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Huang G, Bao Z, Feng L, Zhai J, Wendel JF, Cao X, Zhu Y. A telomere-to-telomere cotton genome assembly reveals centromere evolution and a Mutator transposon-linked module regulating embryo development. Nat Genet 2024:10.1038/s41588-024-01877-6. [PMID: 39147922 DOI: 10.1038/s41588-024-01877-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Accepted: 07/18/2024] [Indexed: 08/17/2024]
Abstract
Assembly of complete genomes can reveal functional genetic elements missing from draft sequences. Here we present the near-complete telomere-to-telomere and contiguous genome of the cotton species Gossypium raimondii. Our assembly identified gaps and misoriented or misassembled regions in previous assemblies and produced 13 centromeres, with 25 chromosomal ends having telomeres. In contrast to satellite-rich Arabidopsis and rice centromeres, cotton centromeres lack phased CENH3 nucleosome positioning patterns and probably evolved by invasion from long terminal repeat retrotransposons. In-depth expression profiling of transposable elements revealed a previously unannotated DNA transposon (MuTC01) that interacts with miR2947 to produce trans-acting small interfering RNAs (siRNAs), one of which targets the newly evolved LEC2 (LEC2b) to produce phased siRNAs. Systematic genome editing experiments revealed that this tripartite module, miR2947-MuTC01-LEC2b, controls the morphogenesis of complex folded embryos characteristic of Gossypium and its close relatives in the cotton tribe. Our study reveals a trans-acting siRNA-based tripartite regulatory pathway for embryo development in higher plants.
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Affiliation(s)
- Gai Huang
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, China.
- Institute for Advanced Studies, Wuhan University, Wuhan, China.
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China.
| | - Zhigui Bao
- Max Planck Institute for Biology Tübingen, Tübingen, Germany
| | - Li Feng
- Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
| | - Jixian Zhai
- Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
| | - Jonathan F Wendel
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA, USA
| | - Xiaofeng Cao
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Yuxian Zhu
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, China.
- Institute for Advanced Studies, Wuhan University, Wuhan, China.
- Hubei Hongshan Laboratory, Wuhan, China.
- Taikang Center for Life and Medical Sciences, Wuhan University, Wuhan, China.
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Xia W, Wang S, Liu X, Chen Y, Lin C, Liu R, Liu H, Li J, Zhu J. Chromosome-level genome provides new insight into the overwintering process of Korla pear (Pyrus sinkiangensis Yu). BMC PLANT BIOLOGY 2024; 24:773. [PMID: 39138412 PMCID: PMC11323677 DOI: 10.1186/s12870-024-05490-x] [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: 04/16/2024] [Accepted: 08/06/2024] [Indexed: 08/15/2024]
Abstract
Korla pear has a unique taste and aroma and is a breeding parent of numerous pear varieties. It is susceptible to Valsa mali var. pyri, which invades bark wounded by freezing injury. Its genetic relationships have not been fully defined and could offer insight into the mechanism for freezing tolerance and disease resistance. We generated a high-quality, chromosome-level genome assembly for Korla pear via the Illumina and PacBio circular consensus sequencing (CCS) platforms and high-throughput chromosome conformation capture (Hi-C). The Korla pear genome is ~ 496.63 Mb, and 99.18% of it is assembled to 17 chromosomes. Collinearity and phylogenetic analyses indicated that Korla might be derived from Pyrus pyrifolia and that it diverged ~ 3.9-4.6 Mya. During domestication, seven late embryogenesis abundant (LEA), two dehydrin (DHN), and 54 disease resistance genes were lost from Korla pear compared with P. betulifolia. Moreover, 21 LEA and 31 disease resistance genes were common to the Korla pear and P. betulifolia genomes but were upregulated under overwintering only in P. betulifolia because key cis elements were missing in Korla pear. Gene deletion and downregulation during domestication reduced freezing tolerance and disease resistance in Korla pear. These results could facilitate the breeding of novel pear varieties with high biotic and abiotic stress resistance.
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Affiliation(s)
- Wenwen Xia
- Key Laboratory of Agricultural Biotechnology, College of Life Science, Shihezi University, Shihezi, 832000, China
| | - Saisai Wang
- Key Laboratory of Agricultural Biotechnology, College of Life Science, Shihezi University, Shihezi, 832000, China
| | - Xiaoyan Liu
- Key Laboratory of Agricultural Biotechnology, College of Life Science, Shihezi University, Shihezi, 832000, China
| | - Yifei Chen
- Key Laboratory of Agricultural Biotechnology, College of Life Science, Shihezi University, Shihezi, 832000, China
| | - Caixia Lin
- Xinjiang Production and Construction Crops, Institute of Agricultural Sciences, Tiemenguan, 841007, China
| | - Ruina Liu
- Key Laboratory of Agricultural Biotechnology, College of Life Science, Shihezi University, Shihezi, 832000, China
| | - Hailiang Liu
- Key Laboratory of Agricultural Biotechnology, College of Life Science, Shihezi University, Shihezi, 832000, China
- Institute for Regenerative Medicine, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, 200123, China
| | - Jin Li
- Key Laboratory of Agricultural Biotechnology, College of Life Science, Shihezi University, Shihezi, 832000, China.
| | - Jianbo Zhu
- Key Laboratory of Agricultural Biotechnology, College of Life Science, Shihezi University, Shihezi, 832000, China.
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Liao M, Xu M, Hu R, Xu Z, Bonvillain C, Li Y, Li X, Luo X, Wang J, Wang J, Zhao S, Gu Z. The chromosome-level genome assembly of the red swamp crayfish Procambarus clarkii. Sci Data 2024; 11:885. [PMID: 39143139 PMCID: PMC11325019 DOI: 10.1038/s41597-024-03718-x] [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: 11/20/2023] [Accepted: 07/31/2024] [Indexed: 08/16/2024] Open
Abstract
Red swamp crayfish, Procambarus clarkii, is the most cultured freshwater crayfish species. It attracts significant research attention due to its considerable economic importance. However, the limited availability of genome information has impeded further genetic studies and breeding programs. By utilizing Illumina, PacBio, and Hi-C sequencing technologies, we present a more comprehensive and continuous chromosome-level assembly for P. clarkii than the published one. The final genome size is 4.03 Gb, consisting of 2,358 scaffolds with a N50 of 42.87 Mb. Notably, 3.68 Gb, corresponding to 91.42% of the genome, was anchored to 94 chromosomes. The assembly comprises 70.64% repetitive sequences, including 5.21% tandem repeats and 65.40% transposable elements. Additionally, a total of 4,456 non-coding RNAs and 28,852 protein-coding genes were predicted in the P. clarkii genome, with 96.26% of the genes were annotated. This high-quality genome assembly not only represents a significant improvement for the genome of P. clarkii and provides insights into the unique genome evolution, but also offers valuable information for developing freshwater aquaculture and accelerating genetic breeding.
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Affiliation(s)
- Mingcong Liao
- College of Fisheries and Shuangshui Shuanglü Institute, Huazhong Agricultural University, Wuhan, 430070, China
- Hubei Hongshan laboratory, Wuhan, 430070, China
| | - Meng Xu
- Department of Ecology and Institute of Hydrobiology, Jinan University, Guangzhou, 510632, China
- BGI Institute of Applied Agriculture, BGI-Shenzhen, Shenzhen, 518120, China
| | - Ruixue Hu
- College of Fisheries and Shuangshui Shuanglü Institute, Huazhong Agricultural University, Wuhan, 430070, China
- Hubei Hongshan laboratory, Wuhan, 430070, China
| | - Zhiwei Xu
- College of Fisheries and Shuangshui Shuanglü Institute, Huazhong Agricultural University, Wuhan, 430070, China
- Hubei Hongshan laboratory, Wuhan, 430070, China
| | - Christopher Bonvillain
- Department of Biological Sciences, Nicholls State University, P.O. Box 2021, Thibodaux, Louisiana, 70310, USA
| | - Ying Li
- College of Fisheries and Shuangshui Shuanglü Institute, Huazhong Agricultural University, Wuhan, 430070, China
- Hubei Hongshan laboratory, Wuhan, 430070, China
| | - Xu Li
- BGI Institute of Applied Agriculture, BGI-Shenzhen, Shenzhen, 518120, China
| | - Xiaohong Luo
- College of Fisheries and Shuangshui Shuanglü Institute, Huazhong Agricultural University, Wuhan, 430070, China
- Hubei Hongshan laboratory, Wuhan, 430070, China
| | - Jianghua Wang
- College of Fisheries and Shuangshui Shuanglü Institute, Huazhong Agricultural University, Wuhan, 430070, China
| | - Jie Wang
- Genetic engineering research center, School of Life Sciences, Chongqing University, Chongqing, 401331, China
| | - Shancen Zhao
- BGI Institute of Applied Agriculture, BGI-Shenzhen, Shenzhen, 518120, China
| | - Zemao Gu
- College of Fisheries and Shuangshui Shuanglü Institute, Huazhong Agricultural University, Wuhan, 430070, China.
