1
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Zhang H, Liu Q, Lu J, Wu L, Cheng Z, Qiao G, Huang X. Genomic and transcriptomic analyses of a social hemipteran provide new insights into insect sociality. Mol Ecol Resour 2024:e14019. [PMID: 39262229 DOI: 10.1111/1755-0998.14019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Revised: 08/17/2024] [Accepted: 09/02/2024] [Indexed: 09/13/2024]
Abstract
The origin of sociality represents one of the most important evolutionary transitions. Insect sociality evolved in some hemipteran aphids, which can produce soldiers and normal nymphs with distinct morphology and behaviour through parthenogenesis. The lack of genomic data resources has hindered the investigations into molecular mechanisms underlying their social evolution. Herein, we generated the first chromosomal-level genome of a social hemipteran (Pseudoregma bambucicola) with highly specialized soldiers and performed comparative genomic and transcriptomic analyses to elucidate the molecular signatures and regulatory mechanisms of caste differentiation. P. bambucicola has a larger known aphid genome of 582.2 Mb with an N50 length of 11.24 Mb, and about 99.6% of the assembly was anchored to six chromosomes with a scaffold N50 of 98.27 Mb. A total of 14,027 protein-coding genes were predicted and 37.33% of the assembly were identified as repeat sequences. The social evolution is accompanied by a variety of changes in genome organization, including expansion of gene families related to transcription factors, transposable elements, as well as species-specific expansions of certain sugar transporters and UGPases involved in carbohydrate metabolism. We also characterized large candidate gene sets linked to caste differentiation and found evidence of expression regulation and positive selection acting on energy metabolism and muscle structure, explaining the soldier-specific traits including morphological and behavioural specialization, developmental arrest and infertility. Overall, this study offers new insights into the molecular basis of social aphids and the evolution of insect sociality and also provides valuable data resources for further comparative and functional studies.
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Affiliation(s)
- Hui Zhang
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Qian Liu
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Jianjun Lu
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Liying Wu
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Zhentao Cheng
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Gexia Qiao
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Xiaolei Huang
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, China
- Fujian Provincial Key Laboratory of Insect Ecology, Fujian Agriculture and Forestry University, Fuzhou, China
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2
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Balao F, Medrano M, Bazaga P, Paun O, Alonso C. Long-term methylome changes after experimental seed demethylation and their interaction with recurrent water stress in Erodium cicutarium (Geraniaceae). PLANT BIOLOGY (STUTTGART, GERMANY) 2024. [PMID: 39250311 DOI: 10.1111/plb.13713] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2024] [Accepted: 08/09/2024] [Indexed: 09/11/2024]
Abstract
The frequencies and lengths of drought periods are increasing in subtropical and temperate regions worldwide. Epigenetic responses to water stress could be key for plant resilience to these largely unpredictable challenges. Experimental DNA demethylation, together with application of a stress factor is an appropriate strategy to reveal the contribution of epigenetics to plant responses to stress. We analysed leaf cytosine methylation changes in adult plants of the annual Mediterranean herb, Erodium cicutarium, in a greenhouse, after seed demethylation with 5-Azacytidine and/or recurrent water stress. We used bisulfite RADseq (BsRADseq) and a newly reported reference genome for E. cicutarium to characterize methylation changes in a 2 × 2 factorial design, controlling for plant relatedness. In the long term, 5-Azacytidine treatment alone caused both hypo- and hyper-methylation at individual cytosines, with substantial hypomethylation in CG contexts. In control conditions, drought resulted in a decrease in methylation in all but CHH contexts. In contrast, the genome of plants that experienced recurrent water stress and had been treated with 5-Azacytidine increased DNA methylation level by ca. 5%. Seed demethylation and recurrent drought produced a highly significant interaction in terms of global and context-specific cytosine methylation. Most methylation changes occurred around genic regions and within Transposable Elements. The annotation of these Differentially Methylated Regions associated with genes included several with a potential role in stress responses (e.g., PAL, CDKC, and ABCF), confirming an epigenetic contribution in response to stress at the molecular level.
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Affiliation(s)
- F Balao
- Departamento de Biología Vegetal y Ecología, Universidad de Sevilla, Sevilla, Spain
| | - M Medrano
- Estación Biológica de Doñana, CSIC, Sevilla, Spain
| | - P Bazaga
- Estación Biológica de Doñana, CSIC, Sevilla, Spain
| | - O Paun
- Department of Botany and Biodiversity Research, University of Vienna, Vienna, Austria
| | - C Alonso
- Estación Biológica de Doñana, CSIC, Sevilla, Spain
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3
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Chen XY, Zhou BF, Shi Y, Liu H, Liang YY, Ingvarsson PK, Wang B. Evolution of the Correlated Genomic Variation Landscape Across a Divergence Continuum in the Genus Castanopsis. Mol Biol Evol 2024; 41:msae191. [PMID: 39248185 PMCID: PMC11421576 DOI: 10.1093/molbev/msae191] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2024] [Revised: 08/27/2024] [Accepted: 09/03/2024] [Indexed: 09/10/2024] Open
Abstract
The heterogeneous landscape of genomic variation has been well documented in population genomic studies. However, disentangling the intricate interplay of evolutionary forces influencing the genetic variation landscape over time remains challenging. In this study, we assembled a chromosome-level genome for Castanopsis eyrei and sequenced the whole genomes of 276 individuals from 12 Castanopsis species, spanning a broad divergence continuum. We found highly correlated genomic variation landscapes across these species. Furthermore, variations in genetic diversity and differentiation along the genome were strongly associated with recombination rates and gene density. These results suggest that long-term linked selection and conserved genomic features have contributed to the formation of a common genomic variation landscape. By examining how correlations between population summary statistics change throughout the species divergence continuum, we determined that background selection alone does not fully explain the observed patterns of genomic variation; the effects of recurrent selective sweeps must be considered. We further revealed that extensive gene flow has significantly influenced patterns of genomic variation in Castanopsis species. The estimated admixture proportion correlated positively with recombination rate and negatively with gene density, supporting a scenario of selection against gene flow. Additionally, putative introgression regions exhibited strong signals of positive selection, an enrichment of functional genes, and reduced genetic burdens, indicating that adaptive introgression has played a role in shaping the genomes of hybridizing species. This study provides insights into how different evolutionary forces have interacted in driving the evolution of the genomic variation landscape.
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Affiliation(s)
- Xue-Yan Chen
- Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
- State Key Laboratory of Plant Diversity and Specialty Crops & Key Laboratory of National Forestry and Grassland Administration on Plant Conservation and Utilization in Southern China, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
- South China National Botanical Garden, Guangzhou, China
- University of the Chinese Academy of Sciences, Beijing, China
| | - Biao-Feng Zhou
- Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
- State Key Laboratory of Plant Diversity and Specialty Crops & Key Laboratory of National Forestry and Grassland Administration on Plant Conservation and Utilization in Southern China, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
- South China National Botanical Garden, Guangzhou, China
| | - Yong Shi
- Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
- State Key Laboratory of Plant Diversity and Specialty Crops & Key Laboratory of National Forestry and Grassland Administration on Plant Conservation and Utilization in Southern China, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
- South China National Botanical Garden, Guangzhou, China
| | - Hui Liu
- Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
- State Key Laboratory of Plant Diversity and Specialty Crops & Key Laboratory of National Forestry and Grassland Administration on Plant Conservation and Utilization in Southern China, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
- South China National Botanical Garden, Guangzhou, China
| | - Yi-Ye Liang
- Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
- State Key Laboratory of Plant Diversity and Specialty Crops & Key Laboratory of National Forestry and Grassland Administration on Plant Conservation and Utilization in Southern China, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
- South China National Botanical Garden, Guangzhou, China
| | - Pär K Ingvarsson
- Linnean Center for Plant Biology, Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Baosheng Wang
- Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
- State Key Laboratory of Plant Diversity and Specialty Crops & Key Laboratory of National Forestry and Grassland Administration on Plant Conservation and Utilization in Southern China, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
- South China National Botanical Garden, Guangzhou, China
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4
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Wu S, Morotti ALM, Yang J, Wang E, Tatsis EC. Single-cell RNA sequencing facilitates the elucidation of the complete biosynthesis of the antidepressant hyperforin in St. John's wort. MOLECULAR PLANT 2024; 17:1439-1457. [PMID: 39135343 DOI: 10.1016/j.molp.2024.08.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2024] [Revised: 08/05/2024] [Accepted: 08/07/2024] [Indexed: 08/27/2024]
Abstract
Hyperforin is the compound responsible for the effectiveness of St. John's wort (Hypericum perforatum) as an antidepressant, but its complete biosynthetic pathway remains unknown. Gene discovery based on co-expression analysis of bulk RNA-sequencing data or genome mining failed to discover the missing steps in hyperforin biosynthesis. In this study, we sequenced the 1.54-Gb tetraploid H. perforatum genome assembled into 32 chromosomes with the scaffold N50 value of 42.44 Mb. By single-cell RNA sequencing, we identified a type of cell, "Hyper cells", wherein hyperforin biosynthesis de novo takes place in both the leaves and flowers. Through pathway reconstitution in yeast and tobacco, we identified and characterized four transmembrane prenyltransferases (HpPT1-4) that are localized at the plastid envelope and complete the hyperforin biosynthetic pathway. The hyperforin polycyclic scaffold is created by a reaction cascade involving an irregular isoprenoid coupling and a tandem cyclization. Our findings reveal how and where hyperforin is biosynthesized, enabling synthetic-biology reconstitution of the complete pathway. Thus, this study not only deepens our comprehension of specialized metabolism at the cellular level but also provides strategic guidance for elucidation of the biosynthetic pathways of other specializied metabolites in plants.
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Affiliation(s)
- Song Wu
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China; University of Chinese Academy of Sciences, Shanghai 200032, China
| | - Ana Luisa Malaco Morotti
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
| | - Jun Yang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
| | - Ertao Wang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
| | - Evangelos C Tatsis
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China; CEPAMS - CAS-JIC Centre of Excellence for Plant and Microbial Science, Shanghai 200032, China.
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5
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Zhao Y, Wang J, Xiao Q, Liu G, Li Y, Zha X, He Z, Kang J. New insights into decoding the lifestyle of endophytic Fusarium lateritium Fl617 via comparing genomes. Genomics 2024; 116:110925. [PMID: 39178998 DOI: 10.1016/j.ygeno.2024.110925] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2024] [Revised: 08/15/2024] [Accepted: 08/20/2024] [Indexed: 08/26/2024]
Abstract
Fungal-plant interactions have persisted for 460 million years, and almost all terrestrial plants on Earth have endophytic fungi. However, the mechanism of symbiosis between endophytic fungi and host plants has been inconclusive. In this dissertation, we used a strain of endophytic Fusarium lateritium (Fl617), which was found in the previous stage to promote disease resistance in tomato, and selected the pathogenic Fusarium oxysporum Fo4287 and endophytic Fusarium oxysporum Fo47, which are in the same host and the closest relatives of Fl617, to carry out a comparative genomics analysis of the three systems and to provide a new perspective for the elucidation of the special lifestyle of the fungal endophytes. We found that endophytic F. lateritium has a smaller genome, fewer clusters and genes associated with pathogenicity, and fewer plant cell wall degrading enzymes (PCWDEs). There were also relatively fewer secondary metabolisms and typical Fusarium spp. toxins, and a lack of the key Fusarium spp. pathogenicity factor, secreted in xylem (SIX), but the endophytic fungi may be more sophisticated in their regulation of the colonization process. It is hypothesized that the endophytic fungi may have maintained their symbiosis with plants due to the relatively homogeneous microenvironment in plants for a long period of time, considering only plant interactions and discarding the relevant pathogenicity factors, and that their endophytic evolutionary tendency may tend to be genome streamlining and to enhance the fineness of the regulation of plant interactions, thus maintaining their symbiotic status with plants.
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Affiliation(s)
- Yan Zhao
- Department of Plant Pathology, College of Agriculture, Guizhou University, Guiyang 550025, China; Engineering and Research Center for Southwest Biopharmaceutical Resource of National Education Ministry of China, Guizhou University, Guiyang 550025, China
| | - Jiankang Wang
- Department of Plant Pathology, College of Agriculture, Guizhou University, Guiyang 550025, China; Engineering and Research Center for Southwest Biopharmaceutical Resource of National Education Ministry of China, Guizhou University, Guiyang 550025, China
| | - Qing Xiao
- Engineering and Research Center for Southwest Biopharmaceutical Resource of National Education Ministry of China, Guizhou University, Guiyang 550025, China; Key Laboratory of Green Pesticide and Agricultural Bioengineering, Guizhou University, Guiyang 550025, China
| | - Guihua Liu
- Engineering and Research Center for Southwest Biopharmaceutical Resource of National Education Ministry of China, Guizhou University, Guiyang 550025, China; Key Laboratory of Green Pesticide and Agricultural Bioengineering, Guizhou University, Guiyang 550025, China
| | - Yongjie Li
- Engineering and Research Center for Southwest Biopharmaceutical Resource of National Education Ministry of China, Guizhou University, Guiyang 550025, China; Key Laboratory of Green Pesticide and Agricultural Bioengineering, Guizhou University, Guiyang 550025, China
| | - Xingping Zha
- Department of Plant Pathology, College of Agriculture, Guizhou University, Guiyang 550025, China; Engineering and Research Center for Southwest Biopharmaceutical Resource of National Education Ministry of China, Guizhou University, Guiyang 550025, China
| | - Zhangjiang He
- Department of Plant Pathology, College of Agriculture, Guizhou University, Guiyang 550025, China; Engineering and Research Center for Southwest Biopharmaceutical Resource of National Education Ministry of China, Guizhou University, Guiyang 550025, China.
| | - Jichuan Kang
- Engineering and Research Center for Southwest Biopharmaceutical Resource of National Education Ministry of China, Guizhou University, Guiyang 550025, China.
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6
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Lu HR, Mao CY, Zhang LJ, He JW, Wang XS, Zhang XY, Fan WL, Huang ZZ, Zong L, Cui CH, Wu FM, Wang XL, Zou Z, Li XY, Ge SQ. High-quality reference genome of cowpea beetle Callosobruchus maculatus. Sci Data 2024; 11:799. [PMID: 39025902 PMCID: PMC11258224 DOI: 10.1038/s41597-024-03638-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2024] [Accepted: 07/11/2024] [Indexed: 07/20/2024] Open
Abstract
Callosobruchus maculatus is one of the most competitive stored grain pests, which causes a great loss to agricultural economy. However, due to an inadequacy of high-quality reference genome, the molecular mechanisms for olfactory and hypoxic adaptations to stored environments are unknown and require to be revealed urgently, which will contribute to the detection and prevention of the invasive pests C. maculatus. Here, we presented a high-quality chromosome-level genome of C. maculatus based on Illumina, Nanopore and Hi-C sequencing data. The total size was 1.2 Gb, and 65.17% (797.47 Mb) of it was identified to be repeat sequences. Among assembled chromosomes, chromosome 10 was considered the X chromosome according to the evidence of reads coverage and homologous genes among species. The current version of high-quality genome provides preferable data resources for the adaptive evolution research of C. maculatus.
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Affiliation(s)
- Hao-Ran Lu
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Chu-Yang Mao
- University of Chinese Academy of Sciences, Beijing, China
- Key Laboratory of Genetic Evolution & Animal Models, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Li-Jie Zhang
- Science and Technical Research Center of China Customs, Beijing, China
| | - Jin-Wu He
- Northwestern Polytechnical University, Xian, China
| | - Xie-Shuang Wang
- University of Chinese Academy of Sciences, Beijing, China
- State Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Xin-Ying Zhang
- University of Chinese Academy of Sciences, Beijing, China
- State Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Wei-Li Fan
- State Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- College of Life Sciences, Hebei University, Baoding, China
| | - Zheng-Zhong Huang
- State Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Le Zong
- University of Chinese Academy of Sciences, Beijing, China
- State Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Chu-Han Cui
- College of Life Sciences, Hebei University, Baoding, China
| | - Feng-Ming Wu
- State Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Xue-Li Wang
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Zhen Zou
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.
- University of Chinese Academy of Sciences, Beijing, China.
| | - Xue-Yan Li
- University of Chinese Academy of Sciences, Beijing, China.
- Key Laboratory of Genetic Evolution & Animal Models, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China.
- Yunnan Key Laboratory of Biodiversity Information, Yunnan, 650223, China.
| | - Si-Qin Ge
- University of Chinese Academy of Sciences, Beijing, China.
- State Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.
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7
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Shi CY, Qin GL, Qin YC, Lu LY, Guan DL, Gao LX. A high-quality chromosome-level genome assembly of the endangered tree Kmeria septentrionalis. Sci Data 2024; 11:775. [PMID: 39003271 PMCID: PMC11246460 DOI: 10.1038/s41597-024-03617-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Accepted: 07/05/2024] [Indexed: 07/15/2024] Open
Abstract
Kmeria septentrionalis is a critically endangered tree endemic to Guangxi, China, and is listed on the International Union for Conservation of Nature's Red List. The lack of genetic information and high-quality genome data has hindered conservation efforts and studies on this species. In this study, we present a chromosome-level genome assembly of K. septentrionalis. The genome was initially assembled to be 2.57 Gb, with a contig N50 of 11.93 Mb. Hi-C guided genome assembly allowed us to anchor 98.83% of the total length of the initial contigs onto 19 pseudochromosomes, resulting in a scaffold N50 of 135.08 Mb. The final chromosome-level genome, spaning 2.54 Gb, achieved a BUSCO completeness of 98.9% and contained 1.67 Gb repetitive elements and 35,927 coding genes. This high-quality genome assembly provides a valuable resource for understanding the genetic basis of conservation-related traits and biological properties of this endangered tree species. Furthermore, it lays a critical foundation for evolutionary studies within the Magnoliaceae family.
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Affiliation(s)
- Chen-Yu Shi
- Guangxi Key Laboratory of Sericulture Ecology and Applied Intelligent Technology, School of Chemistry and Bioengineering, Hechi University, Hechi, 546300, China
| | - Guo-Le Qin
- Guangxi Key Laboratory of Sericulture Ecology and Applied Intelligent Technology, School of Chemistry and Bioengineering, Hechi University, Hechi, 546300, China
| | - Ying-Can Qin
- Guangxi Key Laboratory of Sericulture Ecology and Applied Intelligent Technology, School of Chemistry and Bioengineering, Hechi University, Hechi, 546300, China
| | - Lin-Yuan Lu
- Guangxi Key Laboratory of Sericulture Ecology and Applied Intelligent Technology, School of Chemistry and Bioengineering, Hechi University, Hechi, 546300, China
| | - De-Long Guan
- Guangxi Key Laboratory of Sericulture Ecology and Applied Intelligent Technology, School of Chemistry and Bioengineering, Hechi University, Hechi, 546300, China.
| | - Li-Xia Gao
- Guangxi Key Laboratory of Sericulture Ecology and Applied Intelligent Technology, School of Chemistry and Bioengineering, Hechi University, Hechi, 546300, China.
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8
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Li J, Fan Y, Li N, Guo Y, Wang W, Feng K, He W, Li F, Huang J, Xu Y, Xiao L, Feng Y. Comparative genomics analysis reveals sequence characteristics potentially related to host preference in Cryptosporidium xiaoi. Int J Parasitol 2024; 54:379-390. [PMID: 38492779 DOI: 10.1016/j.ijpara.2024.03.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Revised: 02/26/2024] [Accepted: 03/12/2024] [Indexed: 03/18/2024]
Abstract
Cryptosporidium spp. are important diarrhea-associated pathogens in humans and livestock. Among the known species, Cryptosporidium xiaoi, which causes cryptosporidiosis in sheep and goats, was previously recognized as a genotype of the bovine-specific Cryptosporidium bovis based on their high sequence identity in the ssrRNA gene. However, the lack of genomic data has limited characterization of the genetic differences between the two closely related species. In this study, we sequenced the genomes of two C. xiaoi isolates and performed comparative genomic analysis to identify the sequence uniqueness of this ovine-adapted species compared with other Cryptosporidium spp. Our results showed that C. xiaoi is genetically related to C. bovis as shown by their 95.8% genomic identity and similar gene content. Consistent with this, both C. xiaoi and C. bovis appear to have fewer genes encoding mitochondrial metabolic enzymes and invasion-related protein families. However, they appear to possess several species-specific genes. Further analysis indicates that the sequence differences between these two Cryptosporidium spp. are mainly in 24 highly polymorphic genes, half of which are located in the subtelomeric regions. Some of these subtelomeric genes encode secretory proteins that have undergone positive selection. In addition, the genomes of two C. xiaoi isolates, identified as subtypes XXIIIf and XXIIIh, share 99.9% nucleotide sequence identity, with six highly divergent genes encoding putative secretory proteins. Therefore, these species-specific genes and sequence polymorphism in subtelomeric genes probably contribute to the different host preference of C. xiaoi and C. bovis.