- Hubei Hongshan laboratory, Wuhan, 430070, China.
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Ribeiro Tomé LM, Quintanilha-Peixoto G, Costa-Rezende DH, Salvador-Montoya CA, Cardoso D, S Araújo D, Freitas JM, Bielefeld Nardoto G, Alves-Silva G, Drechsler-Santos ER, Góes-Neto A. Comparative genomics and stable isotope analysis reveal the saprotrophic-pathogenic lifestyle of a neotropical fungus. mBio 2024; 15:e0142324. [PMID: 39012152 PMCID: PMC11325261 DOI: 10.1128/mbio.01423-24] [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: 06/03/2024] [Accepted: 06/20/2024] [Indexed: 07/17/2024] Open
Abstract
In terrestrial forested ecosystems, fungi may interact with trees in at least three distinct ways: (i) associated with roots as symbionts; (ii) as pathogens in roots, trunks, leaves, flowers, and fruits; or (iii) decomposing dead tree tissues on soil or even on dead tissues in living trees. Distinguishing the latter two nutrition modes is rather difficult in Hymenochaetaceae (Basidiomycota) species. Herein, we have used an integrative approach of comparative genomics, stable isotopes, host tree association, and bioclimatic data to investigate the lifestyle ecology of the scarcely known neotropical genus Phellinotus, focusing on the unique species Phellinotus piptadeniae. This species is strongly associated with living Piptadenia gonoacantha (Fabaceae) trees in the Atlantic Forest domain on a relatively high precipitation gradient. Phylogenomics resolved P. piptadeniae in a clade that also includes both plant pathogens and typical wood saprotrophs. Furthermore, both genome-predicted Carbohydrate-Active Enzymes (CAZy) and stable isotopes (δ13C and δ15N) revealed a rather flexible lifestyle for the species. Altogether, our findings suggest that P. piptadeniae has been undergoing a pathotrophic specialization in a particular tree species while maintaining all the metabolic repertoire of a wood saprothroph. IMPORTANCE This is the first genomic description for Phellinotus piptadeniae. This basidiomycete is found across a broad range of climates and ecosystems in South America, including regions threatened by extensive agriculture. This fungus is also relevant considering its pathotrophic-saprotrophic association with Piptadenia goanocantha, which we began to understand with these new results that locate this species among biotrophic and necrotrophic fungi.
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Affiliation(s)
- Luiz Marcelo Ribeiro Tomé
- Department of Microbiology, Molecular and Computational Biology of Fungi Laboratory, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Gabriel Quintanilha-Peixoto
- Department of Microbiology, Molecular and Computational Biology of Fungi Laboratory, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Diogo Henrique Costa-Rezende
- Departamento de Ciências Biológicas, Programa de Pós-graduação em Botânica, Universidade Estadual de Feira de Santana, Feira de Santana, Brazil
| | - Carlos A Salvador-Montoya
- MIND.Funga (Monitoring and Inventorying Neotropical Diversity of Fungi) - MICOLAB, Universidade Federal de Santa Catarina, Florianópolis, Brazil
- Fundación Miguel Lillo, Instituto Criptogámico-Sección Micología, San Miguel de Tucumán, Argentina
- Organización Juvenil "Hongos Perú", Cusco, Santiago, Peru
| | - Domingos Cardoso
- Instituto de Pesquisas Jardim Botânico do Rio de Janeiro (JBRJ), Rio de Janeiro, Brazil
- Instituto de Biologia, Universidade Federal da Bahia, Salvador, Brazil
| | - Daniel S Araújo
- Program in Bioinformatics, Loyola University Chicago, Chicago, Illinois, USA
| | | | | | - Genivaldo Alves-Silva
- MIND.Funga (Monitoring and Inventorying Neotropical Diversity of Fungi) - MICOLAB, Universidade Federal de Santa Catarina, Florianópolis, Brazil
| | - Elisandro Ricardo Drechsler-Santos
- MIND.Funga (Monitoring and Inventorying Neotropical Diversity of Fungi) - MICOLAB, Universidade Federal de Santa Catarina, Florianópolis, Brazil
| | - Aristóteles Góes-Neto
- Department of Microbiology, Molecular and Computational Biology of Fungi Laboratory, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
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Chen BZ, Yang ZJ, Wang WB, Hao TT, Yu PB, Dong Y, Yu WB. Chromosome-level genome assembly and annotation of Flueggea virosa (Phyllanthaceae). Sci Data 2024; 11:875. [PMID: 39138223 PMCID: PMC11322648 DOI: 10.1038/s41597-024-03681-7] [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: 05/30/2024] [Accepted: 07/25/2024] [Indexed: 08/15/2024] Open
Abstract
Flueggea virosa (Roxb. ex Willd.) Royle, an evergreen shrub and small tree in the Phyllanthaceae family, holds significant potential in garden landscaping and pharmacological applications. However, the lack of genomic data has hindered further scientific understanding of its horticultural and medicinal values. In this study, we have assembled a haplotype-resolved genome of F. virosa for the first time. The two haploid genomes, named haplotype A genome and haplotype B genome, are 487.33 Mb and 477.53 Mb in size, respectively, with contig N50 lengths of 31.45 Mb and 32.81 Mb. More than 99% of the assembled sequences were anchored to 13 pairs of pseudo-chromosomes. Furthermore, 21,587 and 21,533 protein-coding genes were predicted in haplotype A and haplotype B genomes, respectively. The availability of this chromosome-level genome fills the gap in genomic data for F. virosa and provides valuable resources for molecular studies of this species, supporting future research on speciation, functional genomics, and comparative genomics within the Phyllanthaceae family.
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Affiliation(s)
- Bao-Zheng Chen
- College of Food Science and Technology, Yunnan Agricultural University, Kunming, Yunnan, 650201, China
- Yunnan Provincial Key Laboratory of Biological Big Data, Yunnan Agricultural University, Kunming, Yunnan, 650201, China
| | - Zi-Jiang Yang
- Bioinformatics group, Wageningen University and Research, Wageningen, Netherlands
| | - Wei-Bin Wang
- Yunnan Provincial Key Laboratory of Biological Big Data, Yunnan Agricultural University, Kunming, Yunnan, 650201, China
| | - Ting-Ting Hao
- Yunnan Provincial Key Laboratory of Biological Big Data, Yunnan Agricultural University, Kunming, Yunnan, 650201, China
| | - Peng-Ban Yu
- Center for Integrative Conservation and Yunnan Key Laboratory for the Conservation of Tropical Rainforests and Asian Elephants, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, Yunnan, 666303, China
| | - Yang Dong
- Yunnan Provincial Key Laboratory of Biological Big Data, Yunnan Agricultural University, Kunming, Yunnan, 650201, China.
| | - Wen-Bin Yu
- Center for Integrative Conservation and Yunnan Key Laboratory for the Conservation of Tropical Rainforests and Asian Elephants, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, Yunnan, 666303, China.
- Southeast Asia Biodiversity Research Institute, Chinese Academy of Sciences, Mengla, Yunnan, 666303, China.
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Chen BZ, Li DW, Wang WJ, Xin YX, Wang WB, Li XZ, Hao TT, Dong Y, Yu WB. Chromosome-level and haplotype-resolved genome assembly of Dracaena cambodiana (Asparagaceae). Sci Data 2024; 11:873. [PMID: 39138230 PMCID: PMC11322170 DOI: 10.1038/s41597-024-03670-w] [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: 01/30/2024] [Accepted: 07/23/2024] [Indexed: 08/15/2024] Open
Abstract
Dracaena cambodiana Pierre ex Gagn. (Asparagaceae) is the source plant of Dragon's blood and has high ornamental values in gardening. Currently, this species is classified as the second-class state-protected species in the National Key Protected Wild Plants (NKPWP) of China. However, limited genomic data has hindered a more comprehensive scientific understanding of the processes involved in the production of Dragon's blood and the related conservation genomics research. In this study, we assembled a haplotype-resolved genome of D. cambodiana. The haploid genomes, haplotype A and haplotype B, are 1,015.22 Mb and 1,003.13 Mb in size, respectively. The completeness of haplotype A and haplotype B genomes was 98.60% and 98.20%, respectively, using the "embryophyta_10" dataset. Haplotype A and haplotype B genomes contained 27,361 and 27,066 protein-coding genes, respectively, with nearly all being functionally annotated. These findings provide new insights into the genomic characteristics of D. cambodiana and will offer additional genomic resources for studying the biosynthesis mechanism of Dragon's blood and the horticultural application of Dragon trees.
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Affiliation(s)
- Bao-Zheng Chen
- College of Food Science and Technology, Yunnan Agricultural University, Kunming, Yunnan, 650201, China
- Yunnan Provincial Key Laboratory of Biological Big Data, Yunnan Agricultural University, Kunming, Yunnan, 650201, China
| | - Da-Wei Li
- Yunnan Provincial Key Laboratory of Biological Big Data, Yunnan Agricultural University, Kunming, Yunnan, 650201, China
| | - Wei-Jia Wang
- Center for Integrative Conservation and Yunnan Key Laboratory for the Conservation of Tropical Rainforests and Asian Elephants, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, Yunnan, 666303, China
| | - Ya-Xuan Xin
- Center for Integrative Conservation and Yunnan Key Laboratory for the Conservation of Tropical Rainforests and Asian Elephants, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, Yunnan, 666303, China
| | - Wei-Bin Wang
- Yunnan Provincial Key Laboratory of Biological Big Data, Yunnan Agricultural University, Kunming, Yunnan, 650201, China
| | - Xu-Zhen Li
- Yunnan Provincial Key Laboratory of Biological Big Data, Yunnan Agricultural University, Kunming, Yunnan, 650201, China
| | - Ting-Ting Hao
- Yunnan Provincial Key Laboratory of Biological Big Data, Yunnan Agricultural University, Kunming, Yunnan, 650201, China
| | - Yang Dong
- Yunnan Provincial Key Laboratory of Biological Big Data, Yunnan Agricultural University, Kunming, Yunnan, 650201, China.
| | - Wen-Bin Yu
- Center for Integrative Conservation and Yunnan Key Laboratory for the Conservation of Tropical Rainforests and Asian Elephants, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, Yunnan, 666303, China.
- Southeast Asia Biodiversity Research Institute, Chinese Academy of Sciences, Mengla, Yunnan, 666303, China.
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He L, Wang Y, Wang Y, Zhang RG, Wang Y, Hörandl E, Ma T, Mao YF, Mank JE, Ming R. Allopolyploidization from two dioecious ancestors leads to recurrent evolution of sex chromosomes. Nat Commun 2024; 15:6893. [PMID: 39134553 PMCID: PMC11319354 DOI: 10.1038/s41467-024-51158-3] [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: 03/13/2024] [Accepted: 07/31/2024] [Indexed: 08/15/2024] Open
Abstract
Polyploidization presents an unusual challenge for species with sex chromosomes, as it can lead to complex combinations of sex chromosomes that disrupt reproductive development. This is particularly true for allopolyploidization between species with different sex chromosome systems. Here, we assemble haplotype-resolved chromosome-level genomes of a female allotetraploid weeping willow (Salix babylonica) and a male diploid S. dunnii. We show that weeping willow arose from crosses between a female ancestor from the Salix-clade, which has XY sex chromosomes on chromosome 7, and a male ancestor from the Vetrix-clade, which has ancestral XY sex chromosomes on chromosome 15. We find that weeping willow has one pair of sex chromosomes, ZW on chromosome 15, that derived from the ancestral XY sex chromosomes in the male ancestor of the Vetrix-clade. Moreover, the ancestral 7X chromosomes from the female ancestor of the Salix-clade have reverted to autosomal inheritance. Duplicated intact ARR17-like genes on the four homologous chromosomes 19 likely have contributed to the maintenance of dioecy during polyploidization and sex chromosome turnover. Taken together, our results suggest the rapid evolution and reversion of sex chromosomes following allopolyploidization in weeping willow.
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Affiliation(s)
- Li He
- Eastern China Conservation Centre for Wild Endangered Plant Resources, Shanghai Chenshan Botanical Garden, Shanghai, 201602, China.
| | - Yuàn Wang
- Eastern China Conservation Centre for Wild Endangered Plant Resources, Shanghai Chenshan Botanical Garden, Shanghai, 201602, China
| | - Yi Wang
- Eastern China Conservation Centre for Wild Endangered Plant Resources, Shanghai Chenshan Botanical Garden, Shanghai, 201602, China
- Laboratory of Systematic Evolution and Biogeography of Woody Plants, School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, 100083, China
| | - Ren-Gang Zhang
- Yunnan Key Laboratory for Integrative Conservation of Plant Species with Extremely Small Populations, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
- University of Chinese Academy of Sciences, Beijing, 101408, China
| | - Yuán Wang
- Eastern China Conservation Centre for Wild Endangered Plant Resources, Shanghai Chenshan Botanical Garden, Shanghai, 201602, China
| | - Elvira Hörandl
- Department of Systematics, Biodiversity and Evolution of Plants (with Herbarium), University of Göttingen, Göttingen, Germany
| | - Tao Ma
- Key Laboratory for Bio‑Resource and Eco‑Environment of Ministry of Education & Sichuan Zoige Alpine Wetland Ecosystem National Observation and Research Station, College of Life Science, Sichuan University, Chengdu, China
| | - Yan-Fei Mao
- CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Judith E Mank
- Department of Zoology and Biodiversity Research Centre, University of British Columbia, Vancouver, BC, Canada
| | - Ray Ming
- Centre for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
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Hu Y, Wei X, Chu Z, Wei F, Peng Y, Huang B, Dong L, Wei K, Li W. Chromosome-level assembly and evolution analysis of the Trichosanthes truncata genome. Sci Data 2024; 11:872. [PMID: 39134552 PMCID: PMC11319624 DOI: 10.1038/s41597-024-03608-2] [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: 12/07/2023] [Accepted: 07/05/2024] [Indexed: 08/15/2024] Open
Abstract
Trichosanthes truncata C. B. Clarke, an important medicinal plant, is a dioecious plant belonging to the Cucurbitaceae family. This study presents a chromosomal-level reference genome assembly for T. truncata. Through the integration of PacBio high-fidelity sequencing and high-throughput chromosome conformation capture technology, a final genome sequence of 637.41 Mb was assembled, with an N50 of 57.24 Mb and consisting of 11 pseudochromosomes. Additionally, 97.21 Mb of repetitive sequences and 36,172 protein-coding genes were annotated. This high-quality genome assembly is of utmost significance for studying the molecular mechanisms underlying the biosynthesis of bioactive compounds. Furthermore, this study provided valuable insights into plant comparative genomics research.