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Affiliation(s)
- Jiayu Li
- State Key Laboratory for Animal Disease Control and Prevention, South China Agricultural University, Guangzhou 510642, China
| | - Yingying Fan
- State Key Laboratory for Animal Disease Control and Prevention, South China Agricultural University, Guangzhou 510642, China
| | - Na Li
- State Key Laboratory for Animal Disease Control and Prevention, South China Agricultural University, Guangzhou 510642, China
| | - Yaqiong Guo
- State Key Laboratory for Animal Disease Control and Prevention, South China Agricultural University, Guangzhou 510642, China
| | - Weijian Wang
- State Key Laboratory for Animal Disease Control and Prevention, South China Agricultural University, Guangzhou 510642, China
| | - Kangli Feng
- State Key Laboratory for Animal Disease Control and Prevention, South China Agricultural University, Guangzhou 510642, China
| | - Wei He
- State Key Laboratory for Animal Disease Control and Prevention, South China Agricultural University, Guangzhou 510642, China
| | - Falei Li
- State Key Laboratory for Animal Disease Control and Prevention, South China Agricultural University, Guangzhou 510642, China
| | - Jianbo Huang
- State Key Laboratory for Animal Disease Control and Prevention, South China Agricultural University, Guangzhou 510642, China
| | - Yanhua Xu
- State Key Laboratory for Animal Disease Control and Prevention, South China Agricultural University, Guangzhou 510642, China
| | - Lihua Xiao
- State Key Laboratory for Animal Disease Control and Prevention, South China Agricultural University, Guangzhou 510642, China.
| | - Yaoyu Feng
- State Key Laboratory for Animal Disease Control and Prevention, South China Agricultural University, Guangzhou 510642, China.
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Zhang J, Dong KL, Ren MZ, Wang ZW, Li JH, Sun WJ, Zhao X, Fu XX, Ye JF, Liu B, Zhang DM, Wang MZ, Zeng G, Niu YT, Lu LM, Su JX, Liu ZJ, Soltis PS, Soltis DE, Chen ZD. Coping with alpine habitats: genomic insights into the adaptation strategies of Triplostegia glandulifera (Caprifoliaceae). HORTICULTURE RESEARCH 2024; 11:uhae077. [PMID: 38779140 PMCID: PMC11109519 DOI: 10.1093/hr/uhae077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/15/2023] [Accepted: 03/08/2024] [Indexed: 05/25/2024]
Abstract
How plants find a way to thrive in alpine habitats remains largely unknown. Here we present a chromosome-level genome assembly for an alpine medicinal herb, Triplostegia glandulifera (Caprifoliaceae), and 13 transcriptomes from other species of Dipsacales. We detected a whole-genome duplication event in T. glandulifera that occurred prior to the diversification of Dipsacales. Preferential gene retention after whole-genome duplication was found to contribute to increasing cold-related genes in T. glandulifera. A series of genes putatively associated with alpine adaptation (e.g. CBFs, ERF-VIIs, and RAD51C) exhibited higher expression levels in T. glandulifera than in its low-elevation relative, Lonicera japonica. Comparative genomic analysis among five pairs of high- vs low-elevation species, including a comparison of T. glandulifera and L. japonica, indicated that the gene families related to disease resistance experienced a significantly convergent contraction in alpine plants compared with their lowland relatives. The reduction in gene repertory size was largely concentrated in clades of genes for pathogen recognition (e.g. CNLs, prRLPs, and XII RLKs), while the clades for signal transduction and development remained nearly unchanged. This finding reflects an energy-saving strategy for survival in hostile alpine areas, where there is a tradeoff with less challenge from pathogens and limited resources for growth. We also identified candidate genes for alpine adaptation (e.g. RAD1, DMC1, and MSH3) that were under convergent positive selection or that exhibited a convergent acceleration in evolutionary rate in the investigated alpine plants. Overall, our study provides novel insights into the high-elevation adaptation strategies of this and other alpine plants.
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Affiliation(s)
- Jian Zhang
- State Key Laboratory of Plant Diversity and Specialty Crops & Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- China National Botanical Garden, Beijing 100093, China
| | - Kai-Lin Dong
- State Key Laboratory of Plant Diversity and Specialty Crops & Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- China National Botanical Garden, Beijing 100093, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Miao-Zhen Ren
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an 710069, China
| | - Zhi-Wen Wang
- PubBio-Tech Services Corporation, Wuhan 430070, China
| | - Jian-Hua Li
- Biology Department, Hope College, Holland, MI 49423, USA
| | - Wen-Jing Sun
- State Key Laboratory of Plant Diversity and Specialty Crops & Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- China National Botanical Garden, Beijing 100093, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiang Zhao
- PubBio-Tech Services Corporation, Wuhan 430070, China
| | - Xin-Xing Fu
- College of Life Sciences, Northwest Normal University, Lanzhou 730070, China
| | - Jian-Fei Ye
- School of Ecology, Shenzhen Campus of Sun Yat-sen University, Shenzhen 518107, China
| | - Bing Liu
- State Key Laboratory of Plant Diversity and Specialty Crops & Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- China National Botanical Garden, Beijing 100093, China
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan 430074, China
| | - Da-Ming Zhang
- State Key Laboratory of Plant Diversity and Specialty Crops & Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- China National Botanical Garden, Beijing 100093, China
| | - Mo-Zhu Wang
- State Key Laboratory of Plant Diversity and Specialty Crops & Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- China National Botanical Garden, Beijing 100093, China
| | - Gang Zeng
- Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun 666303, China
| | - Yan-Ting Niu
- State Key Laboratory of Plant Diversity and Specialty Crops & Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- China National Botanical Garden, Beijing 100093, China
| | - Li-Min Lu
- State Key Laboratory of Plant Diversity and Specialty Crops & Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- China National Botanical Garden, Beijing 100093, China
| | - Jun-Xia Su
- School of Life Science, Shanxi Normal University, Taiyuan 030031, China
| | - Zhong-Jian Liu
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Pamela S Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA
| | - Douglas E Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA
- Department of Biology, University of Florida, Gainesville, FL 32611-7800, USA
| | - Zhi-Duan Chen
- State Key Laboratory of Plant Diversity and Specialty Crops & Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- China National Botanical Garden, Beijing 100093, China
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan 430074, China
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10
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Han Z, Wang Z, Rittschof D, Huang Z, Chen L, Hao H, Yao S, Su P, Huang M, Zhang YY, Ke C, Feng D. New genes helped acorn barnacles adapt to a sessile lifestyle. Nat Genet 2024; 56:970-981. [PMID: 38654131 DOI: 10.1038/s41588-024-01733-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Accepted: 03/21/2024] [Indexed: 04/25/2024]
Abstract
Barnacles are the only sessile lineages among crustaceans, and their sessile life begins with the settlement of swimming larvae (cyprids) and the formation of protective shells. These processes are crucial for adaptation to a sessile lifestyle, but the underlying molecular mechanisms remain poorly understood. While investigating these mechanisms in the acorn barnacle, Amphibalanus amphitrite, we discovered a new gene, bcs-6, which is involved in the energy metabolism of cyprid settlement and originated from a transposon by acquiring the promoter and cis-regulatory element. Unlike mollusks, the barnacle shell comprises alternate layers of chitin and calcite and requires another new gene, bsf, which generates silk-like fibers that efficiently bind chitin and aggregate calcite in the aquatic environment. Our findings highlight the importance of exploring new genes in unique adaptative scenarios, and the results will provide important insights into gene origin and material development.
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Affiliation(s)
- Zhaofang Han
- State Key Laboratory of Mariculture Breeding, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Zhixuan Wang
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Daniel Rittschof
- Division of Marine Science and Conservation, Nicholas School of the Environment, Duke University, Beaufort, NC, USA
| | - Zekun Huang
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Liying Chen
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Huanhuan Hao
- State-Province Joint Engineering Laboratory of Marine Bioproducts and Technology, Xiamen University, Xiamen, China
| | - Shanshan Yao
- State-Province Joint Engineering Laboratory of Marine Bioproducts and Technology, Xiamen University, Xiamen, China
| | - Pei Su
- State Key Laboratory of Mariculture Breeding, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Miaoqin Huang
- State Key Laboratory of Mariculture Breeding, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Yuan-Ye Zhang
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, China.
| | - Caihuan Ke
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China.
| | - Danqing Feng
- State Key Laboratory of Mariculture Breeding, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China.
- State-Province Joint Engineering Laboratory of Marine Bioproducts and Technology, Xiamen University, Xiamen, China.
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11
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Ma Q, Liu HS, Li HJ, Bai WP, Gao QF, Wu SD, Yin XX, Chen QQ, Shi YQ, Gao TG, Bao AK, Yin HJ, Li L, Rowland O, Hepworth SR, Luan S, Wang SM. Genomic analysis reveals phylogeny of Zygophyllales and mechanism for water retention of a succulent xerophyte. PLANT PHYSIOLOGY 2024; 195:617-639. [PMID: 38285060 DOI: 10.1093/plphys/kiae040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Revised: 11/30/2023] [Accepted: 12/21/2023] [Indexed: 01/30/2024]
Abstract
Revealing the genetic basis for stress-resistant traits in extremophile plants will yield important information for crop improvement. Zygophyllum xanthoxylum, an extant species of the ancient Mediterranean, is a succulent xerophyte that can maintain a favorable water status under desert habitats; however, the genetic basis of this adaptive trait is poorly understood. Furthermore, the phylogenetic position of Zygophyllales, to which Z. xanthoxylum belongs, remains controversial. In this study, we sequenced and assembled the chromosome-level genome of Z. xanthoxylum. Phylogenetic analysis showed that Zygophyllales and Myrtales form a separated taxon as a sister to the clade comprising fabids and malvids, clarifying the phylogenetic position of Zygophyllales at whole-genome scale. Analysis of genomic and transcriptomic data revealed multiple critical mechanisms underlying the efficient osmotic adjustment using Na+ and K+ as "cheap" osmolytes that Z. xanthoxylum has evolved through the expansion and synchronized expression of genes encoding key transporters/channels and their regulators involved in Na+/K+ uptake, transport, and compartmentation. It is worth noting that ZxCNGC1;1 (cyclic nucleotide-gated channels) and ZxCNGC1;2 constituted a previously undiscovered energy-saving pathway for Na+ uptake. Meanwhile, the core genes involved in biosynthesis of cuticular wax also featured an expansion and upregulated expression, contributing to the water retention capacity of Z. xanthoxylum under desert environments. Overall, these findings boost the understanding of evolutionary relationships of eudicots, illustrate the unique water retention mechanism in the succulent xerophyte that is distinct from glycophyte, and thus provide valuable genetic resources for the improvement of stress tolerance in crops and insights into the remediation of sodic lands.
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Affiliation(s)
- Qing Ma
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems; College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730020, China
| | - Hai-Shuang Liu
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems; College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730020, China
| | - Hu-Jun Li
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems; College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730020, China
| | - Wan-Peng Bai
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems; College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730020, China
| | - Qi-Fei Gao
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA
| | - Sheng-Dan Wu
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems; College of Ecology, Lanzhou University, Lanzhou 730000, China
| | - Xiu-Xia Yin
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems; College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730020, China
| | - Qin-Qin Chen
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems; College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730020, China
| | - Ya-Qi Shi
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems; College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730020, China
| | - Tian-Ge Gao
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems; College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730020, China
| | - Ai-Ke Bao
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems; College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730020, China
| | - Hong-Ju Yin
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems; College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730020, China
| | - Li Li
- Institute of Grassland, Xinjiang Academy of Animal Science, Urumqi 830000, China
| | - Owen Rowland
- Department of Biology and Institute of Biochemistry, Carleton University, Ottawa, Ontario K1S 5B6, Canada
| | - Shelley R Hepworth
- Department of Biology and Institute of Biochemistry, Carleton University, Ottawa, Ontario K1S 5B6, Canada
| | - Sheng Luan
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA
| | - Suo-Min Wang
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems; College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730020, China
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12
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Meng K, Liao W, Wei S, Chen S, Li M, Ma Y, Fan Q. Chromosome-scale genome assembly and annotation of Cotoneaster glaucophyllus. Sci Data 2024; 11:406. [PMID: 38649372 PMCID: PMC11035681 DOI: 10.1038/s41597-024-03246-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Accepted: 04/10/2024] [Indexed: 04/25/2024] Open
Abstract
Cotoneaster glaucophyllus is a semi-evergreen plant that blossoms in late summer, producing dense, attractive, fragrant white flowers with significant ornamental and ecological value. Here, a chromosome-scale genome assembly was obtained by integrating PacBio and Illumina sequencing data with the aid of Hi-C technology. The genome assembly was 563.3 Mb in length, with contig N50 and scaffold N50 values of ~6 Mb and ~31 Mb, respectively. Most (95.59%) of the sequences were anchored onto 17 pseudochromosomes (538.4 Mb). We predicted 35,856 protein-coding genes, 1,401 miRNAs, 655 tRNAs, 425 rRNAs, and 795 snRNAs. The functions of 34,967 genes (97.52%) were predicted. The availability of this chromosome-level genome will provide valuable resources for molecular studies of this species, facilitating future research on speciation, functional genomics, and comparative genomics within the Rosaceae family.
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Affiliation(s)
- Kaikai Meng
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China
- Guangxi Key Laboratory of Quality and Safety Control for Subtropical Fruits, Guangxi Subtropical Crops Research Institute, Nanning, 530001, China
| | - Wenbo Liao
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China
| | - Shaolong Wei
- Guangxi Key Laboratory of Quality and Safety Control for Subtropical Fruits, Guangxi Subtropical Crops Research Institute, Nanning, 530001, China
| | - Sufang Chen
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China
| | - Mingwan Li
- College of Forestry, Henan Agricultural University, Zhengzhou, 450002, China
| | - Yongpeng Ma
- State Key Laboratory of Plant Diversity and Specialty Crops, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China.
| | - Qiang Fan
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China.
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13
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Marcet-Houben M, Cruz F, Gómez-Garrido J, Alioto TS, Nunez-Rodriguez JC, Mesanza N, Gut M, Iturritxa E, Gabaldon T. Genomics of the expanding pine pathogen Lecanosticta acicola reveals patterns of ongoing genetic admixture. mSystems 2024; 9:e0092823. [PMID: 38364101 PMCID: PMC10949461 DOI: 10.1128/msystems.00928-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Accepted: 01/09/2024] [Indexed: 02/18/2024] Open
Abstract
Lecanosticta acicola is the causal agent for brown spot needle blight that affects pine trees across the northern hemisphere. Based on marker genes and microsatellite data, two distinct lineages have been identified that were introduced into Europe on two separate occasions. Despite their overall distinct geographic distribution, they have been found to coexist in regions of northern Spain and France. Here, we present the first genome-wide study of Lecanosticta acicola, including assembly of the reference genome and a population genomics analysis of 70 natural isolates from northern Spain. We show that most of the isolates belong to the southern lineage but show signs of introgression with northern lineage isolates, indicating mating between the two lineages. We also identify phenotypic differences between the two lineages based on the activity profiles of 20 enzymes, with introgressed strains being more phenotypically similar to members of the southern lineage. In conclusion, we show undergoing genetic admixture between the two main lineages of L. acicola in a region of recent expansion. IMPORTANCE Lecanosticta acicola is a fungal pathogen causing severe defoliation, growth reduction, and even death in more than 70 conifer species. Despite the increasing incidence of this species, little is known about its population dynamics. Two divergent lineages have been described that have now been found together in regions of France and Spain, but it is unknown how these mixed populations evolve. Here we present the first reference genome for this important plant pathogenic fungi and use it to study the population genomics of 70 isolates from an affected forest in the north of Spain. We find signs of introgression between the two main lineages, indicating that active mating is occurring in this region which could propitiate the appearance of novel traits in this species. We also study the phenotypic differences across this population based on enzymatic activities on 20 compounds.
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Affiliation(s)
- Marina Marcet-Houben
- Barcelona Supercomputing Centre (BSC-CNS), Barcelona, Spain
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
- Centro de Investigación Biomédica En Red de Enfermedades Infecciosas (CIBERINFEC), Barcelona, Spain
| | - Fernando Cruz
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Jéssica Gómez-Garrido
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Tyler S. Alioto
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Juan Carlos Nunez-Rodriguez
- Barcelona Supercomputing Centre (BSC-CNS), Barcelona, Spain
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Nebai Mesanza
- Instituto Vasco de Investigación y Desarrollo Agrario (BRTA), Arkaute, Araba, Spain
| | - Marta Gut
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Eugenia Iturritxa
- Instituto Vasco de Investigación y Desarrollo Agrario (BRTA), Arkaute, Araba, Spain
| | - Toni Gabaldon
- Barcelona Supercomputing Centre (BSC-CNS), Barcelona, Spain
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
- Centro de Investigación Biomédica En Red de Enfermedades Infecciosas (CIBERINFEC), Barcelona, Spain
- Catalan Institution for Research and Advanced Studies (ICREA), Barcelona, Spain
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14
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Hu Z, Fan Z, Li S, Wang M, Huang M, Ma X, Liu W, Wang Y, Yu Y, Li Y, Sun Y, Li X, Li J, Yin H. Genomics insights into flowering and floral pattern formation: regional duplication and seasonal pattern of gene expression in Camellia. BMC Biol 2024; 22:50. [PMID: 38414012 PMCID: PMC10900828 DOI: 10.1186/s12915-024-01851-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Accepted: 02/20/2024] [Indexed: 02/29/2024] Open
Abstract
BACKGROUND The formation and domestication of ornamental traits are influenced by various aspects, such as the recognition of esthetic values and cultural traditions. Camellia japonica is widely appreciated and domesticated around the world mainly due to its rich variations in ornamental traits. Ornamental camellias have a diverse range of resources, including different bud variations from Camellia spp. as well as inter- and intra- specific hybridization. Despite research on the formation of ornamental traits, a basic understanding of their genetics and genomics is still lacking. RESULTS Here, we report the chromosomal-level reference genome of C. japonica through combining multiple DNA-sequencing technologies and obtain a high-density genetic linkage map of 4255 markers by sequencing 98 interspecific F1 hybrids between C. japonica and C. chekiangoleosa. We identify two whole-genome duplication events in C. japonica: one is a shared ancient γ event, and the other is revealed to be specific to genus Camellia. Based on the micro-collinearity analysis, we find large-scale segmental duplication of chromosome 8, resulting to two copies of the AGAMOUS loci, which may play a key role in the domestication of floral shapes. To explore the regulatory mechanisms of seasonal flowering, we have analyzed year-round gene expression patterns of C. japonica and C. azalea-a sister plant of continuous flowering that has been widely used for cross breeding. Through comparative analyses of gene co-expression networks and annual gene expression patterns, we show that annual expression rhythms of some important regulators of seasonal growth and development, including GIGANTEA and CONSTANS of the photoperiod pathway, have been disrupted in C. azalea. Furthermore, we reveal that the distinctive expression patterns of FLOWERING LOCUS T can be correlated with the seasonal activities of flowering and flushing. We demonstrate that the regulatory module involved in GIGANTEA, CONSTANS, and FLOWERING LOCUS T is central to achieve seasonality. CONCLUSIONS Through the genomic and comparative genomics characterizations of ornamental Camellia spp., we propose that duplication of chromosomal segments as well as the establishment of gene expression patterns has played a key role in the formation of ornamental traits (e.g., flower shape, flowering time). This work provides a valuable genomic platform for understanding the molecular basis of ornamental traits.
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Affiliation(s)
- Zhikang Hu
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, 311400, Zhejiang, China
- College of Information Science and Technology, Nanjing Forestry University, Nanjing, 210037, China
- Key Laboratory of Forest Genetics and Breeding, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, 311400, Zhejiang, China
| | - Zhengqi Fan
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, 311400, Zhejiang, China
- Key Laboratory of Forest Genetics and Breeding, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, 311400, Zhejiang, China
| | - Sijia Li
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, 311400, Zhejiang, China
- College of Information Science and Technology, Nanjing Forestry University, Nanjing, 210037, China
- Key Laboratory of Forest Genetics and Breeding, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, 311400, Zhejiang, China
| | - Minyan Wang
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, 311400, Zhejiang, China
- Key Laboratory of Forest Genetics and Breeding, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, 311400, Zhejiang, China
| | - Mingchuan Huang
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, 311400, Zhejiang, China
- College of Horticulture, Qingdao Agricultural University, Qingdao, 266109, Shandong, China
| | - Xianjin Ma
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, 311400, Zhejiang, China
- Key Laboratory of Forest Genetics and Breeding, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, 311400, Zhejiang, China
| | - Weixin Liu
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, 311400, Zhejiang, China
- Key Laboratory of Forest Genetics and Breeding, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, 311400, Zhejiang, China
| | - Yupeng Wang
- College of Information Science and Technology, Nanjing Forestry University, Nanjing, 210037, China
| | - Yifan Yu
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, 311400, Zhejiang, China
- College of Information Science and Technology, Nanjing Forestry University, Nanjing, 210037, China
- Key Laboratory of Forest Genetics and Breeding, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, 311400, Zhejiang, China
| | - Yaxuan Li
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, 311400, Zhejiang, China
- College of Information Science and Technology, Nanjing Forestry University, Nanjing, 210037, China
- Key Laboratory of Forest Genetics and Breeding, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, 311400, Zhejiang, China
| | - Yingkun Sun
- College of Horticulture, Qingdao Agricultural University, Qingdao, 266109, Shandong, China
| | - Xinlei Li
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, 311400, Zhejiang, China
- Key Laboratory of Forest Genetics and Breeding, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, 311400, Zhejiang, China
| | - Jiyuan Li
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, 311400, Zhejiang, China
- Key Laboratory of Forest Genetics and Breeding, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, 311400, Zhejiang, China
| | - Hengfu Yin
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, 311400, Zhejiang, China.
- Key Laboratory of Forest Genetics and Breeding, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, 311400, Zhejiang, China.
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15
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Yang Z, Yang Q, Liu Q, Li X, Wang L, Zhang Y, Ke Z, Lu Z, Shen H, Li J, Zhou W. A chromosome-level genome assembly of Agave hybrid NO.11648 provides insights into the CAM photosynthesis. HORTICULTURE RESEARCH 2024; 11:uhad269. [PMID: 38333731 PMCID: PMC10848310 DOI: 10.1093/hr/uhad269] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Accepted: 12/06/2023] [Indexed: 02/10/2024]
Abstract
The subfamily Agavoideae comprises crassulacean acid metabolism (CAM), C3, and C4 plants with a young age of speciation and slower mutation accumulation, making it a model crop for studying CAM evolution. However, the genetic mechanism underlying CAM evolution remains unclear because of lacking genomic information. This study assembled the genome of Agave hybrid NO.11648, a constitutive CAM plant belonging to subfamily Agavoideae, at the chromosome level using data generated from high-throughput chromosome conformation capture, Nanopore, and Illumina techniques, resulting in 30 pseudo-chromosomes with a size of 4.87 Gb and scaffold N50 of 186.42 Mb. The genome annotation revealed 58 841 protein-coding genes and 76.91% repetitive sequences, with the dominant repetitive sequences being the I-type repeats (Copia and Gypsy accounting for 18.34% and 13.5% of the genome, respectively). Our findings also provide support for a whole genome duplication event in the lineage leading to A. hybrid, which occurred after its divergence from subfamily Asparagoideae. Moreover, we identified a gene duplication event in the phosphoenolpyruvate carboxylase kinase (PEPCK) gene family and revealed that three PEPCK genes (PEPCK3, PEPCK5, and PEPCK12) were involved in the CAM pathway. More importantly, we identified transcription factors enriched in the circadian rhythm, MAPK signaling, and plant hormone signal pathway that regulate the PEPCK3 expression by analysing the transcriptome and using yeast one-hybrid assays. Our results shed light on CAM evolution and offer an essential resource for the molecular breeding program of Agave spp.
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Affiliation(s)
- Ziping Yang
- Zhanjiang Key Laboratory of Tropical Crop Genetic Improvement, South Subtropical Crops Research Institute, Chinese Academy of Tropical Agricultural Sciences, 524091 Zhanjiang, Guangdong, China
| | - Qian Yang
- Zhanjiang Key Laboratory of Tropical Crop Genetic Improvement, South Subtropical Crops Research Institute, Chinese Academy of Tropical Agricultural Sciences, 524091 Zhanjiang, Guangdong, China
| | - Qi Liu
- Wuhan Onemore-tech Co., Ltd, 430076 Wuhan, Hubei, China
| | - Xiaolong Li
- Biomarker Technologies Corporation, 101300 Beijing, China
| | - Luli Wang
- Zhanjiang Key Laboratory of Tropical Crop Genetic Improvement, South Subtropical Crops Research Institute, Chinese Academy of Tropical Agricultural Sciences, 524091 Zhanjiang, Guangdong, China
| | - Yanmei Zhang
- Zhanjiang Key Laboratory of Tropical Crop Genetic Improvement, South Subtropical Crops Research Institute, Chinese Academy of Tropical Agricultural Sciences, 524091 Zhanjiang, Guangdong, China
| | - Zhi Ke
- Zhanjiang Key Laboratory of Tropical Crop Genetic Improvement, South Subtropical Crops Research Institute, Chinese Academy of Tropical Agricultural Sciences, 524091 Zhanjiang, Guangdong, China
| | - Zhiwei Lu
- Zhanjiang Key Laboratory of Tropical Crop Genetic Improvement, South Subtropical Crops Research Institute, Chinese Academy of Tropical Agricultural Sciences, 524091 Zhanjiang, Guangdong, China
| | - Huibang Shen
- Zhanjiang Key Laboratory of Tropical Crop Genetic Improvement, South Subtropical Crops Research Institute, Chinese Academy of Tropical Agricultural Sciences, 524091 Zhanjiang, Guangdong, China
| | - Junfeng Li
- Zhanjiang Key Laboratory of Tropical Crop Genetic Improvement, South Subtropical Crops Research Institute, Chinese Academy of Tropical Agricultural Sciences, 524091 Zhanjiang, Guangdong, China
| | - Wenzhao Zhou
- Zhanjiang Key Laboratory of Tropical Crop Genetic Improvement, South Subtropical Crops Research Institute, Chinese Academy of Tropical Agricultural Sciences, 524091 Zhanjiang, Guangdong, China
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Pu Y, Zhou Y, Liu J, Zhang H. A high-quality chromosomal genome assembly of the sea cucumber Chiridota heheva and its hydrothermal adaptation. Gigascience 2024; 13:giad107. [PMID: 38171490 PMCID: PMC10764150 DOI: 10.1093/gigascience/giad107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2023] [Revised: 07/05/2023] [Accepted: 11/22/2023] [Indexed: 01/05/2024] Open
Abstract
BACKGROUND Chiridota heheva is a cosmopolitan holothurian well adapted to diverse deep-sea ecosystems, especially chemosynthetic environments. Besides high hydrostatic pressure and limited light, high concentrations of metal ions also represent harsh conditions in hydrothermal environments. Few holothurian species can live in such extreme conditions. Therefore, it is valuable to elucidate the adaptive genetic mechanisms of C. heheva in hydrothermal environments. FINDINGS Herein, we report a high-quality reference genome assembly of C. heheva from the Kairei vent, which is the first chromosome-level genome of Apodida. The chromosome-level genome size was 1.43 Gb, with a scaffold N50 of 53.24 Mb and BUSCO completeness score of 94.5%. Contig sequences were clustered, ordered, and assembled into 19 natural chromosomes. Comparative genome analysis found that the expanded gene families and positively selected genes of C. heheva were involved in the DNA damage repair process. The expanded gene families and the unique genes contributed to maintaining iron homeostasis in an iron-enriched environment. The positively selected gene RFC2 with 10 positively selected sites played an essential role in DNA repair under extreme environments. CONCLUSIONS This first chromosome-level genome assembly of C. heheva reveals the hydrothermal adaptation of holothurians. As the first chromosome-level genome of order Apodida, this genome will provide the resource for investigating the evolution of class Holothuroidea.
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Affiliation(s)
- Yujin Pu
- Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya 572000, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yang Zhou
- Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya 572000, China
| | - Jun Liu
- Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya 572000, China
| | - Haibin Zhang
- Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya 572000, China
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17
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Hong X, Liu H, Wang Y, Li M, Ji L, Wang K, Wei C, Li W, Chen C, Yu L, Zhu X, Liu X. A chromosome-level genome assembly of the Asian giant softshell turtle Pelochelys cantorii. Sci Data 2023; 10:754. [PMID: 37914689 PMCID: PMC10620421 DOI: 10.1038/s41597-023-02667-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Accepted: 10/19/2023] [Indexed: 11/03/2023] Open
Abstract
The Asian giant softshell turtle Pelochelys cantorii is one of the largest aquatic turtles in China and has been designated a First Grade Protected Animal in China. To advance conservation research, a combination of Illumina short-read, PacBio long-read, and Hi-C scaffolding technologies was used to develop a high-quality chromosome-level genome assembly for P. cantorii. A total of 262.77 Gb of clean data were produced (121.6 × depth) and then the genome was assembled into 2.16 Gb with a contig N50 of 41.44 Mb and scaffold N50 length of 120.17 Mb, respectively. Moreover, about 99.98% assembly genome sequences were clustered and ordered onto 33 pseudochromosomes. Genome annotation revealed that 21,833 protein-coding genes were predicted, and 96.40% of them were annotated. This new chromosome-level assembly will be an enabling resource for genetic and genomic studies to support fundamental insight into P. cantorii biology.
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Affiliation(s)
- Xiaoyou Hong
- Key Laboratory of Tropical and Subtropical Fishery Resources Application and Cultivation, Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, 510380, China
| | - Haiyang Liu
- Key Laboratory of Tropical and Subtropical Fishery Resources Application and Cultivation, Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, 510380, China
| | - Yakun Wang
- Key Laboratory of Tropical and Subtropical Fishery Resources Application and Cultivation, Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, 510380, China
| | - Mingzhi Li
- Guangzhou Bio&data Technology Co., Ltd, Guangzhou, 510555, China
| | - Liqin Ji
- Key Laboratory of Tropical and Subtropical Fishery Resources Application and Cultivation, Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, 510380, China
| | - Kaikuo Wang
- Key Laboratory of Tropical and Subtropical Fishery Resources Application and Cultivation, Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, 510380, China
- College of Life Science and Fisheries, Shanghai Ocean University, Shanghai, 201306, China
| | - Chengqing Wei
- Key Laboratory of Tropical and Subtropical Fishery Resources Application and Cultivation, Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, 510380, China
| | - Wei Li
- Key Laboratory of Tropical and Subtropical Fishery Resources Application and Cultivation, Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, 510380, China
| | - Chen Chen
- Key Laboratory of Tropical and Subtropical Fishery Resources Application and Cultivation, Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, 510380, China
| | - Lingyun Yu
- Key Laboratory of Tropical and Subtropical Fishery Resources Application and Cultivation, Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, 510380, China
| | - Xinping Zhu
- Key Laboratory of Tropical and Subtropical Fishery Resources Application and Cultivation, Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, 510380, China.
- College of Life Science and Fisheries, Shanghai Ocean University, Shanghai, 201306, China.
| | - Xiaoli Liu
- Key Laboratory of Tropical and Subtropical Fishery Resources Application and Cultivation, Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, 510380, China.
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18
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Chaturvedi A, Li X, Dhandapani V, Marshall H, Kissane S, Cuenca-Cambronero M, Asole G, Calvet F, Ruiz-Romero M, Marangio P, Guigó R, Rago D, Mirbahai L, Eastwood N, Colbourne J, Zhou J, Mallon E, Orsini L. The hologenome of Daphnia magna reveals possible DNA methylation and microbiome-mediated evolution of the host genome. Nucleic Acids Res 2023; 51:9785-9803. [PMID: 37638757 PMCID: PMC10570034 DOI: 10.1093/nar/gkad685] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Revised: 07/07/2023] [Accepted: 08/09/2023] [Indexed: 08/29/2023] Open
Abstract
Properties that make organisms ideal laboratory models in developmental and medical research are often the ones that also make them less representative of wild relatives. The waterflea Daphnia magna is an exception, by both sharing many properties with established laboratory models and being a keystone species, a sentinel species for assessing water quality, an indicator of environmental change and an established ecotoxicology model. Yet, Daphnia's full potential has not been fully exploited because of the challenges associated with assembling and annotating its gene-rich genome. Here, we present the first hologenome of Daphnia magna, consisting of a chromosomal-level assembly of the D. magna genome and the draft assembly of its metagenome. By sequencing and mapping transcriptomes from exposures to environmental conditions and from developmental morphological landmarks, we expand the previously annotates gene set for this species. We also provide evidence for the potential role of gene-body DNA-methylation as a mutagen mediating genome evolution. For the first time, our study shows that the gut microbes provide resistance to commonly used antibiotics and virulence factors, potentially mediating Daphnia's environmental-driven rapid evolution. Key findings in this study improve our understanding of the contribution of DNA methylation and gut microbiota to genome evolution in response to rapidly changing environments.
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Affiliation(s)
- Anurag Chaturvedi
- Environmental Genomics Group, School of Biosciences, and Institute for Interdisciplinary Data Science and AI, the University of Birmingham, Birmingham B15 2TT, UK
| | - Xiaojing Li
- Environmental Genomics Group, School of Biosciences, and Institute for Interdisciplinary Data Science and AI, the University of Birmingham, Birmingham B15 2TT, UK
| | - Vignesh Dhandapani
- Environmental Genomics Group, School of Biosciences, and Institute for Interdisciplinary Data Science and AI, the University of Birmingham, Birmingham B15 2TT, UK
| | - Hollie Marshall
- Environmental Genomics Group, School of Biosciences, and Institute for Interdisciplinary Data Science and AI, the University of Birmingham, Birmingham B15 2TT, UK
- Department of Genetics and Genome Biology, the University of Leicester, Leicester LE1 7RH, UK
| | - Stephen Kissane
- Environmental Genomics Group, School of Biosciences, and Institute for Interdisciplinary Data Science and AI, the University of Birmingham, Birmingham B15 2TT, UK
| | - Maria Cuenca-Cambronero
- Environmental Genomics Group, School of Biosciences, and Institute for Interdisciplinary Data Science and AI, the University of Birmingham, Birmingham B15 2TT, UK
- Aquatic Ecology Group, University of Vic - Central University of Catalonia, 08500 Vic, Spain
| | - Giovanni Asole
- Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology (BIST), Barcelona, Catalonia, Spain
| | - Ferriol Calvet
- Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology (BIST), Barcelona, Catalonia, Spain
| | - Marina Ruiz-Romero
- Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology (BIST), Barcelona, Catalonia, Spain
| | - Paolo Marangio
- Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology (BIST), Barcelona, Catalonia, Spain
| | - Roderic Guigó
- Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology (BIST), Barcelona, Catalonia, Spain
| | - Daria Rago
- Environmental Genomics Group, School of Biosciences, and Institute for Interdisciplinary Data Science and AI, the University of Birmingham, Birmingham B15 2TT, UK
| | - Leda Mirbahai
- Warwick Medical School, University of Warwick, Coventry CV4 7AL, UK
| | - Niamh Eastwood
- Environmental Genomics Group, School of Biosciences, and Institute for Interdisciplinary Data Science and AI, the University of Birmingham, Birmingham B15 2TT, UK
| | - John K Colbourne
- Environmental Genomics Group, School of Biosciences, and Institute for Interdisciplinary Data Science and AI, the University of Birmingham, Birmingham B15 2TT, UK
| | - Jiarui Zhou
- Environmental Genomics Group, School of Biosciences, and Institute for Interdisciplinary Data Science and AI, the University of Birmingham, Birmingham B15 2TT, UK
| | - Eamonn Mallon
- Department of Genetics and Genome Biology, the University of Leicester, Leicester LE1 7RH, UK
| | - Luisa Orsini
- Environmental Genomics Group, School of Biosciences, and Institute for Interdisciplinary Data Science and AI, the University of Birmingham, Birmingham B15 2TT, UK
- The Alan Turing Institute, British Library, London NW1 2DB, UK
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19
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Cruz F, Gómez-Garrido J, Gut M, Alioto TS, Pons J, Alós J, Barcelo-Serra M. Chromosome-level assembly and annotation of the Xyrichtys novacula (Linnaeus, 1758) genome. DNA Res 2023; 30:dsad021. [PMID: 37797305 PMCID: PMC10590160 DOI: 10.1093/dnares/dsad021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Revised: 09/15/2023] [Accepted: 10/04/2023] [Indexed: 10/07/2023] Open
Abstract
The pearly razorfish (Xyrichtys novacula), commonly known as raor in the Balearic Islands, is a wrasse within the family Labridae. This fish species has particular biological and socio-cultural characteristics making it an ideal model organism in the fields of behavioural ecology, molecular ecology and conservation biology. In this study, we present the first annotated chromosome-level assembly for this species. Sequencing involved a combination of long reads with Oxford Nanopore Technologies, Illumina paired-end short reads (2 × 151 bp), Hi-C and RNA-seq from different tissues. The nuclear genome assembly has a scaffold N50 of 34.33 Mb, a total assembly span of 775.53 Mb and 99.63% of the sequence assembled into 24 superscaffolds, consistent with its known karyotype. Quality metrics revealed a consensus accuracy (QV) of 42.92 and gene completeness > 98%. The genome annotation resulted in 26,690 protein-coding genes and 12,737 non-coding transcripts. The coding regions encoded 39,613 unique protein products, 93% of them with assigned function. Overall, the publication of the X. novacula's reference genome will broaden the scope and impact of genomic research conducted on this iconic and colourful species.
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Affiliation(s)
- Fernando Cruz
- Centro Nacional de Análisis Genómico (CNAG), C/Baldiri Reixac 4, 08028 Barcelona, Spain
| | - Jèssica Gómez-Garrido
- Centro Nacional de Análisis Genómico (CNAG), C/Baldiri Reixac 4, 08028 Barcelona, Spain
| | - Marta Gut
- Centro Nacional de Análisis Genómico (CNAG), C/Baldiri Reixac 4, 08028 Barcelona, Spain
| | - Tyler S Alioto
- Centro Nacional de Análisis Genómico (CNAG), C/Baldiri Reixac 4, 08028 Barcelona, Spain
| | - Joan Pons
- Institut Mediterrani d’Estudis Avançats, IMEDEA (UIB-CSIC), C/Miquel Marquès 21, 07190 Esporles, Illes Balears, Spain
| | - Josep Alós
- Institut Mediterrani d’Estudis Avançats, IMEDEA (UIB-CSIC), C/Miquel Marquès 21, 07190 Esporles, Illes Balears, Spain
| | - Margarida Barcelo-Serra
- Institut Mediterrani d’Estudis Avançats, IMEDEA (UIB-CSIC), C/Miquel Marquès 21, 07190 Esporles, Illes Balears, Spain
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20
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Ma L, Yang C, Xiao D, Liu X, Jiang X, Lin H, Ying Z, Lin Y. Chromosome-level assembly of Dictyophora rubrovolvata genome using third-generation DNA sequencing and Hi-C analysis. G3 (BETHESDA, MD.) 2023; 13:jkad102. [PMID: 37178144 PMCID: PMC10411574 DOI: 10.1093/g3journal/jkad102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2023] [Revised: 01/15/2023] [Accepted: 04/14/2023] [Indexed: 05/15/2023]
Abstract
Dictyophora rubrovolvata, a rare edible mushroom with both nutritional and medicinal values, was regarded as the "queen of the mushroom" for its attractive appearance. Dictyophora rubrovolvata has been widely cultivated in China in recent years, and many researchers were focusing on its nutrition, culture condition, and artificial cultivation. Due to a lack of genomic information, research on bioactive substances, cross breeding, lignocellulose degradation, and molecular biology is limited. In this study, we report a chromosome-level reference genome of D. rubrovolvata using the PacBio single-molecule real-time-sequencing technique and high-throughput chromosome conformation capture (Hi-C) technologies. A total of 1.83 Gb circular consensus sequencing reads representing ∼983.34 coverage of the D. rubrovolvata genome were generated. The final genome was assembled into 136 contigs with a total length of 32.89 Mb. The scaffold and contig N50 length were 2.71 and 2.48 Mb, respectively. After chromosome-level scaffolding, 11 chromosomes with a total length of 28.24 Mb were constructed. Genome annotation further revealed that 9.86% of the genome was composed of repetitive sequences, and a total of 508 noncoding RNA (rRNA: 329, tRNA: 150, ncRNA: 29) were annotated. In addition, 9,725 protein-coding genes were predicted, among which 8,830 (90.79%) genes were predicted using homology or RNA-seq. Benchmarking Universal Single-Copy Orthologs results further revealed that there were 80.34% complete single-copy fungal orthologs. In this study, a total of 360 genes were annotated as belonging to the carbohydrate-active enzymes family. Further analysis also predicted 425 cytochromes P450 genes, which can be classified into 41 families. This highly accurate, chromosome-level reference genome of D. rubrovolvata will provide essential genomic information for understanding the molecular mechanism in its fruiting body formation during morphological development and facilitate the exploitation of medicinal compounds produced by this mushroom.