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Affiliation(s)
- Ying Hu
- National Center for Traditional Chinese Medicine Inheritance and Innovation, Guangxi Botanical Garden of Medicinal Plants, Nanning, 530023, China
- Guangxi Key Laboratory of Medicinal Resources Protection and Genetic Improvement, Guangxi Botanical Garden of Medicinal Plants, Nanning, 530023, China
| | - Xiaomei Wei
- National Center for Traditional Chinese Medicine Inheritance and Innovation, Guangxi Botanical Garden of Medicinal Plants, Nanning, 530023, China
- Guangxi Key Laboratory of Medicinal Resources Protection and Genetic Improvement, Guangxi Botanical Garden of Medicinal Plants, Nanning, 530023, China
| | - Zhuannan Chu
- Institute of Horticulture, Anhui Academy of Agricultural Sciences, Hefei, 230001, China
| | - Fan Wei
- National Center for Traditional Chinese Medicine Inheritance and Innovation, Guangxi Botanical Garden of Medicinal Plants, Nanning, 530023, China
- Guangxi Key Laboratory of Medicinal Resources Protection and Genetic Improvement, Guangxi Botanical Garden of Medicinal Plants, Nanning, 530023, China
| | - Yude Peng
- National Center for Traditional Chinese Medicine Inheritance and Innovation, Guangxi Botanical Garden of Medicinal Plants, Nanning, 530023, China
| | - Baoyou Huang
- National Center for Traditional Chinese Medicine Inheritance and Innovation, Guangxi Botanical Garden of Medicinal Plants, Nanning, 530023, China
| | - Ling Dong
- Institute of Horticulture, Anhui Academy of Agricultural Sciences, Hefei, 230001, China
| | - Kunhua Wei
- National Center for Traditional Chinese Medicine Inheritance and Innovation, Guangxi Botanical Garden of Medicinal Plants, Nanning, 530023, China.
- Guangxi Key Laboratory of Medicinal Resources Protection and Genetic Improvement, Guangxi Botanical Garden of Medicinal Plants, Nanning, 530023, China.
| | - Weiwen Li
- Institute of Horticulture, Anhui Academy of Agricultural Sciences, Hefei, 230001, China.
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9
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Wang W, Ge Q, Wen J, Zhang H, Guo Y, Li Z, Xu Y, Ji D, Chen C, Guo L, Xu M, Shi C, Fan G, Xie C. Horizontal gene transfer and symbiotic microorganisms regulate the adaptive evolution of intertidal algae, Porphyra sense lato. Commun Biol 2024; 7:976. [PMID: 39128935 PMCID: PMC11317521 DOI: 10.1038/s42003-024-06663-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: 02/10/2024] [Accepted: 07/31/2024] [Indexed: 08/13/2024] Open
Abstract
Intertidal algae may adapt to environmental challenges by acquiring genes from other organisms and relying on symbiotic microorganisms. Here, we obtained a symbiont-free and chromosome-level genome of Pyropia haitanensis (47.2 Mb), a type of intertidal algae, by using multiple symbiont screening methods. We identified 286 horizontal gene transfer (HGT) genes, 251 of which harbored transposable elements (TEs), reflecting the importance of TEs for facilitating the transfer of genes into P. haitanensis. Notably, the bulked segregant analysis revealed that two HGT genes, sirohydrochlorin ferrochelatase and peptide-methionine (R)-S-oxide reductase, play a significant role in the adaptation of P. haitanensis to heat stress. Besides, we found Pseudomonas, Actinobacteria, and Bacteroidetes are the major taxa among the symbiotic bacteria of P. haitanensis (nearly 50% of the HGT gene donors). Among of them, a heat-tolerant actinobacterial strain (Saccharothrix sp.) was isolated and revealed to be associated with the heat tolerance of P. haitanensis through its regulatory effects on the genes involved in proline synthesis (proC), redox homeostasis (ggt), and protein folding (HSP20). These findings contribute to our understanding of the adaptive evolution of intertidal algae, expanding our knowledge of the HGT genes and symbiotic microorganisms to enhance their resilience and survival in challenging intertidal environments.
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Affiliation(s)
- Wenlei Wang
- Fisheries College, Jimei University, Xiamen, 361021, China
- State Key Laboratory of Mariculture Breeding, Fisheries College of Jimei university, Ningde, China
- Fujian Engineering Research Center of Aquatic Breeding and Healthy Aquaculture, Xiamen, 361021, China
| | - Qijin Ge
- BGI Research, Qingdao, 266555, China
| | - Jian Wen
- Fisheries College, Jimei University, Xiamen, 361021, China
- State Key Laboratory of Mariculture Breeding, Fisheries College of Jimei university, Ningde, China
| | - Han Zhang
- Fisheries College, Jimei University, Xiamen, 361021, China
- State Key Laboratory of Mariculture Breeding, Fisheries College of Jimei university, Ningde, China
| | - Yanling Guo
- Fisheries College, Jimei University, Xiamen, 361021, China
- State Key Laboratory of Mariculture Breeding, Fisheries College of Jimei university, Ningde, China
| | - Zongtang Li
- Fisheries College, Jimei University, Xiamen, 361021, China
- State Key Laboratory of Mariculture Breeding, Fisheries College of Jimei university, Ningde, China
| | - Yan Xu
- Fisheries College, Jimei University, Xiamen, 361021, China
- State Key Laboratory of Mariculture Breeding, Fisheries College of Jimei university, Ningde, China
| | - Dehua Ji
- Fisheries College, Jimei University, Xiamen, 361021, China
- State Key Laboratory of Mariculture Breeding, Fisheries College of Jimei university, Ningde, China
| | - Changsheng Chen
- Fisheries College, Jimei University, Xiamen, 361021, China
- State Key Laboratory of Mariculture Breeding, Fisheries College of Jimei university, Ningde, China
| | | | | | - Chengcheng Shi
- BGI Research, Qingdao, 266555, China
- Qingdao Key Laboratory of Marine Genomics, BGI Research, Qingdao, 266555, China
| | - Guangyi Fan
- BGI Research, Qingdao, 266555, China.
- Qingdao Key Laboratory of Marine Genomics, BGI Research, Qingdao, 266555, China.
- BGI Research, Shenzhen, 518083, China.
| | - Chaotian Xie
- Fisheries College, Jimei University, Xiamen, 361021, China.
- State Key Laboratory of Mariculture Breeding, Fisheries College of Jimei university, Ningde, China.
- Fujian Engineering Research Center of Aquatic Breeding and Healthy Aquaculture, Xiamen, 361021, China.
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10
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Zhang J, Guo Y, Su J, Yu G, Ma Z, Qin C. The first high-quality genome assembly and annotation of Anthocidaris crassispina. Sci Data 2024; 11:866. [PMID: 39127825 DOI: 10.1038/s41597-024-03733-y] [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: 03/08/2024] [Accepted: 08/02/2024] [Indexed: 08/12/2024] Open
Abstract
Anthocidaris crassispina is a very popular edible sea urchin distributed along the coast of the South China Sea. In this study, we performed whole-genome sequencing and generated a chromosome-level assembly of this species. The total length of the genomic contig sequence was 891.02 Mb, and contig N50 was 808.15 kb when Hifiasm was used for assembly. The Hi-C library was constructed and sequenced, yielding approximately 68.61 Gb of data. After Hi-C assembly, approximately 886.72 Mb of sequence was able to be mapped onto 21 chromosomes, accounting for 99.52% of the total genome length. Among the sequences located on the chromosomes, those for which the order and direction could be determined accounted for approximately 826.82 Mb, or 93.24% of the total length. These results provide valuable resources for further study of A. crassispina at the genetic level.
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Affiliation(s)
- Jia Zhang
- South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China
- National Agricultural Experimental Station for Fishery Resources and Environment Dapeng, Shenzhen, China
- Key Laboratory of Efficient Utilization and Processing of Marine Fishery Resources of Hainan Province, Sanya Tropical Fisheries Research Institute, Sanya, China
| | - Yu Guo
- South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China
- National Agricultural Experimental Station for Fishery Resources and Environment Dapeng, Shenzhen, China
- Key Laboratory of Efficient Utilization and Processing of Marine Fishery Resources of Hainan Province, Sanya Tropical Fisheries Research Institute, Sanya, China
- Hainan Seed Industry Laboratory, Sanya, China
| | - Jiaqi Su
- South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China
- Key Laboratory of Efficient Utilization and Processing of Marine Fishery Resources of Hainan Province, Sanya Tropical Fisheries Research Institute, Sanya, China
| | - Gang Yu
- South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China
- Key Laboratory of Efficient Utilization and Processing of Marine Fishery Resources of Hainan Province, Sanya Tropical Fisheries Research Institute, Sanya, China
| | - Zhenhua Ma
- South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China
- Key Laboratory of Efficient Utilization and Processing of Marine Fishery Resources of Hainan Province, Sanya Tropical Fisheries Research Institute, Sanya, China
| | - Chuanxin Qin
- South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China.