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Affiliation(s)
- Lu Ma
- Institute of Edible Mushroom, Fujian Academy of Agricultural Sciences, Fuzhou 350012, China
- National and Local Joint Engineering Research Center for Breeding and Cultivation of Featured Edible Muhsroom, Fujian Academy of Agricultural Sciences, Fuzhou 350012, China
| | - Chi Yang
- Institute of Edible Mushroom, Fujian Academy of Agricultural Sciences, Fuzhou 350012, China
- National and Local Joint Engineering Research Center for Breeding and Cultivation of Featured Edible Muhsroom, Fujian Academy of Agricultural Sciences, Fuzhou 350012, China
| | - Donglai Xiao
- Institute of Edible Mushroom, Fujian Academy of Agricultural Sciences, Fuzhou 350012, China
- National and Local Joint Engineering Research Center for Breeding and Cultivation of Featured Edible Muhsroom, Fujian Academy of Agricultural Sciences, Fuzhou 350012, China
| | - Xiaoyu Liu
- Institute of Edible Mushroom, Fujian Academy of Agricultural Sciences, Fuzhou 350012, China
- National and Local Joint Engineering Research Center for Breeding and Cultivation of Featured Edible Muhsroom, Fujian Academy of Agricultural Sciences, Fuzhou 350012, China
| | - Xiaoling Jiang
- Institute of Edible Mushroom, Fujian Academy of Agricultural Sciences, Fuzhou 350012, China
- National and Local Joint Engineering Research Center for Breeding and Cultivation of Featured Edible Muhsroom, Fujian Academy of Agricultural Sciences, Fuzhou 350012, China
| | - Hui Lin
- Institute of Edible Mushroom, Fujian Academy of Agricultural Sciences, Fuzhou 350012, China
- National and Local Joint Engineering Research Center for Breeding and Cultivation of Featured Edible Muhsroom, Fujian Academy of Agricultural Sciences, Fuzhou 350012, China
| | - Zhenghe Ying
- Institute of Edible Mushroom, Fujian Academy of Agricultural Sciences, Fuzhou 350012, China
- National and Local Joint Engineering Research Center for Breeding and Cultivation of Featured Edible Muhsroom, Fujian Academy of Agricultural Sciences, Fuzhou 350012, China
| | - Yanquan Lin
- Institute of Edible Mushroom, Fujian Academy of Agricultural Sciences, Fuzhou 350012, China
- National and Local Joint Engineering Research Center for Breeding and Cultivation of Featured Edible Muhsroom, Fujian Academy of Agricultural Sciences, Fuzhou 350012, China
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21
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Yang Y, Zeng L, Wang T, Wu L, Wu X, Xia J, Meng Z, Liu X. Assembly of Genome and Resequencing Provide Insights into Genetic Differentiation between Parents of Hulong Hybrid Grouper ( Epinephelus fuscoguttatus ♀ × E. lanceolatus ♂). Int J Mol Sci 2023; 24:12007. [PMID: 37569383 PMCID: PMC10418399 DOI: 10.3390/ijms241512007] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Revised: 07/22/2023] [Accepted: 07/25/2023] [Indexed: 08/13/2023] Open
Abstract
The Hulong hybrid grouper was bred from the brown-marbled grouper (Epinephelus fuscoguttatus) ♀ and the giant grouper (E. lanceolatus) ♂, combining the advantageous traits of both parents. Possessing an excellent performance, this hybrid's cultivation promotes the development of the grouper industry. Its male parent, the giant grouper, possesses the fastest growth and the largest body size among all coral-reef-dwelling fish. This species is not only an economically important species in marine aquaculture, but it is also an ideal male parent in the interspecific crossing of grouper species. In the present study, a high-quality chromosome-level genome of the giant grouper was constructed with a total length of 1.06 Gb, consisting of 24 chromosomes and 69 scaffolds. To analyze the genetic differences between the parents of the Hulong hybrid grouper, the structural variations (SVs) between both parental genomes were detected, and a total of 46,643 SVs were obtained. High-quality SNPs were identified from resequencing data. There were significant differences between the two genomes, and the average FST reached 0.685. A total of 234 highly differentiated regions were detected with an FST > 0.9. The protein-coding genes involved in SVs and highly differentiated regions were significantly enriched in metabolic pathways, including fatty metabolism, carbohydrate metabolism, amino acid metabolism and the TCA cycle. These genes may be related to the differences in feeding preferences and the ability to digest carbohydrates between the two grouper species under natural conditions. In addition, protein-coding genes related to the cell cycle and p53-signaling pathway were also detected. These genes may play important roles in the regulation of body size and growth performance. This research provides genomic resources for further breeding works and evolutionary analyses.
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Affiliation(s)
- Yang Yang
- State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals and Guangdong Provincial Key Laboratory for Aquatic Economic Animals, Life Sciences School, Sun Yat-sen University, Guangzhou 510275, China; (Y.Y.); (L.Z.); (T.W.); (L.W.); (X.W.); (J.X.)
- Key Laboratory of Tropical Marine Fish Germplasm Innovation and Utilization, Ministry of Agriculture, Sanya 572025, China
- Key Laboratory of Tropical Aquatic Germplasm of Hainan Province, Sanya 572025, China
| | - Leilei Zeng
- State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals and Guangdong Provincial Key Laboratory for Aquatic Economic Animals, Life Sciences School, Sun Yat-sen University, Guangzhou 510275, China; (Y.Y.); (L.Z.); (T.W.); (L.W.); (X.W.); (J.X.)
| | - Tong Wang
- State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals and Guangdong Provincial Key Laboratory for Aquatic Economic Animals, Life Sciences School, Sun Yat-sen University, Guangzhou 510275, China; (Y.Y.); (L.Z.); (T.W.); (L.W.); (X.W.); (J.X.)
| | - Lina Wu
- State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals and Guangdong Provincial Key Laboratory for Aquatic Economic Animals, Life Sciences School, Sun Yat-sen University, Guangzhou 510275, China; (Y.Y.); (L.Z.); (T.W.); (L.W.); (X.W.); (J.X.)
| | - Xi Wu
- State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals and Guangdong Provincial Key Laboratory for Aquatic Economic Animals, Life Sciences School, Sun Yat-sen University, Guangzhou 510275, China; (Y.Y.); (L.Z.); (T.W.); (L.W.); (X.W.); (J.X.)
| | - Junhong Xia
- State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals and Guangdong Provincial Key Laboratory for Aquatic Economic Animals, Life Sciences School, Sun Yat-sen University, Guangzhou 510275, China; (Y.Y.); (L.Z.); (T.W.); (L.W.); (X.W.); (J.X.)
- Southern Laboratory of Ocean Science and Engineering, Zhuhai 519000, China
| | - Zining Meng
- State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals and Guangdong Provincial Key Laboratory for Aquatic Economic Animals, Life Sciences School, Sun Yat-sen University, Guangzhou 510275, China; (Y.Y.); (L.Z.); (T.W.); (L.W.); (X.W.); (J.X.)
- Southern Laboratory of Ocean Science and Engineering, Zhuhai 519000, China
| | - Xiaochun Liu
- State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals and Guangdong Provincial Key Laboratory for Aquatic Economic Animals, Life Sciences School, Sun Yat-sen University, Guangzhou 510275, China; (Y.Y.); (L.Z.); (T.W.); (L.W.); (X.W.); (J.X.)
- Southern Laboratory of Ocean Science and Engineering, Zhuhai 519000, China
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22
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Li J, Li N, Roellig DM, Zhao W, Guo Y, Feng Y, Xiao L. High subtelomeric GC content in the genome of a zoonotic Cryptosporidium species. Microb Genom 2023; 9:mgen001052. [PMID: 37399068 PMCID: PMC10438818 DOI: 10.1099/mgen.0.001052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Accepted: 05/24/2023] [Indexed: 07/04/2023] Open
Abstract
Cryptosporidium canis is a zoonotic species causing cryptosporidiosis in humans in addition to its natural hosts dogs and other fur animals. To understand the genetic basis for host adaptation, we sequenced the genomes of C. canis from dogs, minks, and foxes and conducted a comparative genomics analysis. While the genomes of C. canis have similar gene contents and organisations, they (~41.0 %) and C. felis (39.6 %) have GC content much higher than other Cryptosporidium spp. (24.3-32.9 %) sequenced to date. The high GC content is mostly restricted to subtelomeric regions of the eight chromosomes. Most of these GC-balanced genes encode Cryptosporidium-specific proteins that have intrinsically disordered regions and are involved in host-parasite interactions. Natural selection appears to play a more important role in the evolution of codon usage in GC-balanced C. canis, and most of the GC-balanced genes have undergone positive selection. While the identity in whole genome sequences between the mink- and dog-derived isolates is 99.9 % (9365 SNVs), it is only 96.0 % (362 894 SNVs) between them and the fox-derived isolate. In agreement with this, the fox-derived isolate possesses more subtelomeric genes encoding invasion-related protein families. Therefore, the change in subtelomeric GC content appears to be responsible for the more GC-balanced C. canis genomes, and the fox-derived isolate could represent a new Cryptosporidium species.
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Affiliation(s)
- Jiayu Li
- State Key Laboratory for Animal Disease Control and Prevention, South China Agricultural University, Guangzhou 510642, PR China
| | - Na Li
- State Key Laboratory for Animal Disease Control and Prevention, South China Agricultural University, Guangzhou 510642, PR China
| | - Dawn M. Roellig
- Division of Foodborne, Waterborne, and Environmental Diseases, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA
| | - Wentao Zhao
- State Key Laboratory for Animal Disease Control and Prevention, South China Agricultural University, Guangzhou 510642, PR China
| | - Yaqiong Guo
- State Key Laboratory for Animal Disease Control and Prevention, South China Agricultural University, Guangzhou 510642, PR China
| | - Yaoyu Feng
- State Key Laboratory for Animal Disease Control and Prevention, South China Agricultural University, Guangzhou 510642, PR China
| | - Lihua Xiao
- State Key Laboratory for Animal Disease Control and Prevention, South China Agricultural University, Guangzhou 510642, PR China
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23
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Shi X, Xia X, Mei J, Gong Z, Zhang J, Xiao Y, Duan C, Liu W. Genome Sequence Resource of a Colletotrichum graminicola Field Strain from China. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2023; 36:447-451. [PMID: 37097710 DOI: 10.1094/mpmi-10-22-0210-a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
The maize anthracnose stalk rot and leaf blight diseases caused by the fungal pathogen Colletotrichum graminicola is emerging as an important threat to corn production worldwide. In this work, we provide an improved genome assembly of a C. graminicola strain (TZ-3) by using the PacBio Sequel II and Illumina high-throughput sequencing technologies. The genome of TZ-3 consists of 36 contigs with a length of 59.3 Mb. After correction and evaluation with the Illumina sequencing data and BUSCO, this genome showed a high assembly quality and integrity. Gene annotation of this genome predicted 11,911 protein-coding genes, among which 983 secreted protein-coding genes and 332 effector genes were predicted. Compared with previous genomes of C. graminicola strains, TZ-3 genome is superior in nearly all parameters. The genome assembly and annotation will enhance our knowledge of the genetic makeup of the pathogen and molecular mechanisms underlying its pathogenicity and will provide valuable insights into genome variation across different regions. [Formula: see text] Copyright © 2023 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.
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Affiliation(s)
- Xuetao Shi
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Gene Editing Technologies (Hainan), Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518000, China
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Xinyao Xia
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Jie Mei
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Ziwen Gong
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Junqi Zhang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Yutao Xiao
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Gene Editing Technologies (Hainan), Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518000, China
| | - Canxing Duan
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Wende Liu
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
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Wu RX, Miao BB, Han FY, Niu SF, Liang YS, Liang ZB, Wang QH. Chromosome-Level Genome Assembly Provides Insights into the Evolution of the Special Morphology and Behaviour of Lepturacanthus savala. Genes (Basel) 2023; 14:1268. [PMID: 37372448 DOI: 10.3390/genes14061268] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Revised: 06/13/2023] [Accepted: 06/13/2023] [Indexed: 06/29/2023] Open
Abstract
Savalani hairtail Lepturacanthus savala is a widely distributed fish along the Indo-Western Pacific coast, and contributes substantially to trichiurid fishery resources worldwide. In this study, the first chromosome-level genome assembly of L. savala was obtained by PacBio SMRT-Seq, Illumina HiSeq, and Hi-C technologies. The final assembled L. savala genome was 790.02 Mb with contig N50 and scaffold N50 values of 19.01 Mb and 32.77 Mb, respectively. The assembled sequences were anchored to 24 chromosomes by using Hi-C data. Combined with RNA sequencing data, 23,625 protein-coding genes were predicted, of which 96.0% were successfully annotated. In total, 67 gene family expansions and 93 gene family contractions were detected in the L. savala genome. Additionally, 1825 positively selected genes were identified. Based on a comparative genomic analysis, we screened a number of candidate genes associated with the specific morphology, behaviour-related immune system, and DNA repair mechanisms in L. savala. Our results preliminarily revealed mechanisms underlying the special morphological and behavioural characteristics of L. savala from a genomic perspective. Furthermore, this study provides valuable reference data for subsequent molecular ecology studies of L. savala and whole-genome analyses of other trichiurid fishes.
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Affiliation(s)
- Ren-Xie Wu
- College of Fisheries, Guangdong Ocean University, Zhanjiang 524088, China
| | - Ben-Ben Miao
- College of Fisheries, Guangdong Ocean University, Zhanjiang 524088, China
| | - Fang-Yuan Han
- College of Fisheries, Guangdong Ocean University, Zhanjiang 524088, China
| | - Su-Fang Niu
- College of Fisheries, Guangdong Ocean University, Zhanjiang 524088, China
| | - Yan-Shan Liang
- College of Fisheries, Guangdong Ocean University, Zhanjiang 524088, China
| | - Zhen-Bang Liang
- College of Fisheries, Guangdong Ocean University, Zhanjiang 524088, China
| | - Qing-Hua Wang
- College of Fisheries, Guangdong Ocean University, Zhanjiang 524088, China
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Guo X, Hu X, Li J, Shao B, Wang Y, Wang L, Li K, Lin D, Wang H, Gao Z, Jiao Y, Wen Y, Ji H, Ma C, Ge S, Jiang W, Jin X. The Sapria himalayana genome provides new insights into the lifestyle of endoparasitic plants. BMC Biol 2023; 21:134. [PMID: 37280593 DOI: 10.1186/s12915-023-01620-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Accepted: 05/09/2023] [Indexed: 06/08/2023] Open
Abstract
BACKGROUND Sapria himalayana (Rafflesiaceae) is an endoparasitic plant characterized by a greatly reduced vegetative body and giant flowers; however, the mechanisms underlying its special lifestyle and greatly altered plant form remain unknown. To illustrate the evolution and adaptation of S. himalayasna, we report its de novo assembled genome and key insights into the molecular basis of its floral development, flowering time, fatty acid biosynthesis, and defense responses. RESULTS The genome of S. himalayana is ~ 1.92 Gb with 13,670 protein-coding genes, indicating remarkable gene loss (~ 54%), especially genes involved in photosynthesis, plant body, nutrients, and defense response. Genes specifying floral organ identity and controlling organ size were identified in S. himalayana and Rafflesia cantleyi, and showed analogous spatiotemporal expression patterns in both plant species. Although the plastid genome had been lost, plastids likely biosynthesize essential fatty acids and amino acids (aromatic amino acids and lysine). A set of credible and functional horizontal gene transfer (HGT) events (involving genes and mRNAs) were identified in the nuclear and mitochondrial genomes of S. himalayana, most of which were under purifying selection. Convergent HGTs in Cuscuta, Orobanchaceae, and S. himalayana were mainly expressed at the parasite-host interface. Together, these results suggest that HGTs act as a bridge between the parasite and host, assisting the parasite in acquiring nutrients from the host. CONCLUSIONS Our results provide new insights into the flower development process and endoparasitic lifestyle of Rafflesiaceae plants. The amount of gene loss in S. himalayana is consistent with the degree of reduction in its body plan. HGT events are common among endoparasites and play an important role in their lifestyle adaptation.
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Affiliation(s)
- Xuelian Guo
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences (IBCAS), Beijing, 100093, China
| | - Xiaodi Hu
- Novogene Bioinformatics Institute, Beijing, 100083, China
| | - Jianwu Li
- Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun Township, Mengla County, Yunnan, 666303, China
| | - Bingyi Shao
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences (IBCAS), Beijing, 100093, China
| | - Yajun Wang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences (IBCAS), Beijing, 100093, China
| | - Long Wang
- Novogene Bioinformatics Institute, Beijing, 100083, China
| | - Kui Li
- Novogene Bioinformatics Institute, Beijing, 100083, China
| | - Dongliang Lin
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences (IBCAS), Beijing, 100093, China
| | - Hanchen Wang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences (IBCAS), Beijing, 100093, China
| | - Zhiyuan Gao
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences (IBCAS), Beijing, 100093, China
| | - Yuannian Jiao
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences (IBCAS), Beijing, 100093, China
| | - Yingying Wen
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences (IBCAS), Beijing, 100093, China
| | - Hongyu Ji
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences (IBCAS), Beijing, 100093, China
| | - Chongbo Ma
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences (IBCAS), Beijing, 100093, China
| | - Song Ge
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences (IBCAS), Beijing, 100093, China
| | - Wenkai Jiang
- Novogene Bioinformatics Institute, Beijing, 100083, China.
| | - Xiaohua Jin
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences (IBCAS), Beijing, 100093, China.
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Gomez-Garrido J, Cruz F, Alioto TS, Feiner N, Uller T, Gut M, Sanchez Escudero I, Tavecchia G, Rotger A, Otalora Acevedo KE, Baldo L. Chromosome-level genome assembly of Lilford's wall lizard, Podarcis lilfordi (Günther, 1874) from the Balearic Islands (Spain). DNA Res 2023; 30:dsad008. [PMID: 37137526 PMCID: PMC10214862 DOI: 10.1093/dnares/dsad008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 03/27/2023] [Accepted: 05/01/2023] [Indexed: 05/05/2023] Open
Abstract
The Mediterranean lizard Podarcis lilfordi is an emblematic species of the Balearic Islands. The extensive phenotypic diversity among extant isolated populations makes the species a great insular model system for eco-evolutionary studies, as well as a challenging target for conservation management plans. Here we report the first high-quality chromosome-level assembly and annotation of the P. lilfordi genome, along with its mitogenome, based on a mixed sequencing strategy (10X Genomics linked reads, Oxford Nanopore Technologies long reads and Hi-C scaffolding) coupled with extensive transcriptomic data (Illumina and PacBio). The genome assembly (1.5 Gb) is highly contiguous (N50 = 90 Mb) and complete, with 99% of the sequence assigned to candidate chromosomal sequences and >97% gene completeness. We annotated a total of 25,663 protein-coding genes translating into 38,615 proteins. Comparison to the genome of the related species Podarcis muralis revealed substantial similarity in genome size, annotation metrics, repeat content, and a strong collinearity, despite their evolutionary distance (~18-20 MYA). This genome expands the repertoire of available reptilian genomes and will facilitate the exploration of the molecular and evolutionary processes underlying the extraordinary phenotypic diversity of this insular species, while providing a critical resource for conservation genomics.
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Affiliation(s)
- Jessica Gomez-Garrido
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), 08028 Barcelona, Spain
| | - Fernando Cruz
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), 08028 Barcelona, Spain
| | - Tyler S Alioto
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), 08028 Barcelona, Spain
| | | | - Tobias Uller
- Department of Biology, Lund University, Lund, Sweden
| | - Marta Gut
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), 08028 Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Ignacio Sanchez Escudero
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), 08028 Barcelona, Spain
| | - Giacomo Tavecchia
- Animal Demography and Ecology Unit, IMEDEA, CSIC-UIB, Esporles, Spain
| | - Andreu Rotger
- Animal Demography and Ecology Unit, IMEDEA, CSIC-UIB, Esporles, Spain
| | - Katherin Eliana Otalora Acevedo
- Department of Evolutionary Biology, Ecology and Environmental Sciences, University of Barcelona, Barcelona, Spain
- Fundación Motiva Inteligencia Colectiva, Biodiversity Branch, Tunja, Boyacá, Colombia
| | - Laura Baldo
- Department of Evolutionary Biology, Ecology and Environmental Sciences, University of Barcelona, Barcelona, Spain
- Institute for Research on Biodiversity (IRBio), University of Barcelona, Barcelona, Spain
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Zhou J, Liu A, He F, Zhang Y, Shen L, Yu J, Zhang X. Draft Genome of White-blotched River Stingray Provides Novel Clues for Niche Adaptation and Skeleton Formation. GENOMICS, PROTEOMICS & BIOINFORMATICS 2023; 21:501-514. [PMID: 36470576 PMCID: PMC10787021 DOI: 10.1016/j.gpb.2022.11.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 11/03/2022] [Accepted: 11/28/2022] [Indexed: 12/12/2022]
Abstract
The white-blotched river stingray (Potamotrygon leopoldi) is a cartilaginous fish native to the Xingu River, a tributary of the Amazon River system. As a rare freshwater-dwelling cartilaginous fish in the Potamotrygonidae family in which no member has the genome sequencing information available, P. leopoldi provides the evolutionary details in fish phylogeny, niche adaptation, and skeleton formation. In this study, we present its draft genome of 4.11 Gb comprising 16,227 contigs and 13,238 scaffolds, with contig N50 of 3937 kb and scaffold N50 of 5675 kb in size. Our analysis shows that P. leopoldi is a slow-evolving fish that diverged from elephant sharks about 96 million years ago. Moreover, two gene families related to the immune system (immunoglobulin heavy constant delta genes and T-cell receptor alpha/delta variable genes) exhibit expansion in P. leopoldi only. We also identified the Hox gene clusters in P. leopoldi and discovered that seven Hox genes shared by five representative fish species are missing in P. leopoldi. The RNA sequencing data from P. leopoldi and other three fish species demonstrate that fishes have a more diversified tissue expression spectrum when compared to mammals. Our functional studies suggest that lack of the gc gene encoding vitamin D-binding protein in cartilaginous fishes (both P. leopoldi and Callorhinchus milii) could partly explain the absence of hard bone in their endoskeleton. Overall, this genome resource provides new insights into the niche adaptation, body plan, and skeleton formation of P. leopoldi, as well as the genome evolution in cartilaginous fishes.
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Affiliation(s)
- Jingqi Zhou
- School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Ake Liu
- Department of Life Sciences, Changzhi University, Changzhi 046011, China
| | - Funan He
- Greehey Children's Cancer Research Institute, UT Health San Antonio, San Antonio, TX 78229, USA
| | - Yunbin Zhang
- State Key Laboratory of Cell Biology, Shanghai Key Laboratory of Molecular Andrology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, China
| | - Libing Shen
- International Human Phenome Institutes (Shanghai), Shanghai 200433, China; Institute of Neuroscience, Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai 200031, China.
| | - Jun Yu
- Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Xiang Zhang
- Shanghai Nanmulin Biotechnology Company Limited, Shanghai 200031, China.
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Wang Y, Wang X, Luo Y, Zhang J, Lin Y, Wu J, Zeng B, Liu L, Yan P, Liang J, Guo H, Jin L, Tang Q, Long K, Li M. Spatio-temporal transcriptome dynamics coordinate rapid transition of core crop functions in 'lactating' pigeon. PLoS Genet 2023; 19:e1010746. [PMID: 37289658 PMCID: PMC10249823 DOI: 10.1371/journal.pgen.1010746] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2022] [Accepted: 04/14/2023] [Indexed: 06/10/2023] Open
Abstract
Pigeons (Columba livia) are among a select few avian species that have developed a specialized reproductive mode wherein the parents produce a 'milk' in their crop to feed newborn squabs. Nonetheless, the transcriptomic dynamics and role in the rapid transition of core crop functions during 'lactation' remain largely unexplored. Here, we generated a de novo pigeon genome assembly to construct a high resolution spatio-temporal transcriptomic landscape of the crop epithelium across the entire breeding stage. This multi-omics analysis identified a set of 'lactation'-related genes involved in lipid and protein metabolism, which contribute to the rapid functional transitions in the crop. Analysis of in situ high-throughput chromatin conformation capture (Hi-C) sequencing revealed extensive reorganization of promoter-enhancer interactions linked to the dynamic expression of these 'lactation'-related genes between stages. Moreover, their expression is spatially localized in specific epithelial layers, and can be correlated with phenotypic changes in the crop. These results illustrate the preferential de novo synthesis of 'milk' lipids and proteins in the crop, and provides candidate enhancer loci for further investigation of the regulatory elements controlling pigeon 'lactation'.
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Affiliation(s)
- Yujie Wang
- Livestock and Poultry Multi-omics Key Laboratory of Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Xun Wang
- Livestock and Poultry Multi-omics Key Laboratory of Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Institute of Animal Genetics and Breeding, Sichuan Agricultural University, Chengdu, China
| | - Yi Luo
- Livestock and Poultry Multi-omics Key Laboratory of Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Jiaman Zhang
- Livestock and Poultry Multi-omics Key Laboratory of Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Yu Lin
- Livestock and Poultry Multi-omics Key Laboratory of Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Jie Wu
- Livestock and Poultry Multi-omics Key Laboratory of Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Bo Zeng
- Livestock and Poultry Multi-omics Key Laboratory of Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Institute of Animal Genetics and Breeding, Sichuan Agricultural University, Chengdu, China
| | - Lei Liu
- Livestock and Poultry Multi-omics Key Laboratory of Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Peiqi Yan
- Livestock and Poultry Multi-omics Key Laboratory of Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Jiyuan Liang
- Livestock and Poultry Multi-omics Key Laboratory of Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Hongrui Guo
- College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Long Jin
- Livestock and Poultry Multi-omics Key Laboratory of Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Institute of Animal Genetics and Breeding, Sichuan Agricultural University, Chengdu, China
| | - Qianzi Tang
- Livestock and Poultry Multi-omics Key Laboratory of Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Institute of Animal Genetics and Breeding, Sichuan Agricultural University, Chengdu, China
| | - Keren Long
- Livestock and Poultry Multi-omics Key Laboratory of Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Institute of Animal Genetics and Breeding, Sichuan Agricultural University, Chengdu, China
| | - Mingzhou Li
- Livestock and Poultry Multi-omics Key Laboratory of Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Institute of Animal Genetics and Breeding, Sichuan Agricultural University, Chengdu, China
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29
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Xu L, Wang Y, Dong J, Zhang W, Tang M, Zhang W, Wang K, Chen Y, Zhang X, He Q, Zhang X, Wang K, Wang L, Ma Y, Xia K, Liu L. A chromosome-level genome assembly of radish (Raphanus sativus L.) reveals insights into genome adaptation and differential bolting regulation. PLANT BIOTECHNOLOGY JOURNAL 2023; 21:990-1004. [PMID: 36648398 PMCID: PMC10106849 DOI: 10.1111/pbi.14011] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Revised: 11/29/2022] [Accepted: 01/03/2023] [Indexed: 05/04/2023]
Abstract
High-quality radish (Raphanus sativus) genome represents a valuable resource for agronomical trait improvements and understanding genome evolution among Brassicaceae species. However, existing radish genome assembly remains fragmentary, which greatly hampered functional genomics research and genome-assisted breeding. Here, using a NAU-LB radish inbred line, we generated a reference genome of 476.32 Mb with a scaffold N50 of 56.88 Mb by incorporating Illumina, PacBio and BioNano optical mapping techniques. Utilizing Hi-C data, 448.12 Mb (94.08%) of the assembled sequences were anchored to nine radish chromosomes with 40 306 protein-coding genes annotated. In total, 249.14 Mb (52.31%) comprised the repetitive sequences, among which long terminal repeats (LTRs, 30.31%) were the most abundant class. Beyond confirming the whole-genome triplication (WGT) event in R. sativus lineage, we found several tandem arrayed genes were involved in stress response process, which may account for the distinctive phenotype of high disease resistance in R. sativus. By comparing against the existing Xin-li-mei radish genome, a total of 2 108 573 SNPs, 7740 large insertions, 7757 deletions and 84 inversions were identified. Interestingly, a 647-bp insertion in the promoter of RsVRN1 gene can be directly bound by the DOF transcription repressor RsCDF3, resulting into its low promoter activity and late-bolting phenotype of NAU-LB cultivar. Importantly, introgression of this 647-bp insertion allele, RsVRN1In-536 , into early-bolting genotype could contribute to delayed bolting time, indicating that it is a potential genetic resource for radish late-bolting breeding. Together, this genome resource provides valuable information to facilitate comparative genomic analysis and accelerate genome-guided breeding and improvement in radish.
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Affiliation(s)
- Liang Xu
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Horticultural Crop Biology and Genetic Improvement (East China) of MOAR, College of HorticultureNanjing Agricultural UniversityNanjingChina
| | - Yan Wang
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Horticultural Crop Biology and Genetic Improvement (East China) of MOAR, College of HorticultureNanjing Agricultural UniversityNanjingChina
| | - Junhui Dong
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Horticultural Crop Biology and Genetic Improvement (East China) of MOAR, College of HorticultureNanjing Agricultural UniversityNanjingChina
| | - Wei Zhang
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Horticultural Crop Biology and Genetic Improvement (East China) of MOAR, College of HorticultureNanjing Agricultural UniversityNanjingChina
- College of Horticulture and Landscape ArchitectureYangzhou UniversityYangzhouChina
| | - Mingjia Tang
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Horticultural Crop Biology and Genetic Improvement (East China) of MOAR, College of HorticultureNanjing Agricultural UniversityNanjingChina
| | - Weilan Zhang
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Horticultural Crop Biology and Genetic Improvement (East China) of MOAR, College of HorticultureNanjing Agricultural UniversityNanjingChina
| | - Kai Wang
- School of Life SciencesNantong UniversityNantongChina
| | - Yinglong Chen
- The UWA Institute of Agriculture, and School of Agriculture and EnvironmentThe University of Western AustraliaPerthWAAustralia
| | - Xiaoli Zhang
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Horticultural Crop Biology and Genetic Improvement (East China) of MOAR, College of HorticultureNanjing Agricultural UniversityNanjingChina
| | - Qing He
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Horticultural Crop Biology and Genetic Improvement (East China) of MOAR, College of HorticultureNanjing Agricultural UniversityNanjingChina
| | - Xinyu Zhang
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Horticultural Crop Biology and Genetic Improvement (East China) of MOAR, College of HorticultureNanjing Agricultural UniversityNanjingChina
| | - Kai Wang
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Horticultural Crop Biology and Genetic Improvement (East China) of MOAR, College of HorticultureNanjing Agricultural UniversityNanjingChina
| | - Lun Wang
- College of Horticulture and Landscape ArchitectureYangzhou UniversityYangzhouChina
| | - Yinbo Ma
- College of Horticulture and Landscape ArchitectureYangzhou UniversityYangzhouChina
| | - Kai Xia
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Horticultural Crop Biology and Genetic Improvement (East China) of MOAR, College of HorticultureNanjing Agricultural UniversityNanjingChina
| | - Liwang Liu
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Horticultural Crop Biology and Genetic Improvement (East China) of MOAR, College of HorticultureNanjing Agricultural UniversityNanjingChina
- College of Horticulture and Landscape ArchitectureYangzhou UniversityYangzhouChina
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30
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Lu P, Yang J, Li M, Wen S, Zhang T, Yan C, Liu R, Xiao Y, Wang X, Jiang W. A desert lncRNA HIDEN regulates human endoderm differentiation via interacting with IMP1 and stabilizing FZD5 mRNA. Genome Biol 2023; 24:92. [PMID: 37095549 PMCID: PMC10124006 DOI: 10.1186/s13059-023-02925-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Accepted: 04/07/2023] [Indexed: 04/26/2023] Open
Abstract
BACKGROUND Extensive studies have revealed the function and mechanism of lncRNAs in development and differentiation, but the majority have focused on those lncRNAs adjacent to protein-coding genes. In contrast, lncRNAs located in gene deserts are rarely explored. Here, we utilize multiple differentiation systems to dissect the role of a desert lncRNA, HIDEN (human IMP1-associated "desert" definitive endoderm lncRNA), in definitive endoderm differentiation from human pluripotent stem cells. RESULTS We show that desert lncRNAs are highly expressed with cell-stage-specific patterns and conserved subcellular localization during stem cell differentiation. We then focus on the desert lncRNA HIDEN which is upregulated and plays a vital role during human endoderm differentiation. We find depletion of HIDEN by either shRNA or promoter deletion significantly impairs human endoderm differentiation. HIDEN functionally interacts with RNA-binding protein IMP1 (IGF2BP1), which is also required for endoderm differentiation. Loss of HIDEN or IMP1 results in reduced WNT activity, and WNT agonist rescues endoderm differentiation deficiency caused by the depletion of HIDEN or IMP1. Moreover, HIDEN depletion reduces the interaction between IMP1 protein and FZD5 mRNA and causes the destabilization of FZD5 mRNA, which is a WNT receptor and necessary for definitive endoderm differentiation. CONCLUSIONS These data suggest that desert lncRNA HIDEN facilitates the interaction between IMP1 and FZD5 mRNA, stabilizing FZD5 mRNA which activates WNT signaling and promotes human definitive endoderm differentiation.
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Affiliation(s)
- Pei Lu
- Department of Biological Repositories, Frontier Science Center for Immunology and Metabolism, Medical Research Institute, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan, 430071, China
| | - Jie Yang
- Department of Biological Repositories, Frontier Science Center for Immunology and Metabolism, Medical Research Institute, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan, 430071, China
| | - Mao Li
- Department of Biological Repositories, Frontier Science Center for Immunology and Metabolism, Medical Research Institute, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan, 430071, China
| | - Shanshan Wen
- Department of Biological Repositories, Frontier Science Center for Immunology and Metabolism, Medical Research Institute, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan, 430071, China
| | - Tianzhe Zhang
- Department of Biological Repositories, Frontier Science Center for Immunology and Metabolism, Medical Research Institute, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan, 430071, China
| | - Chenchao Yan
- Department of Biological Repositories, Frontier Science Center for Immunology and Metabolism, Medical Research Institute, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan, 430071, China
| | - Ran Liu
- Department of Biological Repositories, Frontier Science Center for Immunology and Metabolism, Medical Research Institute, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan, 430071, China
- Department of Urology, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China
| | - Yu Xiao
- Department of Biological Repositories, Frontier Science Center for Immunology and Metabolism, Medical Research Institute, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan, 430071, China
- Department of Urology, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China
- Human Genetics Resource Preservation Center of Wuhan University, Wuhan, 430071, China
| | - Xinghuan Wang
- Department of Biological Repositories, Frontier Science Center for Immunology and Metabolism, Medical Research Institute, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan, 430071, China
- Department of Urology, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China
- Human Genetics Resource Preservation Center of Wuhan University, Wuhan, 430071, China
| | - Wei Jiang
- Department of Biological Repositories, Frontier Science Center for Immunology and Metabolism, Medical Research Institute, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan, 430071, China.
- Human Genetics Resource Preservation Center of Wuhan University, Wuhan, 430071, China.
- RNA Institute, Wuhan University, Wuhan, 430071, China.
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Zhang Z, Pei P, Zhang M, Li F, Tang G. Chromosome-level genome assembly of Dastarcus helophoroides provides insights into CYP450 genes expression upon insecticide exposure. PEST MANAGEMENT SCIENCE 2023; 79:1467-1482. [PMID: 36502364 DOI: 10.1002/ps.7319] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 10/26/2022] [Accepted: 12/11/2022] [Indexed: 06/17/2023]
Abstract
BACKGROUND Dastarcus helophoroides is an important natural enemy of cerambycids, and is wildly used in biological control of pests. Nevertheless, the absence of complete genomic information limits the investigation of the underlying molecular mechanisms. Here, a chromosome-level of Dastarcus helophoroides genome is assembled using a combination strategy of Illumina, PacBio, 10x™ Genomics, and Hi-C. RESULTS The final assembly is 609.09 Mb with contig N50, scaffold N50 and GC content of 5.46 Mb, 42.56 Mb and 31.50%, respectively, and 95.25% of the contigs anchor into 13 chromosomes. In total 14 890 protein-coding genes and 65.37% repeat sequences are predicted in the assembly genome. The phylogenetic analysis of single-copy gene families shared among 20 insect species indicates that Dastarcus helophoroides is placed as the sister species to clade (Nitidulidae+Curculionoidea+Chrysomeloidea) + Tenebrionoidea, and diverges from the related species ~242.9 Mya. In total 36 expanded gene families are identified in Dastarcus helophoroides genome, and are functionally related to drug metabolism and metabolism of xenobiotics by cytochrome P450. Some members of CYP4 Clade and CYP6 Clade are up-regulated in Dastarcus helophoroides adults upon insecticide exposure, of which expressions of DhCYP4Q, DhCYP6A14X1 and DhCYP4C1 are significantly up-regulated. The silencing of the three genes leads to adults more sensitive to insecticide and increased knocked-down rate, which may indicate their critical roles in stress resistance and detoxication. CONCLUSION Our study systematically integrated the chromosome-level genome, transcriptome and gene expression of Dastarcus helophoroides, which will provide valuable resources for understanding mechanisms of pesticide metabolism, growth and development, and utilization of the natural enemy in integrated control. © 2022 Society of Chemical Industry.
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Affiliation(s)
- Zhengqing Zhang
- Key Laboratory of National Forestry and Grassland Administration on Management of Western Forest Bio-Disaster, College of Forestry, Northwest A&F University, Yangling, P. R. China
| | - Pei Pei
- Key Laboratory of National Forestry and Grassland Administration on Management of Western Forest Bio-Disaster, College of Forestry, Northwest A&F University, Yangling, P. R. China
| | - Meng Zhang
- Key Laboratory of National Forestry and Grassland Administration on Management of Western Forest Bio-Disaster, College of Forestry, Northwest A&F University, Yangling, P. R. China
| | - Feifei Li
- Key Laboratory of National Forestry and Grassland Administration on Management of Western Forest Bio-Disaster, College of Forestry, Northwest A&F University, Yangling, P. R. China
| | - Guanghui Tang
- Key Laboratory of National Forestry and Grassland Administration on Management of Western Forest Bio-Disaster, College of Forestry, Northwest A&F University, Yangling, P. R. China
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Yang Z, Li X, Yang L, Peng S, Song W, Lin Y, Xiang G, Li Y, Ye S, Ma C, Miao J, Zhang G, Chen W, Yang S, Dong Y. Comparative genomics reveals the diversification of triterpenoid biosynthesis and origin of ocotillol-type triterpenes in Panax. PLANT COMMUNICATIONS 2023:100591. [PMID: 36926697 PMCID: PMC10363511 DOI: 10.1016/j.xplc.2023.100591] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Revised: 01/14/2023] [Accepted: 03/13/2023] [Indexed: 06/18/2023]
Abstract
Gene duplication is assumed to be the major force driving the evolution of metabolite biosynthesis in plants. Freed from functional burdens, duplicated genes can mutate toward novelties until fixed due to selective fitness. However, the extent to which this mechanism has driven the diversification of metabolite biosynthesis remains to be tested. Here we performed comparative genomics analysis and functional characterization to evaluate the impact of gene duplication on the evolution of triterpenoid biosynthesis using Panax species as models. We found that whole-genome duplications (WGDs) occurred independently in Araliaceae and Apiaceae lineages. Comparative genomics revealed the evolutionary trajectories of triterpenoid biosynthesis in plants, which was mainly promoted by WGDs and tandem duplication. Lanosterol synthase (LAS) was likely derived from a tandem duplicate of cycloartenol synthase that predated the emergence of Nymphaeales. Under episodic diversifying selection, the LAS gene duplicates produced by γ whole-genome triplication have given rise to triterpene biosynthesis in core eudicots through neofunctionalization. Moreover, functional characterization revealed that oxidosqualene cyclases (OSCs) responsible for synthesizing dammarane-type triterpenes in Panax species were also capable of producing ocotillol-type triterpenes. Genomic and biochemical evidence suggested that Panax genes encoding the above OSCs originated from the specialization of one OSC gene duplicate produced from a recent WGD shared by Araliaceae (Pg-β). Our results reveal the crucial role of gene duplication in diversification of triterpenoid biosynthesis in plants and provide insight into the origin of ocotillol-type triterpenes in Panax species.
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Affiliation(s)
- Zijiang Yang
- National & Local Joint Engineering Research Center on Germplasm Innovation & Utilization of Chinese Medicinal Materials in Southwest China, Yunnan Agricultural University, Kunming, China; The Key Laboratory of Medicinal Plant Biology of Yunnan Province, Yunnan Agricultural University, Kunming, China
| | - Xiaobo Li
- National & Local Joint Engineering Research Center on Germplasm Innovation & Utilization of Chinese Medicinal Materials in Southwest China, Yunnan Agricultural University, Kunming, China; The Key Laboratory of Medicinal Plant Biology of Yunnan Province, Yunnan Agricultural University, Kunming, China
| | - Ling Yang
- National & Local Joint Engineering Research Center on Germplasm Innovation & Utilization of Chinese Medicinal Materials in Southwest China, Yunnan Agricultural University, Kunming, China; College of Food Science and Technology, Yunnan Agricultural University, Kunming, China
| | - Sufang Peng
- National & Local Joint Engineering Research Center on Germplasm Innovation & Utilization of Chinese Medicinal Materials in Southwest China, Yunnan Agricultural University, Kunming, China; The Key Laboratory of Medicinal Plant Biology of Yunnan Province, Yunnan Agricultural University, Kunming, China
| | - Wanling Song
- National & Local Joint Engineering Research Center on Germplasm Innovation & Utilization of Chinese Medicinal Materials in Southwest China, Yunnan Agricultural University, Kunming, China; The Key Laboratory of Medicinal Plant Biology of Yunnan Province, Yunnan Agricultural University, Kunming, China
| | - Yuan Lin
- National & Local Joint Engineering Research Center on Germplasm Innovation & Utilization of Chinese Medicinal Materials in Southwest China, Yunnan Agricultural University, Kunming, China; The Key Laboratory of Medicinal Plant Biology of Yunnan Province, Yunnan Agricultural University, Kunming, China
| | - Guisheng Xiang
- National & Local Joint Engineering Research Center on Germplasm Innovation & Utilization of Chinese Medicinal Materials in Southwest China, Yunnan Agricultural University, Kunming, China; The Key Laboratory of Medicinal Plant Biology of Yunnan Province, Yunnan Agricultural University, Kunming, China
| | - Ying Li
- National & Local Joint Engineering Research Center on Germplasm Innovation & Utilization of Chinese Medicinal Materials in Southwest China, Yunnan Agricultural University, Kunming, China; The Key Laboratory of Medicinal Plant Biology of Yunnan Province, Yunnan Agricultural University, Kunming, China
| | - Shuang Ye
- National & Local Joint Engineering Research Center on Germplasm Innovation & Utilization of Chinese Medicinal Materials in Southwest China, Yunnan Agricultural University, Kunming, China; The Key Laboratory of Medicinal Plant Biology of Yunnan Province, Yunnan Agricultural University, Kunming, China
| | - Chunhua Ma
- National & Local Joint Engineering Research Center on Germplasm Innovation & Utilization of Chinese Medicinal Materials in Southwest China, Yunnan Agricultural University, Kunming, China; The Key Laboratory of Medicinal Plant Biology of Yunnan Province, Yunnan Agricultural University, Kunming, China
| | - Jianhua Miao
- Guangxi Key Laboratory of Medicinal Resources Protection and Genetic Improvement, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
| | - Guanghui Zhang
- National & Local Joint Engineering Research Center on Germplasm Innovation & Utilization of Chinese Medicinal Materials in Southwest China, Yunnan Agricultural University, Kunming, China; The Key Laboratory of Medicinal Plant Biology of Yunnan Province, Yunnan Agricultural University, Kunming, China
| | - Wei Chen
- National & Local Joint Engineering Research Center on Germplasm Innovation & Utilization of Chinese Medicinal Materials in Southwest China, Yunnan Agricultural University, Kunming, China; Guangxi Key Laboratory of Medicinal Resources Protection and Genetic Improvement, Guangxi Botanical Garden of Medicinal Plants, Nanning, China; Yunnan Plateau Characteristic Agriculture Industry Research Institute, Kunming, China
| | - Shengchao Yang
- National & Local Joint Engineering Research Center on Germplasm Innovation & Utilization of Chinese Medicinal Materials in Southwest China, Yunnan Agricultural University, Kunming, China; The Key Laboratory of Medicinal Plant Biology of Yunnan Province, Yunnan Agricultural University, Kunming, China.
| | - Yang Dong
- National & Local Joint Engineering Research Center on Germplasm Innovation & Utilization of Chinese Medicinal Materials in Southwest China, Yunnan Agricultural University, Kunming, China; Guangxi Key Laboratory of Medicinal Resources Protection and Genetic Improvement, Guangxi Botanical Garden of Medicinal Plants, Nanning, China; Yunnan Plateau Characteristic Agriculture Industry Research Institute, Kunming, China.