- National Agricultural Experimental Station for Fishery Resources and Environment Dapeng, Shenzhen, China.
- Key Laboratory of Efficient Utilization and Processing of Marine Fishery Resources of Hainan Province, Sanya Tropical Fisheries Research Institute, Sanya, China.
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11
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Huang XC, Tang H, Wei X, He Y, Hu S, Wu JY, Xu D, Qiao F, Xue JY, Zhao Y. The gradual establishment of complex coumarin biosynthetic pathway in Apiaceae. Nat Commun 2024; 15:6864. [PMID: 39127760 PMCID: PMC11316762 DOI: 10.1038/s41467-024-51285-x] [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: 01/15/2024] [Accepted: 08/05/2024] [Indexed: 08/12/2024] Open
Abstract
Complex coumarins (CCs) represent characteristic metabolites found in Apiaceae plants, possessing significant medical value. Their essential functional role is likely as protectants against pathogens and regulators responding to environmental stimuli. Utilizing genomes and transcriptomes from 34 Apiaceae plants, including our recently sequenced Peucedanum praeruptorum, we conduct comprehensive phylogenetic analyses to reconstruct the detailed evolutionary process of the CC biosynthetic pathway in Apiaceae. Our results show that three key enzymes - p-coumaroyl CoA 2'-hydroxylase (C2'H), C-prenyltransferase (C-PT), and cyclase - originated successively at different evolutionary nodes within Apiaceae through various means of gene duplications: ectopic and tandem duplications. Neofunctionalization endows these enzymes with novel functions necessary for CC biosynthesis, thus completing the pathway. Candidate genes are cloned for heterologous expression and subjected to in vitro enzymatic assays to test our hypothesis regarding the origins of the key enzymes, and the results precisely validate our evolutionary inferences. Among the three enzymes, C-PTs are likely the primary determinant of the structural diversity of CCs (linear/angular), due to divergent activities evolved to target different positions (C-6 or C-8) of umbelliferone. A key amino acid variation (Ala161/Thr161) is identified and proven to play a crucial role in the alteration of enzymatic activity, possibly resulting in distinct binding forms between enzymes and substrates, thereby leading to different products. In conclusion, this study provides a detailed trajectory for the establishment and evolution of the CC biosynthetic pathway in Apiaceae. It explains why only a portion, not all, of Apiaceae plants can produce CCs and reveals the mechanisms of CC structural diversity among different Apiaceae plants.
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Affiliation(s)
- Xin-Cheng Huang
- College of Horticulture, Bioinformatics Center, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Huanying Tang
- Department of Resources Science of Traditional Chinese Medicines, School of Traditional Chinese Pharmacy, and State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, 210009, Jiangsu, China
| | - Xuefen Wei
- College of Horticulture, Bioinformatics Center, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Yuedong He
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, 410128, Hunan, China
| | - Shuaiya Hu
- College of Horticulture, Bioinformatics Center, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Jia-Yi Wu
- College of Horticulture, Bioinformatics Center, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Dingqiao Xu
- School of Pharmacy, Shaanxi University of Chinese Medicine, Xi'an, 712046, Shaanxi, China
| | - Fei Qiao
- National Key Laboratory for Tropical Crop Breeding, Sanya, 572024, Hainan, China.
- Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, Hainan, China.
| | - Jia-Yu Xue
- College of Horticulture, Bioinformatics Center, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China.
| | - Yucheng Zhao
- Department of Resources Science of Traditional Chinese Medicines, School of Traditional Chinese Pharmacy, and State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, 210009, Jiangsu, China.
- Medical Botanical Garden, China Pharmaceutical University, Nanjing, 210009, Jiangsu, China.
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12
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Xie J, Liu X, Qin Z, Mei S, Tarafder E, Li C, Zeng X, Tian F. Evolution and related pathogenic genes of Pseudodiploöspora longispora on Morchella based on genomic characterization and comparative genomic analysis. Sci Rep 2024; 14:18588. [PMID: 39127740 PMCID: PMC11316761 DOI: 10.1038/s41598-024-69421-4] [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: 01/06/2024] [Accepted: 08/05/2024] [Indexed: 08/12/2024] Open
Abstract
True morels (Morchella) are globally renowned medicinal and edible mushrooms. White mold disease caused by fungi is the main disease of Morchella, which has the characteristics of wide incidence and strong destructiveness. The disparities observed in the isolation rates of different pathogens indicate their varying degrees of host adaptability and competitive survival abilities. In order to elucidate its potential mechanism, this study, the pathogen of white mold disease from Dafang county, Guizhou Province was isolated and purified, identified as Pseudodiploöspora longispora by morphological, molecular biological and pathogenicity tests. Furthermore, high-quality genome of P. longisporus (40.846 Mb) was assembled N50 of 3.09 Mb, predicts 7381 protein-coding genes. Phylogenetic analysis of single-copy homologous genes showed that P. longispora and Zelopaecilomyces penicillatus have the closest evolutionary relationship, diverging into two branches approximately 50 (44.3-61.4) MYA. Additionally, compared with the other two pathogens causing Morchella disease, Z. penicillatus and Cladobotryum protrusum, it was found that they had similar proportions of carbohydrate enzyme types and encoded abundant cell wall degrading enzymes, such as chitinase and glucanase, indicating their important role in disease development. Moreover, the secondary metabolite gene clusters of P. longispora and Z. penicillatus show a high degree of similarity to leucinostatin A and leucinostatin B (peptaibols). Furthermore, a gene cluster with synthetic toxic substance Ochratoxin A was also identified in P. longispora and C. protrusum, indicating that they may pose a potential threat to food safety. This study provides valuable insights into the genome of P. longispora, contributing to pathogenicity research.
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Affiliation(s)
- Jiangtao Xie
- Department of Plant Pathology, College of Agriculture, Guizhou University, Guiyang, Guizhou, China
- Institute of Edible Mushroom, Guizhou University, Guiyang, China
| | - Xue Liu
- Department of Plant Pathology, College of Agriculture, Guizhou University, Guiyang, Guizhou, China
- Institute of Edible Mushroom, Guizhou University, Guiyang, China
| | - Zaili Qin
- Department of Plant Pathology, College of Agriculture, Guizhou University, Guiyang, Guizhou, China
- Institute of Edible Mushroom, Guizhou University, Guiyang, China
| | - Shihui Mei
- Department of Plant Pathology, College of Agriculture, Guizhou University, Guiyang, Guizhou, China
- Institute of Edible Mushroom, Guizhou University, Guiyang, China
| | - Entaj Tarafder
- Department of Plant Pathology, College of Agriculture, Guizhou University, Guiyang, Guizhou, China
| | - Chao Li
- Department of Plant Pathology, College of Agriculture, Guizhou University, Guiyang, Guizhou, China
- Institute of Edible Mushroom, Guizhou University, Guiyang, China
| | - Xiangyu Zeng
- Department of Plant Pathology, College of Agriculture, Guizhou University, Guiyang, Guizhou, China
- Institute of Edible Mushroom, Guizhou University, Guiyang, China
| | - Fenghua Tian
- Department of Plant Pathology, College of Agriculture, Guizhou University, Guiyang, Guizhou, China.
- Engineering Research Center of Chinese Ministry of Education for Edible and Medicinal Fungi, Jilin Agricultural University, Changchun, Jilin, China.
- Guizhou Key Laboratory of Edible Fungi Breeding, Guiyang, China.
- Institute of Edible Mushroom, Guizhou University, Guiyang, China.
- Tianiin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China.