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Lou H, Song L, Li X, Zi H, Chen W, Gao Y, Zheng S, Fei Z, Sun X, Wu J. The Torreya grandis genome illuminates the origin and evolution of gymnosperm-specific sciadonic acid biosynthesis. Nat Commun 2023; 14:1315. [PMID: 36898990 PMCID: PMC10006428 DOI: 10.1038/s41467-023-37038-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Accepted: 02/28/2023] [Indexed: 03/12/2023] Open
Abstract
Torreya plants produce dry fruits with assorted functions. Here, we report the 19-Gb chromosome-level genome assembly of T. grandis. The genome is shaped by ancient whole-genome duplications and recurrent LTR retrotransposon bursts. Comparative genomic analyses reveal key genes involved in reproductive organ development, cell wall biosynthesis and seed storage. Two genes encoding a C18 Δ9-elongase and a C20 Δ5-desaturase are identified to be responsible for sciadonic acid biosynthesis and both are present in diverse plant lineages except angiosperms. We demonstrate that the histidine-rich boxes of the Δ5-desaturase are crucial for its catalytic activity. Methylome analysis reveals that methylation valleys of the T. grandis seed genome harbor genes associated with important seed activities, including cell wall and lipid biosynthesis. Moreover, seed development is accompanied by DNA methylation changes that possibly fuel energy production. This study provides important genomic resources and elucidates the evolutionary mechanism of sciadonic acid biosynthesis in land plants.
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Affiliation(s)
- Heqiang Lou
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, 311300, Zhejiang, China
| | - Lili Song
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, 311300, Zhejiang, China
| | - Xiaolong Li
- Collaborative Innovation Center for Efficient and Green Production of Agriculture in Mountainous Areas of Zhejiang Province, Zhejiang A&F University, Hangzhou, 311300, Zhejiang, China.,Key Laboratory of Quality and Safety Control for Subtropical Fruit and Vegetable, Ministry of Agriculture and Rural Affairs, Hangzhou, 311300, Zhejiang, China
| | - Hailing Zi
- Novogene Bioinformatics Institute, 100083, Beijing, China
| | - Weijie Chen
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, 311300, Zhejiang, China
| | - Yadi Gao
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, 311300, Zhejiang, China
| | - Shan Zheng
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, 311300, Zhejiang, China
| | - Zhangjun Fei
- Boyce Thompson Institute, Cornell University, Ithaca, NY, 14853, USA. .,U.S. Department of Agriculture-Agricultural Research Service, Robert W. Holley Center for Agriculture and Health, Ithaca, NY, 14853, USA.
| | - Xuepeng Sun
- Collaborative Innovation Center for Efficient and Green Production of Agriculture in Mountainous Areas of Zhejiang Province, Zhejiang A&F University, Hangzhou, 311300, Zhejiang, China. .,Key Laboratory of Quality and Safety Control for Subtropical Fruit and Vegetable, Ministry of Agriculture and Rural Affairs, Hangzhou, 311300, Zhejiang, China.
| | - Jiasheng Wu
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, 311300, Zhejiang, China.
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Jiang S, Zhang X, Yang X, Liu C, Wang L, Ma B, Miao Y, Hu J, Tan K, Wang Y, Jiang H, Wang J. A chromosome-level genome assembly of an early matured aromatic Japonica rice variety Qigeng10 to accelerate rice breeding for high grain quality in Northeast China. FRONTIERS IN PLANT SCIENCE 2023; 14:1134308. [PMID: 36909446 PMCID: PMC9995481 DOI: 10.3389/fpls.2023.1134308] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Accepted: 02/10/2023] [Indexed: 06/18/2023]
Abstract
Early-matured aromatic japonica rice from the Northeast is the most popular rice commodity in the Chinese market. The Qigeng10 (QG10) was one of the varieties with the largest planting area in this region in recent years. It was an early-matured japonica rice variety with a lot of superior traits such as semi-dwarf, lodging resistance, long grain, aromatic and good quality. Therefore, a high-quality assembly of Qigeng10 genome is critical and useful for japonica research and breeding. In this study, we produced a high-precision QG10 chromosome-level genome by using a combination of Nanopore and Hi-C platforms. Finally, we assembled the QG10 genome into 77 contigs with an N50 length of 11.80 Mb in 27 scaffolds with an N50 length of 30.55 Mb. The assembled genome size was 378.31Mb with 65 contigs and constituted approximately 99.59% of the 12 chromosomes. We identified a total of 1,080,819 SNPs and 682,392 InDels between QG10 and Nipponbare. We also annotated 57,599 genes by the Ab initio method, homology-based technique, and RNA-seq. Based on the assembled genome sequence, we detected the sequence variation in a total of 63 cloned genes involved in grain yield, grain size, disease tolerance, lodging resistance, fragrance, and many other important traits. Finally, we identified five elite alleles (qTGW2Nipponbare , qTGW3Nanyangzhan , GW5IR24 , GW6Suyunuo , and qGW8Basmati385 ) controlling long grain size, four elite alleles (COLD1Nipponbare , bZIP73Nipponbare , CTB4aKunmingxiaobaigu , and CTB2Kunmingxiaobaigu ) controlling cold tolerance, three non-functional alleles (DTH7Kitaake , Ghd7Hejiang19 , and Hd1Longgeng31 ) for early heading, two resistant alleles (PiaAkihikari and Pid4Digu ) for rice blast, a resistant allele STV11Kasalath for rice stripe virus, an NRT1.1BIR24 allele for higher nitrate absorption activity, an elite allele SCM3Chugoku117 for stronger culms, and the typical aromatic gene badh2-E2 for fragrance in QG10. These results not only help us to better elucidate the genetic mechanisms underlying excellent agronomic traits in QG10 but also have wide-ranging implications for genomics-assisted breeding in early-matured fragrant japonica rice.
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Affiliation(s)
- Shukun Jiang
- Qiqihar Branch of Heilongjiang Academy of Agricultural Sciences, Qiqihar, China
- Heilongjiang Provincial Key Laboratory of Crop Physiology and Ecology in Cold Region, Heilongjiang Provincial Engineering Technology Research Center of Crop Cold Damage, Harbin, China
- Northeast Branch of National Salt-Alkali Tolerant Rice Technology Innovation Center, Harbin, China
| | - Xijuan Zhang
- Heilongjiang Provincial Key Laboratory of Crop Physiology and Ecology in Cold Region, Heilongjiang Provincial Engineering Technology Research Center of Crop Cold Damage, Harbin, China
- Northeast Branch of National Salt-Alkali Tolerant Rice Technology Innovation Center, Harbin, China
- Crop Cultivation and Tillage Institute of Heilongjiang Academy of Agricultural Sciences, Harbin, China
| | - Xianli Yang
- Heilongjiang Provincial Key Laboratory of Crop Physiology and Ecology in Cold Region, Heilongjiang Provincial Engineering Technology Research Center of Crop Cold Damage, Harbin, China
- Northeast Branch of National Salt-Alkali Tolerant Rice Technology Innovation Center, Harbin, China
- Crop Cultivation and Tillage Institute of Heilongjiang Academy of Agricultural Sciences, Harbin, China
| | - Chuanzeng Liu
- Qiqihar Branch of Heilongjiang Academy of Agricultural Sciences, Qiqihar, China
- Northeast Branch of National Salt-Alkali Tolerant Rice Technology Innovation Center, Harbin, China
| | - Lizhi Wang
- Heilongjiang Provincial Key Laboratory of Crop Physiology and Ecology in Cold Region, Heilongjiang Provincial Engineering Technology Research Center of Crop Cold Damage, Harbin, China
- Northeast Branch of National Salt-Alkali Tolerant Rice Technology Innovation Center, Harbin, China
- Crop Cultivation and Tillage Institute of Heilongjiang Academy of Agricultural Sciences, Harbin, China
| | - Bo Ma
- Qiqihar Branch of Heilongjiang Academy of Agricultural Sciences, Qiqihar, China
- Northeast Branch of National Salt-Alkali Tolerant Rice Technology Innovation Center, Harbin, China
| | - Yi Miao
- Qiqihar Branch of Heilongjiang Academy of Agricultural Sciences, Qiqihar, China
- Northeast Branch of National Salt-Alkali Tolerant Rice Technology Innovation Center, Harbin, China
| | - Jifang Hu
- Qiqihar Branch of Heilongjiang Academy of Agricultural Sciences, Qiqihar, China
- Northeast Branch of National Salt-Alkali Tolerant Rice Technology Innovation Center, Harbin, China
| | - Kefei Tan
- Qiqihar Branch of Heilongjiang Academy of Agricultural Sciences, Qiqihar, China
- Northeast Branch of National Salt-Alkali Tolerant Rice Technology Innovation Center, Harbin, China
| | - Yuxian Wang
- Qiqihar Branch of Heilongjiang Academy of Agricultural Sciences, Qiqihar, China
- Northeast Branch of National Salt-Alkali Tolerant Rice Technology Innovation Center, Harbin, China
| | - Hui Jiang
- Keshan Branch of Heilongjiang Academy of Agricultural Sciences, Qiqihar, China
| | - Junhe Wang
- Heilongjiang Provincial Key Laboratory of Crop Physiology and Ecology in Cold Region, Heilongjiang Provincial Engineering Technology Research Center of Crop Cold Damage, Harbin, China
- Crop Cultivation and Tillage Institute of Heilongjiang Academy of Agricultural Sciences, Harbin, China
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35
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Julca I, Mutwil-Anderwald D, Manoj V, Khan Z, Lai SK, Yang LK, Beh IT, Dziekan J, Lim YP, Lim SK, Low YW, Lam YI, Tjia S, Mu Y, Tan QW, Nuc P, Choo LM, Khew G, Shining L, Kam A, Tam JP, Bozdech Z, Schmidt M, Usadel B, Kanagasundaram Y, Alseekh S, Fernie A, Li HY, Mutwil M. Genomic, transcriptomic, and metabolomic analysis of Oldenlandia corymbosa reveals the biosynthesis and mode of action of anti-cancer metabolites. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2023. [PMID: 36807520 DOI: 10.1111/jipb.13469] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Accepted: 02/18/2023] [Indexed: 06/18/2023]
Abstract
Plants accumulate a vast array of secondary metabolites, which constitute a natural resource for pharmaceuticals. Oldenlandia corymbosa belongs to the Rubiaceae family, and has been used in traditional medicine to treat different diseases, including cancer. However, the active metabolites of the plant, their biosynthetic pathway and mode of action in cancer are unknown. To fill these gaps, we exposed this plant to eight different stress conditions and combined different omics data capturing gene expression, metabolic profiles, and anti-cancer activity. Our results show that O. corymbosa extracts are active against breast cancer cell lines and that ursolic acid is responsible for this activity. Moreover, we assembled a high-quality genome and uncovered two genes involved in the biosynthesis of ursolic acid. Finally, we also revealed that ursolic acid causes mitotic catastrophe in cancer cells and identified three high-confidence protein binding targets by Cellular Thermal Shift Assay (CETSA) and reverse docking. Altogether, these results constitute a valuable resource to further characterize the biosynthesis of active metabolites in the Oldenlandia group, while the mode of action of ursolic acid will allow us to further develop this valuable compound.
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Affiliation(s)
- Irene Julca
- School of Biological Sciences, Nanyang Technological University, Singapore, 639798, Singapore
| | | | - Vaishnervi Manoj
- School of Biological Sciences, Nanyang Technological University, Singapore, 639798, Singapore
| | - Zahra Khan
- School of Biological Sciences, Nanyang Technological University, Singapore, 639798, Singapore
| | - Soak Kuan Lai
- School of Biological Sciences, Nanyang Technological University, Singapore, 639798, Singapore
| | - Lay K Yang
- Shared Analytics, Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science, Technology and Research (A*STAR), Singapore, 138671, Singapore
| | - Ing T Beh
- School of Biological Sciences, Nanyang Technological University, Singapore, 639798, Singapore
| | - Jerzy Dziekan
- School of Biological Sciences, Nanyang Technological University, Singapore, 639798, Singapore
| | - Yoon P Lim
- Department of Biochemistry, National University of Singapore, Singapore, 117596, Singapore
| | - Shen K Lim
- School of Biological Sciences, Nanyang Technological University, Singapore, 639798, Singapore
- Department of Biochemistry, National University of Singapore, Singapore, 117596, Singapore
| | - Yee W Low
- Singapore Botanic Gardens, Singapore, 259569, Singapore
| | - Yuen I Lam
- School of Biological Sciences, Nanyang Technological University, Singapore, 639798, Singapore
| | - Seth Tjia
- School of Biological Sciences, Nanyang Technological University, Singapore, 639798, Singapore
| | - Yuguang Mu
- School of Biological Sciences, Nanyang Technological University, Singapore, 639798, Singapore
| | - Qiao W Tan
- School of Biological Sciences, Nanyang Technological University, Singapore, 639798, Singapore
| | - Przemyslaw Nuc
- Department of Gene Expression, Faculty of Biology, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Poznan, 61-614, Poland
| | - Le M Choo
- Singapore Botanic Gardens, Singapore, 259569, Singapore
| | - Gillian Khew
- School of Biological Sciences, Nanyang Technological University, Singapore, 639798, Singapore
- Singapore Botanic Gardens, Singapore, 259569, Singapore
| | - Loo Shining
- School of Biological Sciences, Nanyang Technological University, Singapore, 639798, Singapore
| | - Antony Kam
- School of Biological Sciences, Nanyang Technological University, Singapore, 639798, Singapore
| | - James P Tam
- School of Biological Sciences, Nanyang Technological University, Singapore, 639798, Singapore
| | - Zbynek Bozdech
- School of Biological Sciences, Nanyang Technological University, Singapore, 639798, Singapore
| | | | - Bjoern Usadel
- IBG-4 Bioinformatics, Forschungszentrum Jülich, Jülich, 52428, Germany
| | - Yoganathan Kanagasundaram
- Shared Analytics, Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science, Technology and Research (A*STAR), Singapore, 138671, Singapore
| | - Saleh Alseekh
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Potsdam-Golm, 14476, Germany
- Center of Plant Systems Biology and Biotechnology, Plovdiv, 4000, Bulgaria
| | - Alisdair Fernie
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Potsdam-Golm, 14476, Germany
- Center of Plant Systems Biology and Biotechnology, Plovdiv, 4000, Bulgaria
| | - Hoi Y Li
- School of Biological Sciences, Nanyang Technological University, Singapore, 639798, Singapore
| | - Marek Mutwil
- School of Biological Sciences, Nanyang Technological University, Singapore, 639798, Singapore
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Gao Y, Xu J, Li Z, Zhang Y, Riera N, Xiong Z, Ouyang Z, Liu X, Lu Z, Seymour D, Zhong B, Wang N. Citrus genomic resources unravel putative genetic determinants of Huanglongbing pathogenicity. iScience 2023; 26:106024. [PMID: 36824272 PMCID: PMC9941208 DOI: 10.1016/j.isci.2023.106024] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2022] [Revised: 11/08/2022] [Accepted: 01/17/2023] [Indexed: 01/24/2023] Open
Abstract
Citrus HLB caused by Candidatus Liberibacter asiaticus is a pathogen-triggered immune disease. Here, we identified putative genetic determinants of HLB pathogenicity by integrating citrus genomic resources to characterize the pan-genome of accessions that differ in their response to HLB. Genome-wide association mapping and analysis of allele-specific expression between susceptible, tolerant, and resistant accessions further refined candidates underlying the response to HLB. We first developed a phased diploid assembly of Citrus sinensis 'Newhall' genome and produced resequencing data for 91 citrus accessions that differ in their response to HLB. These data were combined with previous resequencing data from 356 accessions for genome-wide association mapping of the HLB response. Genes determinants for HLB pathogenicity were associated with host immune response, ROS production, and antioxidants. Overall, this study has provided a significant resource of citrus genomic data and identified candidate genes to be further explored to understand the genetic determinants of HLB pathogenicity.
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Affiliation(s)
- Yuxia Gao
- National Navel Orange Engineering Research Center, Gannan Normal University, Ganzhou, Jiangxi, China
| | - Jin Xu
- Citrus Research and Education Center, Department of Microbiology and Cell Science, IFAS, University of Florida, Lake Alfred, FL, USA
| | - Zhilong Li
- National Navel Orange Engineering Research Center, Gannan Normal University, Ganzhou, Jiangxi, China
| | - Yunzeng Zhang
- Citrus Research and Education Center, Department of Microbiology and Cell Science, IFAS, University of Florida, Lake Alfred, FL, USA
| | - Nadia Riera
- Citrus Research and Education Center, Department of Microbiology and Cell Science, IFAS, University of Florida, Lake Alfred, FL, USA
| | - Zhiwei Xiong
- National Navel Orange Engineering Research Center, Gannan Normal University, Ganzhou, Jiangxi, China
| | - Zhigang Ouyang
- National Navel Orange Engineering Research Center, Gannan Normal University, Ganzhou, Jiangxi, China
| | - Xinjun Liu
- National Navel Orange Engineering Research Center, Gannan Normal University, Ganzhou, Jiangxi, China
| | - Zhanjun Lu
- National Navel Orange Engineering Research Center, Gannan Normal University, Ganzhou, Jiangxi, China
| | | | - Balian Zhong
- National Navel Orange Engineering Research Center, Gannan Normal University, Ganzhou, Jiangxi, China
| | - Nian Wang
- Citrus Research and Education Center, Department of Microbiology and Cell Science, IFAS, University of Florida, Lake Alfred, FL, USA
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Li Y, Wang S, Zhang Z, Luo J, Lin GL, Deng WD, Guo Z, Han FM, Wang LL, Li J, Wu SF, Liu HQ, He S, Murphy RW, Zhang ZJ, Cooper DN, Wu DD, Zhang YP. Large-Scale Chromosomal Changes Lead to Genome-Level Expression Alterations, Environmental Adaptation, and Speciation in the Gayal (Bos frontalis). Mol Biol Evol 2023; 40:6980758. [PMID: 36625089 PMCID: PMC9874039 DOI: 10.1093/molbev/msad006] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Revised: 12/20/2022] [Accepted: 01/05/2023] [Indexed: 01/11/2023] Open
Abstract
Determining the functional consequences of karyotypic changes is invariably challenging because evolution tends to obscure many of its own footprints, such as accumulated mutations, recombination events, and demographic perturbations. Here, we describe the assembly of a chromosome-level reference genome of the gayal (Bos frontalis) thereby revealing the structure, at base-pair-level resolution, of a telo/acrocentric-to-telo/acrocentric Robertsonian translocation (2;28) (T/A-to-T/A rob[2;28]). The absence of any reduction in the recombination rate or genetic introgression within the fusion region of gayal served to challenge the long-standing view of a role for fusion-induced meiotic dysfunction in speciation. The disproportionate increase noted in the distant interactions across pro-chr2 and pro-chr28, and the change in open-chromatin accessibility following rob(2;28), may, however, have led to the various gene expression irregularities observed in the gayal. Indeed, we found that many muscle-related genes, located synthetically on pro-chr2 and pro-chr28, exhibited significant changes in expression. This, combined with genome-scale structural variants and expression alterations in genes involved in myofibril composition, may have driven the rapid sarcomere adaptation of gayal to its rugged mountain habitat. Our findings not only suggest that large-scale chromosomal changes can lead to alterations in genome-level expression, thereby promoting both adaptation and speciation, but also illuminate novel avenues for studying the relationship between karyotype evolution and speciation.