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13
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Chen Y, Zhang X, Wang L, Fang M, Lu R, Ma Y, Huang Y, Chen X, Sheng W, Shi L, Zheng Z, Qiu Y. Telomere-to-telomere genome assembly of Eleocharis dulcis and expression profiles during corm development. Sci Data 2024; 11:869. [PMID: 39127691 PMCID: PMC11316796 DOI: 10.1038/s41597-024-03717-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: 01/08/2024] [Accepted: 07/31/2024] [Indexed: 08/12/2024] Open
Abstract
Eleocharis dulcis (Burm. f.) Trin. ex Hensch., commonly known as Chinese water chestnut, is a traditional aquatic vegetable in China, and now is widely cultivated throughout the world because of its high nutritional value and unique tastes. Here, we report the assembly of a 493.24 Mb telomere-to-telomere (T2T) genome of E. dulcis accomplished by integrating ONT ultra-long reads, PacBio long reads and Hi-C data. The reference genome was anchored onto 111 gap-free chromosomes, containing 48.31% repeat elements and 33,493 predicted protein-coding genes. Whole genome duplication (WGD) and inter-genomic synteny analyses indicated that chromosome breakage and genome duplication in E. dulcis possibly occurred multiple times during genome evolution after its divergence from a common ancestor with Rhynchospora breviuscula at ca. 35.6 Mya. A comparative time-course transcriptome analysis of corm development revealed different patterns of gene expression between cultivated and wild accessions with the highest number of differentially expressed genes (DEGs, 15,870) at the middle swelling stage and some of the DEGs were significantly enriched for starch metabolic process.
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Affiliation(s)
- Yang Chen
- Provincial Key Laboratory of Characteristic Aquatic Vegetable Breeding and Cultivation, Jinhua Academy of Agricultural Sciences (Zhejiang Institute of Agricultural Machinery), Jinhua, Zhejiang, 321000, China
- Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei, 430074, China
| | - Xinyi Zhang
- Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei, 430074, China
| | - Lingyun Wang
- Provincial Key Laboratory of Characteristic Aquatic Vegetable Breeding and Cultivation, Jinhua Academy of Agricultural Sciences (Zhejiang Institute of Agricultural Machinery), Jinhua, Zhejiang, 321000, China
| | - Mingya Fang
- Provincial Key Laboratory of Characteristic Aquatic Vegetable Breeding and Cultivation, Jinhua Academy of Agricultural Sciences (Zhejiang Institute of Agricultural Machinery), Jinhua, Zhejiang, 321000, China
| | - Ruisen Lu
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, Jiangsu, 210014, China
| | - Yazhen Ma
- Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei, 430074, China
| | - Yan Huang
- Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei, 430074, China
| | - Xiaoyang Chen
- Seed Management Station of Zhejiang Province, Hangzhou, Zhejiang, 310020, China
| | - Wei Sheng
- Provincial Key Laboratory of Characteristic Aquatic Vegetable Breeding and Cultivation, Jinhua Academy of Agricultural Sciences (Zhejiang Institute of Agricultural Machinery), Jinhua, Zhejiang, 321000, China
| | - Lin Shi
- Provincial Key Laboratory of Characteristic Aquatic Vegetable Breeding and Cultivation, Jinhua Academy of Agricultural Sciences (Zhejiang Institute of Agricultural Machinery), Jinhua, Zhejiang, 321000, China
| | - Zhaisheng Zheng
- Provincial Key Laboratory of Characteristic Aquatic Vegetable Breeding and Cultivation, Jinhua Academy of Agricultural Sciences (Zhejiang Institute of Agricultural Machinery), Jinhua, Zhejiang, 321000, China.
| | - Yingxiong Qiu
- Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei, 430074, China.
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14
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Yang W, Yang Z, Yang L, Li Z, Zhang Z, Wei T, Huang R, Li G. Genomic and transcriptomic analyses of the elite rice variety Huizhan provide insight into disease resistance and heat tolerance. Genomics 2024; 116:110915. [PMID: 39134161 DOI: 10.1016/j.ygeno.2024.110915] [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: 03/28/2024] [Revised: 08/09/2024] [Accepted: 08/09/2024] [Indexed: 08/16/2024]
Abstract
The indica rice variety Huizhan shows elite traits of disease resistance and heat tolerance. However, the underlying genetic basis of these traits is not fully understood due to limited genomic resources. Here, we used Nanopore long-read and next-generation sequencing technologies to generate a chromosome-scale genome assembly of Huizhan. Comparative genomics analysis uncovered a large chromosomal inversion and expanded gene families that are associated with plant growth, development and stress responses. Functional rice blast resistance genes, including Pi2, Pib and Ptr, and bacterial blight resistance gene Xa27, contribute to disease resistance of Huizhan. Furthermore, integrated genomics and transcriptomics analyses showed that OsHIRP1, OsbZIP60, the SOD gene family, and various transcription factors are involved in heat tolerance of Huizhan. The high-quality genome assembly and comparative genomics results presented in this study facilitate the use of Huizhan as an elite parental line in developing rice varieties adapted to disease pressure and climate challenges.
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Affiliation(s)
- Wei Yang
- National Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, Hubei Key Laboratory of Plant Pathology, The Center of Crop Nanobiotechnology, Huazhong Agricultural University, Wuhan 430070, China
| | - Zhou Yang
- National Engineering Research Center of Rice (Nanchang), Key Laboratory of Germplasm innovation and Breeding of Double-cropping Rice (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Rice Research Institute, Jiangxi Academy of Agricultural Sciences, Nanchang 330200, China
| | - Lei Yang
- National Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, Hubei Key Laboratory of Plant Pathology, The Center of Crop Nanobiotechnology, Huazhong Agricultural University, Wuhan 430070, China
| | - Zheng Li
- National Engineering Research Center of Rice (Nanchang), Key Laboratory of Germplasm innovation and Breeding of Double-cropping Rice (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Rice Research Institute, Jiangxi Academy of Agricultural Sciences, Nanchang 330200, China; National Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, Hubei Key Laboratory of Plant Pathology, The Center of Crop Nanobiotechnology, Huazhong Agricultural University, Wuhan 430070, China
| | - Zhaowu Zhang
- State Key Laboratory of Agricultural Genomics, BGI Research, Shenzhen 518083, China; BGI Research, Wuhan 430074, China
| | - Tong Wei
- State Key Laboratory of Agricultural Genomics, BGI Research, Shenzhen 518083, China; BGI Research, Wuhan 430074, China
| | - Renliang Huang
- National Engineering Research Center of Rice (Nanchang), Key Laboratory of Germplasm innovation and Breeding of Double-cropping Rice (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Rice Research Institute, Jiangxi Academy of Agricultural Sciences, Nanchang 330200, China.
| | - Guotian Li
- National Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, Hubei Key Laboratory of Plant Pathology, The Center of Crop Nanobiotechnology, Huazhong Agricultural University, Wuhan 430070, China.
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15
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Duan M, Yang S, Li X, Tang X, Cheng Y, Luo J, Wang J, Song H, Wang Q, Zhu GX. Chromosome-level genome assembly and annotation of the Rhabdophis nuchalis (Hubei keelback). Sci Data 2024; 11:850. [PMID: 39117633 PMCID: PMC11310211 DOI: 10.1038/s41597-024-03708-z] [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: 05/23/2024] [Accepted: 07/30/2024] [Indexed: 08/10/2024] Open
Abstract
Rhabdophis nuchalis, a snake widely distributed in China, possesses a unique trait: glands beneath the skin on its neck and back, known as nucho-dorsal glands. These features make it a valuable subject for studying genetic diversity and the evolution of complex traits. In this study, we obtained a high-quality chromosome-level reference genome of R. nuchalis using MGI short-read sequencing, PacBio Revio long-read sequencing, and Hi-C sequencing techniques. The final assembly comprised 1.92 Gb of the R. nuchalis genome, anchored to 20 chromosomes (including 9 macrochromosomes and 11 microchromosomes), with a contig N50 of 104.79 Mb, a scaffold N50 of 204.96 Mb, and a BUSCO completeness of 97.50%. Additionally, we annotated a total of 1.09 Gb of repetitive sequences (which constitute 56.51% of the entire genome) and identified 22,057 protein-coding genes. This high-quality reference genome of R. nuchalis furnishes essential genomic data for comprehending the genetic diversity and evolutionary history of the species, as well as for facilitating species conservation efforts and comparative genomics studies.