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Affiliation(s)
- Yan Li
- Corresponding authors: E-mails: ;
| | | | | | | | | | | | | | | | - Li-Li Wang
- Biomarker Technologies Corporation, Beijing, China
| | - Jie Li
- State Key Laboratory for Conservation and Utilization of Bio-resource in Yunnan and School of Ecology and Environmental Science, Yunnan University, Kunming, China
| | - Shi-Fang Wu
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - He-Qun Liu
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Sheng He
- Nujiang Livestock Technology Promotion Station, Nujiang, China
| | - Robert W Murphy
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China,Centre for Biodiversity and Conservation Biology, Royal Ontario Museum, Toronto, ON, Canada
| | - Zi-Jie Zhang
- State Key Laboratory for Conservation and Utilization of Bio-resource in Yunnan and School of Ecology and Environmental Science, Yunnan University, Kunming, China
| | - David N Cooper
- Institute of Medical Genetics, Cardiff University, Cardiff, United Kingdom
| | - Dong-Dong Wu
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China,Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China,Kunming Natural History Museum of Zoology, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
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Jiang D, Liu Q, Sun J, Liu S, Fan G, Wang L, Zhang Y, Seim I, An S, Liu X, Li Q, Zheng X. The gold-ringed octopus (Amphioctopus fangsiao) genome and cerebral single-nucleus transcriptomes provide insights into the evolution of karyotype and neural novelties. BMC Biol 2022; 20:289. [PMID: 36575497 PMCID: PMC9795677 DOI: 10.1186/s12915-022-01500-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Accepted: 12/08/2022] [Indexed: 12/28/2022] Open
Abstract
BACKGROUND Coleoid cephalopods have distinctive neural and morphological characteristics compared to other invertebrates. Early studies reported massive genomic rearrangements occurred before the split of octopus and squid lineages (Proc Natl Acad Sci U S A 116:3030-5, 2019), which might be related to the neural innovations of their brain, yet the details remain elusive. Here we combine genomic and single-nucleus transcriptome analyses to investigate the octopod chromosome evolution and cerebral characteristics. RESULTS We present a chromosome-level genome assembly of a gold-ringed octopus, Amphioctopus fangsiao, and a single-nucleus transcriptome of its supra-esophageal brain. Chromosome-level synteny analyses estimate that the chromosomes of the ancestral octopods experienced multiple chromosome fission/fusion and loss/gain events by comparing with the nautilus genome as outgroup, and that a conserved genome organization was detected during the evolutionary process from the last common octopod ancestor to their descendants. Besides, protocadherin, GPCR, and C2H2 ZNF genes are thought to be highly related to the neural innovations in cephalopods (Nature 524:220-4, 2015), and the chromosome analyses pinpointed several collinear modes of these genes on the octopod chromosomes, such as the collinearity between PCDH and C2H2 ZNF, as well as between GPCR and C2H2 ZNF. Phylogenetic analyses show that the expansion of the octopod protocadherin genes is driven by a tandem-duplication mechanism on one single chromosome, including two separate expansions at 65 million years ago (Ma) and 8-14 Ma, respectively. Furthermore, we identify eight cell types (i.e., cholinergic and glutamatergic neurons) in the supra-esophageal brain of A. fangsiao, and the single-cell expression analyses reveal the co-expression of protocadherin and GPCR in specific neural cells, which may contribute to the neural development and signal transductions in the octopod brain. CONCLUSIONS The octopod genome analyses reveal the dynamic evolutionary history of octopod chromosomes and neural-related gene families. The single-nucleus transcriptomes of the supra-esophageal brain indicate their cellular heterogeneities and functional interactions with other tissues (i.e., gill), which provides a foundation for further octopod cerebral studies.
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Affiliation(s)
- Dianhang Jiang
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Ocean University of China, Qingdao, 266003, China
- Institute of Evolution & Marine Biodiversity (IEMB), Qingdao, 266003, China
| | - Qun Liu
- BGI-QingDao, BGI-Shenzhen, Qingdao, 266555, China
| | - Jin Sun
- Institute of Evolution & Marine Biodiversity (IEMB), Qingdao, 266003, China
| | - Shikai Liu
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Ocean University of China, Qingdao, 266003, China
| | - Guangyi Fan
- BGI-QingDao, BGI-Shenzhen, Qingdao, 266555, China
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, 518083, China
| | - Lihua Wang
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Ocean University of China, Qingdao, 266003, China
- Institute of Evolution & Marine Biodiversity (IEMB), Qingdao, 266003, China
| | - Yaolei Zhang
- BGI-QingDao, BGI-Shenzhen, Qingdao, 266555, China
| | - Inge Seim
- Integrative Biology Laboratory, College of Life Sciences, Nanjing Normal University, Nanjing, 210046, China
- School of Biology and Environmental Science, Queensland University of Technology, Brisbane, 4000, Australia
| | - Shucai An
- The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Xin Liu
- BGI-QingDao, BGI-Shenzhen, Qingdao, 266555, China
| | - Qi Li
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Ocean University of China, Qingdao, 266003, China
| | - Xiaodong Zheng
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Ocean University of China, Qingdao, 266003, China.
- Institute of Evolution & Marine Biodiversity (IEMB), Qingdao, 266003, China.
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Zhang S, Wu Z, Ma D, Zhai J, Han X, Jiang Z, Liu S, Xu J, Jiao P, Li Z. Chromosome-scale assemblies of the male and female Populus euphratica genomes reveal the molecular basis of sex determination and sexual dimorphism. Commun Biol 2022; 5:1186. [PMCID: PMC9636151 DOI: 10.1038/s42003-022-04145-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2022] [Accepted: 10/20/2022] [Indexed: 11/06/2022] Open
Abstract
Reference-quality genomes of both sexes are essential for studying sex determination and sex-chromosome evolution, as their gene contents and expression profiles differ. Here, we present independent chromosome-level genome assemblies for the female (XX) and male (XY) genomes of desert poplar (Populus euphratica), resolving a 22.7-Mb X and 24.8-Mb Y chromosome. We also identified a relatively complete 761-kb sex-linked region (SLR) in the peritelomeric region on chromosome 14 (Y). Within the SLR, recombination around the partial repeats for the feminizing factor ARR17 (ARABIDOPSIS RESPONSE REGULATOR 17) was potentially suppressed by flanking palindromic arms and the dense accumulation of retrotransposons. The inverted small segments S1 and S2 of ARR17 exhibited relaxed selective pressure and triggered sex determination by generating 24-nt small interfering RNAs that induce male-specific hyper-methylation at the promoter of the autosomal targeted ARR17. We also detected two male-specific fusion genes encoding proteins with NB-ARC domains at the breakpoint region of an inversion in the SLR that may be responsible for the observed sexual dimorphism in immune responses. Our results show that the SLR appears to follow proposed evolutionary dynamics for sex chromosomes and advance our understanding of sex determination and the evolution of sex chromosomes in Populus. Reference-quality genomes of both sexes of the dioecious tree species, Populus euphratica, provide further insight into the evolution of Populus sex chromosomes and highlight male-specific fusion genes that may contribute to sexual dimorphism.
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Affiliation(s)
- Shanhe Zhang
- grid.443240.50000 0004 1760 4679College of Life Sciences and Technology, Tarim University/Key Laboratory of Protection and Utilization of Biological Resources in Tarim Basin, Xinjiang Production & Construction Corps/Research Center of Populus Euphratica, Aral, 843300 China
| | - Zhihua Wu
- grid.453534.00000 0001 2219 2654College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua, 321004 China
| | - De Ma
- grid.410753.4Novogene Bioinformatics Institute, Beijing, 100083 China
| | - Juntuan Zhai
- grid.443240.50000 0004 1760 4679College of Life Sciences and Technology, Tarim University/Key Laboratory of Protection and Utilization of Biological Resources in Tarim Basin, Xinjiang Production & Construction Corps/Research Center of Populus Euphratica, Aral, 843300 China
| | - Xiaoli Han
- grid.443240.50000 0004 1760 4679College of Life Sciences and Technology, Tarim University/Key Laboratory of Protection and Utilization of Biological Resources in Tarim Basin, Xinjiang Production & Construction Corps/Research Center of Populus Euphratica, Aral, 843300 China
| | - Zhenbo Jiang
- grid.443240.50000 0004 1760 4679College of Life Sciences and Technology, Tarim University/Key Laboratory of Protection and Utilization of Biological Resources in Tarim Basin, Xinjiang Production & Construction Corps/Research Center of Populus Euphratica, Aral, 843300 China
| | - Shuo Liu
- Hubei Provincial Key Laboratory for Protection and Application of Special Plant Germplasm in Wuling Area of China, College of Life Sciences, South-Central Minzu University, Wuhan, 430074 China
| | - Jingdong Xu
- Hubei Provincial Key Laboratory for Protection and Application of Special Plant Germplasm in Wuling Area of China, College of Life Sciences, South-Central Minzu University, Wuhan, 430074 China
| | - Peipei Jiao
- grid.443240.50000 0004 1760 4679College of Life Sciences and Technology, Tarim University/Key Laboratory of Protection and Utilization of Biological Resources in Tarim Basin, Xinjiang Production & Construction Corps/Research Center of Populus Euphratica, Aral, 843300 China
| | - Zhijun Li
- grid.443240.50000 0004 1760 4679College of Life Sciences and Technology, Tarim University/Key Laboratory of Protection and Utilization of Biological Resources in Tarim Basin, Xinjiang Production & Construction Corps/Research Center of Populus Euphratica, Aral, 843300 China
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Li Y, Xu W, Wang Y, Kou J, Zhang J, Hu S, Zhang L, Wang J, Liu J, Liu H, Luo L, Wang C, Lan J, Hou R, Shen F. An improved, chromosome-level genome of the giant panda (Ailuropoda melanoleuca). Genomics 2022; 114:110501. [PMID: 36270383 DOI: 10.1016/j.ygeno.2022.110501] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Revised: 09/21/2022] [Accepted: 10/04/2022] [Indexed: 01/14/2023]
Abstract
BACKGROUND The iconic giant panda (Ailuropoda melanoleuca), as both a flagship and umbrella species endemic to China, is a world famous symbol for wildlife conservation. The giant panda has several specific biological traits and holds a relatively small place in evolution. A high-quality genome of the giant panda is key to understanding the biology of this vulnerable species. FINDINGS We generated a 2.48-Gb chromosome-level genome (GPv1) of the giant panda named "Jing Jing" with a contig N50 of 28.56 Mb and scaffold N50 of 134.17 Mb, respectively. The total length of chromosomes (n = 21) was 2.39-Gb, accounting for 96.4% of the whole genome. Compared with the previously published four genomes of the giant panda, our genome is characterized by the highest completeness and the correct sequence orientation. A gap-free and 850 kb length of immunoglobulin heavy-chain gene cluster was manually annotated in close proximity to the telomere of chromosome 14. Additionally, we developed an algorithm to predict the centromere position of each chromosome. We also constructed a complete chromatin structure for "Jing Jing", which includes inter-chromosome interaction pattern, A/B compartment, topologically associated domain (TAD), TAD-clique and promoter-enhancer interaction (PEI). CONCLUSIONS We presented an improved chromosome-level genome and complete chromatin structure for the giant panda. This is a valuable resource for the future genetic and genomic studies on giant panda.
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Affiliation(s)
- Yan Li
- Chengdu Research Base of Giant Panda Breeding, China; Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, China
| | - Wei Xu
- Chengdu Research Base of Giant Panda Breeding, China; Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, China
| | - Ye Wang
- Chengdu Research Base of Giant Panda Breeding, China; Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, China
| | - Jie Kou
- Chengdu Research Base of Giant Panda Breeding, China; Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, China
| | - Jiaman Zhang
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, China
| | - Silu Hu
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, China
| | - Liang Zhang
- Chengdu Research Base of Giant Panda Breeding, China; Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, China
| | - Juan Wang
- Chengdu Research Base of Giant Panda Breeding, China; Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, China
| | - Jiawen Liu
- Chengdu Research Base of Giant Panda Breeding, China; Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, China
| | - Hong Liu
- Chengdu Research Base of Giant Panda Breeding, China; Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, China
| | - Li Luo
- Chengdu Research Base of Giant Panda Breeding, China; Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, China
| | - Chengdong Wang
- Chengdu Research Base of Giant Panda Breeding, China; Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, China
| | - Jingchao Lan
- Chengdu Research Base of Giant Panda Breeding, China; Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, China
| | - Rong Hou
- Chengdu Research Base of Giant Panda Breeding, China; Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, China.
| | - Fujun Shen
- Chengdu Research Base of Giant Panda Breeding, China; Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, China.
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da Silva EMG, Rebello KM, Choi YJ, Gregorio V, Paschoal AR, Mitreva M, McKerrow JH, Neves-Ferreira AGDC, Passetti F. Identification of Novel Genes and Proteoforms in Angiostrongylus costaricensis through a Proteogenomic Approach. Pathogens 2022; 11:1273. [PMID: 36365024 PMCID: PMC9694666 DOI: 10.3390/pathogens11111273] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Revised: 10/15/2022] [Accepted: 10/20/2022] [Indexed: 07/22/2023] Open
Abstract
RNA sequencing (RNA-Seq) and mass-spectrometry-based proteomics data are often integrated in proteogenomic studies to assist in the prediction of eukaryote genome features, such as genes, splicing, single-nucleotide (SNVs), and single-amino-acid variants (SAAVs). Most genomes of parasite nematodes are draft versions that lack transcript- and protein-level information and whose gene annotations rely only on computational predictions. Angiostrongylus costaricensis is a roundworm species that causes an intestinal inflammatory disease, known as abdominal angiostrongyliasis (AA). Currently, there is no drug available that acts directly on this parasite, mostly due to the sparse understanding of its molecular characteristics. The available genome of A. costaricensis, specific to the Costa Rica strain, is a draft version that is not supported by transcript- or protein-level evidence. This study used RNA-Seq and MS/MS data to perform an in-depth annotation of the A. costaricensis genome. Our prediction improved the reference annotation with (a) novel coding and non-coding genes; (b) pieces of evidence of alternative splicing generating new proteoforms; and (c) a list of SNVs between the Brazilian (Crissiumal) and the Costa Rica strain. To the best of our knowledge, this is the first time that a multi-omics approach has been used to improve the genome annotation of A. costaricensis. We hope this improved genome annotation can assist in the future development of drugs, kits, and vaccines to treat, diagnose, and prevent AA caused by either the Brazil strain (Crissiumal) or the Costa Rica strain.
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Affiliation(s)
- Esdras Matheus Gomes da Silva
- Instituto Carlos Chagas, Fiocruz, Curitiba 81350-010, PR, Brazil
- Laboratory of Toxinology, Oswaldo Cruz Institute, Fiocruz, Rio de Janeiro 21040-900, RJ, Brazil
| | - Karina Mastropasqua Rebello
- Laboratory of Toxinology, Oswaldo Cruz Institute, Fiocruz, Rio de Janeiro 21040-900, RJ, Brazil
- Laboratory of Integrated Studies in Protozoology, Oswaldo Cruz Institute, Fiocruz, Rio de Janeiro 21040-360, RJ, Brazil
| | - Young-Jun Choi
- Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Vitor Gregorio
- Bioinformatics and Pattern Recognition Group (Bioinfo-CP), Department of Computer Science (DACOM), Federal University of Technology-Parana (UTFPR), Cornélio Procópio 86300-000, PR, Brazil
| | - Alexandre Rossi Paschoal
- Bioinformatics and Pattern Recognition Group (Bioinfo-CP), Department of Computer Science (DACOM), Federal University of Technology-Parana (UTFPR), Cornélio Procópio 86300-000, PR, Brazil
| | - Makedonka Mitreva
- Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - James H. McKerrow
- Center for Discovery and Innovation in Parasitic Diseases, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, CA 92093, USA
| | | | - Fabio Passetti
- Instituto Carlos Chagas, Fiocruz, Curitiba 81350-010, PR, Brazil
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Li M, Wu B, Zhang P, Li Y, Xu W, Wang K, Qiu Q, Zhang J, Li J, Zhang C, Fan J, Feng C, Chen Z. Genomes of Two Flying Squid Species Provide Novel Sights into Adaptations of Cephalopods to Pelagic Life. GENOMICS, PROTEOMICS & BIOINFORMATICS 2022; 20:1053-1065. [PMID: 36216027 DOI: 10.1016/j.gpb.2022.09.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2021] [Revised: 08/25/2022] [Accepted: 09/28/2022] [Indexed: 11/07/2022]
Abstract
Pelagic cephalopods have evolved a series of fascinating traits, such as excellent visual acuity, high-speed agility, and photophores for adaptation to open pelagic oceans. However, the genetic mechanisms underpinning these traits are not well understood. Thus, in this study, we obtained high-quality genomes of two purpleback flying squid species (Sthenoteuthis oualaniensis and Sthenoteuthis sp.), with sizes of 5450 Mb and 5651 Mb, respectively. Comparative genomic analyses revealed that the S-crystallin subfamily SL20-1 associated with visual acuity in the purpleback flying squid lineage was significantly expanded, and the evolution of high-speed agility for the species was accompanied by significant positive selection pressure on genes related to energy metabolism. These molecular signals might have contributed to the evolution of their adaptative predatory and anti-predatory traits. In addition, the transcriptomic analysis provided clear indications of the evolution of the photophores of purpleback flying squids, especially the recruitment of new genes and energy metabolism-related genes which may have played key functional roles in the process.
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Affiliation(s)
- Min Li
- South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510300, China; Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China; Key Laboratory for Sustainable Utilization of Open-Sea Fishery, Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of Fishery Ecology and Environment, Guangzhou 510300, China
| | - Baosheng Wu
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an 710072, China
| | - Peng Zhang
- South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510300, China
| | - Ye Li
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an 710072, China
| | - Wenjie Xu
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an 710072, China
| | - Kun Wang
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an 710072, China
| | - Qiang Qiu
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an 710072, China
| | - Jun Zhang
- South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510300, China
| | - Jie Li
- South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510300, China
| | - Chi Zhang
- Qinghai Province Key Laboratory of Crop Molecular Breeding, Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining 810008, China
| | - Jiangtao Fan
- South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510300, China
| | - Chenguang Feng
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an 710072, China; The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China.
| | - Zuozhi Chen
- South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510300, China; Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China; Key Laboratory for Sustainable Utilization of Open-Sea Fishery, Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of Fishery Ecology and Environment, Guangzhou 510300, China.
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Long read genome assemblies complemented by single cell RNA-sequencing reveal genetic and cellular mechanisms underlying the adaptive evolution of yak. Nat Commun 2022; 13:4887. [PMID: 36068211 PMCID: PMC9448747 DOI: 10.1038/s41467-022-32164-9] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Accepted: 07/20/2022] [Indexed: 12/04/2022] Open
Abstract
Wild yak (Bos mutus) and domestic yak (Bos grunniens) are adapted to high altitude environment and have ecological, economic, and cultural significances on the Qinghai-Tibetan Plateau (QTP). Currently, the genetic and cellular bases underlying adaptations of yak to extreme conditions remains elusive. In the present study, we assembled two chromosome-level genomes, one each for wild yak and domestic yak, and screened structural variants (SVs) through the long-read data of yak and taurine cattle. The results revealed that 6733 genes contained high-FST SVs. 127 genes carrying special type of SVs were differentially expressed in lungs of the taurine cattle and yak. We then constructed the first single-cell gene expression atlas of yak and taurine cattle lung tissues and identified a yak-specific endothelial cell subtype. By integrating SVs and single-cell transcriptome data, we revealed that the endothelial cells expressed the highest proportion of marker genes carrying high-FST SVs in taurine cattle lungs. Furthermore, we identified pathways which were related to the medial thickness and formation of elastic fibers in yak lungs. These findings provide new insights into the high-altitude adaptation of yak and have important implications for understanding the physiological and pathological responses of large mammals and humans to hypoxia. The genetic bases of yak adaptations to extreme conditions remains elusive. This study compares yak and cattle at a genomic and transcriptomic level, revealing a new type of endothelial cell and candidate genes related with elastic fiber formation in yak lungs that might contribute to high altitude adaptation.
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Kong W, Deng X, Liao Z, Wang Y, Zhou M, Wang Z, Li Y. De novo assembly of two chromosome-level rice genomes and bin-based QTL mapping reveal genetic diversity of grain weight trait in rice. FRONTIERS IN PLANT SCIENCE 2022; 13:995634. [PMID: 36072319 PMCID: PMC9443666 DOI: 10.3389/fpls.2022.995634] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/16/2022] [Accepted: 08/01/2022] [Indexed: 06/15/2023]
Abstract
Following the "green revolution," indica and japonica hybrid breeding has been recognized as a new breakthrough in further improving rice yields. However, heterosis-related grain weight QTLs and the basis of yield advantage among subspecies has not been well elucidated. We herein de novo assembled the chromosome level genomes of an indica/xian rice (Luohui 9) and a japonica/geng rice (RPY geng) and found that gene number differences and structural variations between these two genomes contribute to the differences in agronomic traits and also provide two different favorable allele pools to produce better derived recombinant inbred lines (RILs). In addition, we generated a high-generation (> F15) population of 272 RILs from the cross between Luohui 9 and RPY geng and two testcross hybrid populations derived from the crosses of RILs and two cytoplasmic male sterile lines (YTA, indica and Z7A, japonica). Based on three derived populations, we totally identified eight 1,000-grain weight (KGW) QTLs and eight KGW heterosis loci. Of QTLs, qKGW-6.1 and qKGW-8.1 were accepted as novel KGW QTLs that have not been reported previously. Interestingly, allele genotyping results revealed that heading date related gene (Ghd8) in qKGW-8.1 and qLH-KGW-8.1, can affect grain weight in RILs and rice core accessions and may also play an important role in grain weight heterosis. Our results provided two high-quality genomes and novel gene editing targets for grain weight for future rice yield improvement project.