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Affiliation(s)
- Mingwen Duan
- College of Life Science, Sichuan Agricultural University, Ya'an, 625014, China
| | - Shijun Yang
- College of Life Science, Sichuan Agricultural University, Ya'an, 625014, China
| | - Xiufeng Li
- College of Life Science, Sichuan Agricultural University, Ya'an, 625014, China
| | - Xuemei Tang
- College of Life Science, Sichuan Agricultural University, Ya'an, 625014, China
| | - Yuqi Cheng
- Chengdu Zoo, Chengdu, Sichuan Province, 610081, China
| | - Jingxue Luo
- College of Life Science, Sichuan Agricultural University, Ya'an, 625014, China
| | - Ji Wang
- College of Life Science, Sichuan Agricultural University, Ya'an, 625014, China
| | - Huina Song
- College of Life Science, Sichuan Agricultural University, Ya'an, 625014, China
| | - Qin Wang
- College of Life Science, Sichuan Agricultural University, Ya'an, 625014, China
| | - Guang Xiang Zhu
- College of Life Science, Sichuan Agricultural University, Ya'an, 625014, China.
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16
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Wang D, Rastas P, Yi X, Löytynoja A, Kivikoski M, Feng X, Reid K, Merilä J. Improved assembly of the Pungitius pungitius reference genome. G3 (BETHESDA, MD.) 2024; 14:jkae126. [PMID: 38861393 PMCID: PMC11304971 DOI: 10.1093/g3journal/jkae126] [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: 04/24/2024] [Revised: 05/23/2024] [Accepted: 05/30/2024] [Indexed: 06/13/2024]
Abstract
The nine-spined stickleback (Pungitius pungitius) has been increasingly used as a model system in studies of local adaptation and sex chromosome evolution but its current reference genome assembly is far from perfect, lacking distinct sex chromosomes. We generated an improved assembly of the nine-spined stickleback reference genome (98.3% BUSCO completeness) with the aid of linked-read mapping. While the new assembly (v8) was of similar size as the earlier version (v7), we were able to assign 4.4 times more contigs to the linkage groups and improve the contiguity of the genome. Moreover, the new assembly contains a ∼22.8 Mb Y-linked scaffold (LG22) consisting mainly of previously assigned X-contigs, putative Y-contigs, putative centromere contigs, and highly repetitive elements. The male individual showed an even mapping depth on LG12 (pseudo X chromosome) and LG22 (Y-linked scaffold) in the segregating sites, suggesting near-pure X and Y representation in the v8 assembly. A total of 26,803 genes were annotated, and about 33% of the assembly was found to consist of repetitive elements. The high proportion of repetitive elements in LG22 (53.10%) suggests it can be difficult to assemble the complete sequence of the species' Y chromosome. Nevertheless, the new assembly is a significant improvement over the previous version and should provide a valuable resource for genomic studies of stickleback fishes.
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Affiliation(s)
- Dandan Wang
- Area of Ecology and Biodiversity, School of Biological Sciences, The University of Hong Kong, 999077, Hong Kong SAR
| | - Pasi Rastas
- Institute of Biotechnology, University of Helsinki, Helsinki FI-00014, Finland
| | - Xueling Yi
- Area of Ecology and Biodiversity, School of Biological Sciences, The University of Hong Kong, 999077, Hong Kong SAR
| | - Ari Löytynoja
- Institute of Biotechnology, University of Helsinki, Helsinki FI-00014, Finland
- Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki FI-00014, Finland
| | - Mikko Kivikoski
- Ecological Genetics Research Unit, Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki FI-00014, Finland
- Department of Computer Science, University of Helsinki, Helsinki FI-00014, Finland
| | - Xueyun Feng
- Institute of Biotechnology, University of Helsinki, Helsinki FI-00014, Finland
- Ecological Genetics Research Unit, Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki FI-00014, Finland
| | - Kerry Reid
- Area of Ecology and Biodiversity, School of Biological Sciences, The University of Hong Kong, 999077, Hong Kong SAR
| | - Juha Merilä
- Area of Ecology and Biodiversity, School of Biological Sciences, The University of Hong Kong, 999077, Hong Kong SAR
- Ecological Genetics Research Unit, Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki FI-00014, Finland
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17
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Huang C, Cheng Y, Hu Y, Zhang X, Chen J, Zhao T, Si Z, Cao Y, Li Y, Fang L, Guan X, Zhang T. Impacts of parental genomic divergence in non-syntenic regions on cotton heterosis. J Adv Res 2024:S2090-1232(24)00331-X. [PMID: 39111623 DOI: 10.1016/j.jare.2024.08.010] [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: 04/07/2024] [Revised: 08/04/2024] [Accepted: 08/04/2024] [Indexed: 08/10/2024] Open
Abstract
INTRODUCTION Heterosis has revolutionized crop breeding, enhancing global agricultural production. However, the mechanisms underlying heterosis remain obscure. Xiangzamian 2# (XZM2), a super hybrid upland cotton (Gossypium hirsutum L.) characterized by high-yield heterosis, has been developed and extensively planted in China. OBJECTIVES We conducted a systematic analysis of CRI12 and J8891, two parents of XZM2. We aimed to reveal the precise genetic information and the role of non-syntenic divergence in shaping heterosis, laying a foundation for advancing understanding of heterosis. METHODS We de novo assembled high-quality genomes of CRI12 and J8891, and further uncovered abundant genetic variations and non-syntenic regions between the parents. Whole-genome comparison, association analysis, transcriptomic analysis and relative identity-by-descent (rIBD) estimation were conducted to identify structural variations (SVs) and introgressions within non-syntenic blocks and to analyze their impacts on promoting heterosis. RESULTS Parental genetic divergence increased in non-syntenic regions. Furthermore, these regions, accounting for only 16.71% of the total genome, contained more loci with significantly higher heterotic effects, far exceeding the syntenic background. SVs covered 97.26% of non-syntenic sequences and caused widespread gene expression differences in these regions, driving dynamic complementation of gene expression in the hybrid. A set of SVs were responsible for trait improvement and had positive effects on heterosis, contributing larger heritability than short variations. We characterized numerous parental-specific introgressions from G. barbadense. Specifically, a functional introgression segment within non-syntenic blocks introduced an elite haplotype, which significantly increased lint yield and enhanced heterosis. CONCLUSION Our study clarified non-syntenic regions to harbor more loci with higher heterotic effects, revealed their importance in promoting heterosis and supported the crucial role of genetic complementation in heterosis. SVs and introgressions were identified as key factors responsible for non-syntenic divergence between the parents. They had important effects on gene expression and trait improvement, positively contributing to heterosis.
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Affiliation(s)
- Chujun Huang
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, Institute of Crop Science, Plant Precision Breeding Academy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Yu Cheng
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, Institute of Crop Science, Plant Precision Breeding Academy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Yan Hu
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, Institute of Crop Science, Plant Precision Breeding Academy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China; Hainan Institute of Zhejiang University, Sanya 572025, China
| | - Xuemei Zhang
- Annoroad Gene Technology (Beijing) Co., Ltd., Beijing 100176, China
| | - Jinwen Chen
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, Institute of Crop Science, Plant Precision Breeding Academy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Ting Zhao
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, Institute of Crop Science, Plant Precision Breeding Academy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Zhanfeng Si
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, Institute of Crop Science, Plant Precision Breeding Academy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Yiwen Cao
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, Institute of Crop Science, Plant Precision Breeding Academy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China; Hainan Institute of Zhejiang University, Sanya 572025, China
| | - Yiqian Li
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, Institute of Crop Science, Plant Precision Breeding Academy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Lei Fang
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, Institute of Crop Science, Plant Precision Breeding Academy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China; Hainan Institute of Zhejiang University, Sanya 572025, China
| | - Xueying Guan
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, Institute of Crop Science, Plant Precision Breeding Academy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China; Hainan Institute of Zhejiang University, Sanya 572025, China
| | - Tianzhen Zhang
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, Institute of Crop Science, Plant Precision Breeding Academy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China; Hainan Institute of Zhejiang University, Sanya 572025, China.