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Affiliation(s)
- Weilong Kong
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China
| | - Xiaoxiao Deng
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China
| | - Zhenyang Liao
- Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yibin Wang
- Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Mingao Zhou
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China
| | - Zhaohai Wang
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding (Jiangxi Agricultural University), Ministry of Education of the People’s Republic of China, Nanchang, China
| | - Yangsheng Li
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China
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Xu KW, Wei XF, Lin CX, Zhang M, Zhang Q, Zhou P, Fang YM, Xue JY, Duan YF. The chromosome-level holly ( Ilex latifolia) genome reveals key enzymes in triterpenoid saponin biosynthesis and fruit color change. FRONTIERS IN PLANT SCIENCE 2022; 13:982323. [PMID: 36072321 PMCID: PMC9441949 DOI: 10.3389/fpls.2022.982323] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Accepted: 08/04/2022] [Indexed: 05/30/2023]
Abstract
The Ilex L. (hollies) genus of Aquifoliaceae shows high species diversity in tropical and subtropical regions of Asia and South America. Throughout the range of the genus, Ilex species have been widely used in beverage and medicine production and as ornamentals. Here, we assembled a high-quality, chromosome-level genome of Ilex latifolia, which has extremely high economic value because of its useful secondary metabolite production and the high ornamental value of its decorative red berries. The 99.8% genome sequence was anchored to 20 pseudochromosomes, with a total length of 766.02 Mb and a scaffold N50 of 33.45 Mb. Based on the comparative genomic analysis of 14 angiosperm species, we recovered I. latifolia as the sister group to all other campanulids. Two whole-genome duplication (WGD) events were identified in hollies: one shared ancient WGD in the ancestor of all eudicots and a recent and independent WGD in hollies. We performed a genome-wide search to screen candidate genes involved in the biosynthesis of pentacyclic triterpenoid saponins in I. latifolia. Three subfamilies of CYP450 (CYP71A, CYP72A, and CYP716A) appear to have expanded. The transcriptomic analysis of I. latifolia leaves at five developmental stages revealed that two CYP716A genes and one CYP72A gene probably play important roles in this biosynthetic pathway. In addition, we totally identified 12 genes in the biosynthesis pathways of pelargonidin and cyanidin and observed their differential expression in green and red fruit pericarps, suggesting an association between pelargonidin and cyanidin biosynthesis and fruit pericarp color change. The accumulation of pelargonidin and cyanidin is expected to play an important role in the ornamental value of I. latifolia. Altogether, this study elucidated the molecular basis of the medicinal and ornamental value of I. latifolia, providing a data basis and promising clues for further applications.
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Affiliation(s)
- Ke-Wang Xu
- Key Laboratory of National Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, Co-innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, Nanjing, China
| | - Xue-Fen Wei
- College of Horticulture, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing, China
| | - Chen-Xue Lin
- Key Laboratory of National Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, Co-innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, Nanjing, China
| | - Min Zhang
- Key Laboratory of National Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, Co-innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, Nanjing, China
- Jiangsu Academy of Forestry, Nanjing, China
| | - Qiang Zhang
- Key Laboratory of National Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, Co-innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, Nanjing, China
| | - Peng Zhou
- Jiangsu Academy of Forestry, Nanjing, China
| | - Yan-Ming Fang
- Key Laboratory of National Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, Co-innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, Nanjing, China
| | - Jia-Yu Xue
- College of Horticulture, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing, China
| | - Yi-Fan Duan
- Key Laboratory of National Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, Co-innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, Nanjing, China
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Zhang L, Wu R, Mur LAJ, Guo C, Zhao X, Meng H, Yan D, Zhang X, Guan H, Han G, Guo B, Yue F, Wei Y, Zhao P, He W. Assembly of high-quality genomes of the locoweed Oxytropis ochrocephala and its endophyte Alternaria oxytropis provides new evidence for their symbiotic relationship and swainsonine biosynthesis. Mol Ecol Resour 2022; 23:253-272. [PMID: 35932461 DOI: 10.1111/1755-0998.13695] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 07/29/2022] [Accepted: 08/02/2022] [Indexed: 11/29/2022]
Abstract
Locoweeds are perennial forbs poisonous to livestock and cause extreme losses to animal husbandry. Locoweed toxicity is attributed to the symbiotic endophytes in Alternaria sect. Undifilum, which produce a mycotoxin swainsonine (SW). We performed a de novo whole genome sequencing of the most common locoweed in China, Oxytropis ochrocephala (2n = 16), and assembled a high-quality, chromosome-level reference genome. Its genome size is 958.83 Mb with 930.94 Mb (97.09 %) anchored and oriented onto 8 chromosomes, and 31,700 protein-coding genes were annotated. Phylogenetic and collinearity analysis showed it is closely related to Medicago truncatula with a pair of large interchromosomal rearrangements, and both species underwent a whole-genome duplication event. We also derived the genome of A. oxytropis at 74.48 Mb with a contig N50 of 8.87 Mb and 10,657 protein-coding genes, and refined the genes of SW biosynthesis. Multiple Alternaria species containing the swnK gene were grouped into a single clade, but in other genera, swnK's homologues are diverse. Resequencing of 41 A. oxytropis strains revealed one SNP in the SWN cluster causing changes in SW concentration. Comparing the transcriptomes of symbiotic and non-symbiotic interactions identified differentially expressed genes (DEG) linked to defense and secondary metabolism in the host. Within the endophyte DEGs were linked to cell wall degradation, fatty acids and nitrogen metabolism. Symbiosis induced the up-regulation of most of the SW biosynthetic genes. These two genomes and relevant sequencing data should provide valuable genetic resources for the study of the evolution, interaction, and SW biosynthesis in the symbiont.
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Affiliation(s)
- Li Zhang
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Shaanxi, China
| | - Ruolin Wu
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Shaanxi, China
| | - Luis A J Mur
- Institute of Biology, Environmental and Rural Science, Aberystwyth University, Aberystwyth, Ceredigion, UK
| | - Chenchen Guo
- Provincial Key Laboratory of Biotechnology of Shaanxi Province, College of Life Sciences, Northwest University, Shaanxi, China
| | - Xuan Zhao
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Shaanxi, China
| | - Huizhen Meng
- Provincial Key Laboratory of Biotechnology of Shaanxi Province, College of Life Sciences, Northwest University, Shaanxi, China
| | - Di Yan
- Provincial Key Laboratory of Biotechnology of Shaanxi Province, College of Life Sciences, Northwest University, Shaanxi, China
| | - Xiuhong Zhang
- Bureau of Natural Resources, Haiyuan, Ningxia, China
| | - Huirui Guan
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Shaanxi, China
| | - Guodong Han
- Key Laboratory of Grassland Resources of Ministry of Education, College of Grassland, Resources and Environment, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, China
| | - Bin Guo
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Shaanxi, China
| | - Fangzheng Yue
- Biological Disaster Control and Prevention Centre, National Forestry and Grassland Administration, Shenyang, Liaoning, China
| | - Yahui Wei
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Shaanxi, China
| | - Peng Zhao
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Shaanxi, China
| | - Wei He
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Shaanxi, China.,Key Laboratory of Grassland Resources of Ministry of Education, College of Grassland, Resources and Environment, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, China
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He K, Zhao L, Yuan Z, Canario A, Liu Q, Chen S, Guo J, Luo W, Yan H, Zhang D, Li L, Yang S. Chromosome-level genome assembly of largemouth bass (Micropterus salmoides) using PacBio and Hi-C technologies. Sci Data 2022; 9:482. [PMID: 35933561 PMCID: PMC9357066 DOI: 10.1038/s41597-022-01601-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Accepted: 07/27/2022] [Indexed: 11/09/2022] Open
Abstract
The largemouth bass (Micropterus salmoides) has become a cosmopolitan species due to its widespread introduction as game or domesticated fish. Here a high-quality chromosome-level reference genome of M. salmoides was produced by combining Illumina paired-end sequencing, PacBio single molecule sequencing technique (SMRT) and High-through chromosome conformation capture (Hi-C) technologies. Ultimately, the genome was assembled into 844.88 Mb with a contig N50 of 15.68 Mb and scaffold N50 length of 35.77 Mb. About 99.9% assembly genome sequences (844.00 Mb) could be anchored to 23 chromosomes, and 98.03% assembly genome sequences could be ordered and directed. The genome contained 38.19% repeat sequences and 2693 noncoding RNAs. A total of 26,370 protein-coding genes from 3415 gene families were predicted, of which 97.69% were functionally annotated. The high-quality genome assembly will be a fundamental resource to study and understand how M. salmoides adapt to novel and changing environments around the world, and also be expected to contribute to the genetic breeding and other research.
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Affiliation(s)
- Kuo He
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
| | - Liulan Zhao
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
| | - Zihao Yuan
- CAS Key Laboratory of Experimental Marine Biology, CAS Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071, China
| | - Adelino Canario
- Comparative Endocrinology and Integrative Biology, Centre of Marine Sciences, Universidade Do Algarve, Campus de Gambelas, 8005-139, Faro, Portugal
| | - Qiao Liu
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
| | - Siyi Chen
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
| | - Jiazhong Guo
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
| | - Wei Luo
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
| | - Haoxiao Yan
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
| | - Dongmei Zhang
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
| | - Lisen Li
- Comparative Endocrinology and Integrative Biology, Centre of Marine Sciences, Universidade Do Algarve, Campus de Gambelas, 8005-139, Faro, Portugal
| | - Song Yang
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China.
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Xu X, Wang Y, Wang C, Guo G, Yu X, Dai Y, Liu Y, Wei G, He X, Jin G, Zhang Z, Guan Q, Pain A, Wang S, Zhang W, Young ND, Gasser RB, McManus DP, Cao J, Zhou Q, Zhang Q. Chromosome-level genome assembly defines female-biased genes associated with sex determination and differentiation in the human blood fluke Schistosoma japonicum. Mol Ecol Resour 2022; 23:205-221. [PMID: 35844053 DOI: 10.1111/1755-0998.13689] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2021] [Revised: 07/05/2022] [Accepted: 07/11/2022] [Indexed: 12/01/2022]
Abstract
Schistosomiasis is a neglected tropical disease of humans caused by blood flukes of the genus Schistosoma, the only dioecious parasitic flatworm. Although aspects of sex determination, differentiation and reproduction have been studied in some Schistosoma species, almost nothing is known for Schistosoma japonicum, the causative agent of schistosomiasis japonica. This mainly reflects the lack of high-quality genomic and transcriptomic resources for this species. As current genomes for S. japonicum are highly fragmented, we assembled and report a chromosome-level reference genome (seven autosomes, the Z-chromosome and partial W-chromosome), achieving a substantially enhanced gene annotation. Utilizing this genome, we discovered that the sex chromosomes of S. japonicum and its congener S. mansoni independently suppressed recombination during evolution, forming five and two evolutionary strata, respectively. By exploring the W-chromosome and sex-specific transcriptomes, we identified 35 W-linked genes and 257 female-preferentially transcribed genes (FTGs) from our chromosomal assembly and uncovered a signature for sex determination and differentiation in S. japonicum. These FTGs clustering within autosomes or the Z-chromosome exhibit a highly dynamic transcription profile during the pairing of female and male schistosomula, thereby representing a critical phase for the maturation of the female worms and suggesting distinct layers of regulatory control of gene transcription at this development stage. Collectively, these data provide a valuable resource for further functional genomic characterization of S. japonicum, shed light on the evolution of sex chromosomes in this highly virulent human blood fluke, and provide a pathway to identify novel targets for development of intervention tools against schistosomiasis.
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Affiliation(s)
- Xindong Xu
- Laboratory of Molecular Parasitology, Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration of Ministry of Education, Tongji Hospital, and Clinical Center for Brain and Spinal Cord Research School of Medicine, School of Medicine, Tongji University, Shanghai, China
| | - Yifeng Wang
- MOE Laboratory of Biosystems Homeostasis and Protection and Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, China
| | - Changhong Wang
- Laboratory of Molecular Parasitology, Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration of Ministry of Education, Tongji Hospital, and Clinical Center for Brain and Spinal Cord Research School of Medicine, School of Medicine, Tongji University, Shanghai, China
| | - Gangqiang Guo
- Laboratory of Molecular Parasitology, Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration of Ministry of Education, Tongji Hospital, and Clinical Center for Brain and Spinal Cord Research School of Medicine, School of Medicine, Tongji University, Shanghai, China
| | - Xinyu Yu
- National Health Commission Key Laboratory of Parasitic Disease Control and Prevention, Jiangsu Provincial Key Laboratory on Parasite and Vector Control Technology, Jiangsu Institute of Parasitic Diseases, Wuxi, China
| | - Yang Dai
- National Health Commission Key Laboratory of Parasitic Disease Control and Prevention, Jiangsu Provincial Key Laboratory on Parasite and Vector Control Technology, Jiangsu Institute of Parasitic Diseases, Wuxi, China
| | - Yaobao Liu
- National Health Commission Key Laboratory of Parasitic Disease Control and Prevention, Jiangsu Provincial Key Laboratory on Parasite and Vector Control Technology, Jiangsu Institute of Parasitic Diseases, Wuxi, China
| | - Guiying Wei
- Laboratory of Molecular Parasitology, Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration of Ministry of Education, Tongji Hospital, and Clinical Center for Brain and Spinal Cord Research School of Medicine, School of Medicine, Tongji University, Shanghai, China
| | - Xiaohui He
- Laboratory of Molecular Parasitology, Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration of Ministry of Education, Tongji Hospital, and Clinical Center for Brain and Spinal Cord Research School of Medicine, School of Medicine, Tongji University, Shanghai, China
| | - Ge Jin
- Novogene Bioinformatics Institute, Beijing, China
| | - Ziqiu Zhang
- Novogene Bioinformatics Institute, Beijing, China
| | - Qingtian Guan
- Pathogen Genomics Laboratory, Biological and Environmental Sciences and Engineering (BESE) Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Kingdom of Saudi Arabia
| | - Arnab Pain
- Pathogen Genomics Laboratory, Biological and Environmental Sciences and Engineering (BESE) Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Kingdom of Saudi Arabia
| | - Shengyue Wang
- National Research Center for Translational Medicine, State Key Laboratory of Medical Genomics, Ruijin Hospital Affiliated to Shanghai Jiao Tong University (SJTU) School of Medicine, Shanghai, China
| | - Wenbao Zhang
- State Key Laboratory of Pathogenesis, Prevention and Treatment of High Incidence Diseases in Central Asia, Clinical Medical Research Institute, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, China
| | - Neil D Young
- Department of Veterinary Biosciences, Melbourne Veterinary School, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria, Australia
| | - Robin B Gasser
- Department of Veterinary Biosciences, Melbourne Veterinary School, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria, Australia
| | - Donald P McManus
- Department of Immunology, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Jun Cao
- National Health Commission Key Laboratory of Parasitic Disease Control and Prevention, Jiangsu Provincial Key Laboratory on Parasite and Vector Control Technology, Jiangsu Institute of Parasitic Diseases, Wuxi, China.,Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Qi Zhou
- MOE Laboratory of Biosystems Homeostasis and Protection and Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, China.,Department of Neuroscience and Developmental Biology, University of Vienna, Vienna, Austria.,Center for Reproductive Medicine, the Second Affiliated Hospital School of Medicine and Life Sciences Institute, Zhejiang University, Hangzhou, China
| | - Qingfeng Zhang
- Laboratory of Molecular Parasitology, Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration of Ministry of Education, Tongji Hospital, and Clinical Center for Brain and Spinal Cord Research School of Medicine, School of Medicine, Tongji University, Shanghai, China
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Wei H, Ye Y, Huang H, Chen M, Yang Z, Chen X, Zhang C. Chromosome‐level genome assembly for the horned‐gall aphid provides insights into interactions between gall‐making insect and its host plant. Ecol Evol 2022; 12:e8815. [PMID: 35475184 PMCID: PMC9021935 DOI: 10.1002/ece3.8815] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Accepted: 03/25/2022] [Indexed: 11/16/2022] Open
Abstract
The aphid Schlechtendalia chinensis is an economically important insect that can induce horned galls, which are valuable for the medicinal and chemical industries. Up to now, more than twenty aphid genomes have been reported. Most of the sequenced genomes are derived from free‐living aphids. Here, we generated a high‐quality genome assembly from a galling aphid. The final genome assembly is 271.52 Mb, representing one of the smallest sequenced genomes of aphids. The genome assembly is based on contig and scaffold N50 values of the genome sequence are 3.77 Mb and 20.41 Mb, respectively. Nine‐seven percent of the assembled sequences was anchored onto 13 chromosomes. Based on BUSCO analysis, the assembly involved 96.9% of conserved arthropod and 98.5% of the conserved Hemiptera single‐copy orthologous genes. A total of 14,089 protein‐coding genes were predicted. Phylogenetic analysis revealed that S. chinensis diverged from the common ancestor of Eriosoma lanigerum approximately 57 million years ago (MYA). In addition, 35 genes encoding salivary gland proteins showed differentially when S. chinensis forms a gall, suggesting they have potential roles in gall formation and plant defense suppression. Taken together, this high‐quality S. chinensis genome assembly and annotation provide a solid genetic foundation for future research to reveal the mechanism of gall formation and to explore the interaction between aphids and their host plants.
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Affiliation(s)
- Hong‐Yuan Wei
- Key Laboratory of Breeding and Utilization of Resource Insects National Forestry and Grassland Administration Institute of Highland Forest Science Chinese Academy of Forestry Kunming China
| | - Yu‐Xuan Ye
- Institute of Insect Sciences Zhejiang University Hangzhou China
| | - Hai‐Jian Huang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro‐products Key Laboratory of Biotechnology in Plant Protection of MOA of China and Zhejiang Province Institute of Plant Virology Ningbo University Ningbo China
| | - Ming‐Shun Chen
- Department of Entomology Kansas State University Manhattan Kansas USA
| | - Zi‐Xiang Yang
- Key Laboratory of Breeding and Utilization of Resource Insects National Forestry and Grassland Administration Institute of Highland Forest Science Chinese Academy of Forestry Kunming China
| | - Xiao‐Ming Chen
- Key Laboratory of Breeding and Utilization of Resource Insects National Forestry and Grassland Administration Institute of Highland Forest Science Chinese Academy of Forestry Kunming China
| | - Chuan‐Xi Zhang
- Institute of Insect Sciences Zhejiang University Hangzhou China
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro‐products Key Laboratory of Biotechnology in Plant Protection of MOA of China and Zhejiang Province Institute of Plant Virology Ningbo University Ningbo China
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Jiang Y, Hu X, Yuan Y, Guo X, Chase MW, Ge S, Li J, Fu J, Li K, Hao M, Wang Y, Jiao Y, Jiang W, Jin X. The Gastrodia menghaiensis (Orchidaceae) genome provides new insights of orchid mycorrhizal interactions. BMC PLANT BIOLOGY 2022; 22:179. [PMID: 35392808 PMCID: PMC8988336 DOI: 10.1186/s12870-022-03573-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Accepted: 04/01/2022] [Indexed: 06/01/2023]
Abstract
BACKGROUND To illustrate the molecular mechanism of mycoheterotrophic interactions between orchids and fungi, we assembled chromosome-level reference genome of Gastrodia menghaiensis (Orchidaceae) and analyzed the genomes of two species of Gastrodia. RESULTS Our analyses indicated that the genomes of Gastrodia are globally diminished in comparison to autotrophic orchids, even compared to Cuscuta (a plant parasite). Genes involved in arbuscular mycorrhizae colonization were found in genomes of Gastrodia, and many of the genes involved biological interaction between Gatrodia and symbiotic microbionts are more numerous than in photosynthetic orchids. The highly expressed genes for fatty acid and ammonium root transporters suggest that fungi receive material from orchids, although most raw materials flow from the fungi. Many nuclear genes (e.g. biosynthesis of aromatic amino acid L-tryptophan) supporting plastid functions are expanded compared to photosynthetic orchids, an indication of the importance of plastids even in totally mycoheterotrophic species. CONCLUSION Gastrodia menghaiensis has the smallest proteome thus far among angiosperms. Many of the genes involved biological interaction between Gatrodia and symbiotic microbionts are more numerous than in photosynthetic orchids.
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Affiliation(s)
- Yan Jiang
- Institute of Botany, Chinese Academy of Sciences, Xiangshan, Haidian, Beijing, 100093, China
| | - Xiaodi Hu
- Novogene Bioinformatics Institute, Beijing, 100083, China
| | - Yuan Yuan
- National Resource Center for Chinese Meteria Medica, Chinese Academy of Chinese Medical Sciences, Chaoyang, Beijing, 100700, China
| | - Xuelian Guo
- Institute of Botany, Chinese Academy of Sciences, Xiangshan, Haidian, Beijing, 100093, China
| | - Mark W Chase
- Jodrell Laboratory, Royal Botanic Gardens, Kew, Richmond, TW9 3DS, Surrey, UK
- Department of Environment and Agriculture, Curtin University, Perth, WA, Australia
| | - Song Ge
- Institute of Botany, Chinese Academy of Sciences, Xiangshan, Haidian, Beijing, 100093, China
| | - Jianwu Li
- Xishuanbanan Tropical Botanical Gardens, Chinese Academy of Sciences, Menglun, Mengla, Yunnan, China
| | - Jinlong Fu
- Novogene Bioinformatics Institute, Beijing, 100083, China
| | - Kui Li
- Novogene Bioinformatics Institute, Beijing, 100083, China
| | - Meng Hao
- Novogene Bioinformatics Institute, Beijing, 100083, China
| | - Yiming Wang
- Novogene Bioinformatics Institute, Beijing, 100083, China
| | - Yuannian Jiao
- Institute of Botany, Chinese Academy of Sciences, Xiangshan, Haidian, Beijing, 100093, China
| | - Wenkai Jiang
- Novogene Bioinformatics Institute, Beijing, 100083, China
| | - Xiaohua Jin
- Institute of Botany, Chinese Academy of Sciences, Xiangshan, Haidian, Beijing, 100093, China.
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