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Liu N, Lyu X, Zhang X, Zhang G, Zhang Z, Guan X, Chen X, Yang X, Feng Z, Gao Q, Shi W, Deng Y, Sheng K, Ou J, Zhu Y, Wang B, Bu Y, Zhang M, Zhang L, Zhao T, Gong Y. Reference genome sequence and population genomic analysis of peas provide insights into the genetic basis of Mendelian and other agronomic traits. Nat Genet 2024:10.1038/s41588-024-01867-8. [PMID: 39103648 DOI: 10.1038/s41588-024-01867-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Accepted: 07/08/2024] [Indexed: 08/07/2024]
Abstract
Peas are essential for human nutrition and played a crucial role in the discovery of Mendelian laws of inheritance. In this study, we assembled the genome of the elite vegetable pea cultivar 'Zhewan No. 1' at the chromosome level and analyzed resequencing data from 314 accessions, creating a comprehensive map of genetic variation in peas. We identified 235 candidate loci associated with 57 important agronomic traits through genome-wide association studies. Notably, we pinpointed the causal gene haplotypes responsible for four Mendelian traits: stem length (Le/le), flower color (A/a), cotyledon color (I/i) and seed shape (R/r). Additionally, we discovered the genes controlling pod form (Mendelian P/p) and hilum color. Our study also involved constructing a gene expression atlas across 22 tissues, highlighting key gene modules related to pod and seed development. These findings provide valuable pea genomic information and will facilitate the future genome-informed improvement of pea crops.
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Affiliation(s)
- Na Liu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ministry of Agriculture and Rural Affairs Key Laboratory of Vegetable Legumes Germplasm Enhancement and Molecular Breeding in Southern China, Zhejiang Xianghu Laboratory, Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Xiaolong Lyu
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Xueying Zhang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ministry of Agriculture and Rural Affairs Key Laboratory of Vegetable Legumes Germplasm Enhancement and Molecular Breeding in Southern China, Zhejiang Xianghu Laboratory, Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Guwen Zhang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ministry of Agriculture and Rural Affairs Key Laboratory of Vegetable Legumes Germplasm Enhancement and Molecular Breeding in Southern China, Zhejiang Xianghu Laboratory, Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Ziqian Zhang
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Xueying Guan
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Xiaoyang Chen
- Station of Zhejiang Seed Management, Hangzhou, China
| | - Xiaoming Yang
- Crop Research Institute, Gansu Academy of Agricultural Sciences, Lanzhou, China
| | - Zhijuan Feng
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ministry of Agriculture and Rural Affairs Key Laboratory of Vegetable Legumes Germplasm Enhancement and Molecular Breeding in Southern China, Zhejiang Xianghu Laboratory, Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Qiang Gao
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Wanghong Shi
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
- Hainan Institute of Zhejiang University, Sanya, China
| | - Yayuan Deng
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
- Hainan Institute of Zhejiang University, Sanya, China
| | - Kuang Sheng
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Jinwen Ou
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ministry of Agriculture and Rural Affairs Key Laboratory of Vegetable Legumes Germplasm Enhancement and Molecular Breeding in Southern China, Zhejiang Xianghu Laboratory, Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Yumeng Zhu
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Bin Wang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ministry of Agriculture and Rural Affairs Key Laboratory of Vegetable Legumes Germplasm Enhancement and Molecular Breeding in Southern China, Zhejiang Xianghu Laboratory, Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Yuanpeng Bu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ministry of Agriculture and Rural Affairs Key Laboratory of Vegetable Legumes Germplasm Enhancement and Molecular Breeding in Southern China, Zhejiang Xianghu Laboratory, Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Mingfang Zhang
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China.
- Hainan Institute of Zhejiang University, Sanya, China.
| | - Liangsheng Zhang
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China.
- Yazhouwan National Laboratory, Sanya, China.
| | - Ting Zhao
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China.
| | - Yaming Gong
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ministry of Agriculture and Rural Affairs Key Laboratory of Vegetable Legumes Germplasm Enhancement and Molecular Breeding in Southern China, Zhejiang Xianghu Laboratory, Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, China.
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Kileeg Z, Wang P, Mott GA. Chromosome-Scale Assembly and Annotation of Eight Arabidopsis thaliana Ecotypes. Genome Biol Evol 2024; 16:evae169. [PMID: 39101619 DOI: 10.1093/gbe/evae169] [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: 07/06/2024] [Revised: 07/25/2024] [Accepted: 07/27/2024] [Indexed: 08/06/2024] Open
Abstract
The plant Arabidopsis thaliana is a model system used by researchers through much of plant research. Recent efforts have focused on discovering the genomic variation found in naturally occurring ecotypes isolated from around the world. These ecotypes have come from diverse climates and therefore have faced and adapted to a variety of abiotic and biotic stressors. The sequencing and comparative analysis of these genomes can offer insight into the adaptive strategies of plants. While there are a large number of ecotype genome sequences available, the majority were created using short-read technology. Mapping of short-reads containing structural variation to a reference genome bereft of that variation leads to incorrect mapping of those reads, resulting in a loss of genetic information and introduction of false heterozygosity. For this reason, long-read de novo sequencing of genomes is required to resolve structural variation events. In this article, we sequenced the genomes of eight natural variants of A. thaliana using nanopore sequencing. This resulted in highly contiguous assemblies with >95% of the genome contained within five contigs. The sequencing results from this study include five ecotypes from relict and African populations, an area of untapped genetic diversity. With this study, we increase the knowledge of diversity we have across A. thaliana ecotypes and contribute to ongoing production of an A. thaliana pan-genome.
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Affiliation(s)
- Zachary Kileeg
- Department of Biological Sciences, University of Toronto-Scarborough, Toronto, Canada
- Department of Cell and Systems Biology, University of Toronto, Toronto, Canada
| | - Pauline Wang
- Department of Cell and Systems Biology, University of Toronto, Toronto, Canada
- Centre for the Analysis of Genome Evolution & Function, University of Toronto, Toronto, Canada
| | - G Adam Mott
- Department of Biological Sciences, University of Toronto-Scarborough, Toronto, Canada
- Department of Cell and Systems Biology, University of Toronto, Toronto, Canada
- Centre for the Analysis of Genome Evolution & Function, University of Toronto, Toronto, Canada
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20
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Liu Y, Liu J, Sun M, Mao Y, Feng S, Shen S, Liu T, Cao Z, Li Z, Hao Z, Dong J. The genome sequencing and comparative genomics analysis of Rhizoctonia solani reveals a novel effector family owning a uinque domain in Basidiomycetes. Int J Biol Macromol 2024; 278:134328. [PMID: 39098663 DOI: 10.1016/j.ijbiomac.2024.134328] [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: 01/13/2024] [Revised: 06/26/2024] [Accepted: 07/23/2024] [Indexed: 08/06/2024]
Abstract
Rhizoctonia solani is a soil-borne pathogen with 14 anastomosis groups (AGs), and different subgroups are genetically diverse. However, the genetic factors contributing to the pathogenicity of the fungus have not been well characterized. In this study, the genome of R. solani AG1-ZJ was sequenced. As the result, a 41.57 Mb draft genome containing 12,197 putative coding genes was obtained. Comparative genomic analysis of 11 different AGs revealed conservation and unique characteristics between the AGs. Furthermore, a novel effector family containing a 68 amino acid conserved domain unique in basidiomycetous fungi was characterized. Two effectors containing the conserved domain in AG4-JY were identified, and named as RsUEB1 and RsUEB2. Furthermore, the spray-induced gene silencing strategy was used to generate a dsRNA capable of silencing the conserved domain sequence of RsUEB1 and RsUEB2. This dsRNA can significantly reduce the expression of RsUEB1 and RsUEB2 and the pathogenicity of AG4-JY on foxtail millet, maize, rice and wheat. In conclusion, this study provides significant insights into the pathogenicity mechanisms of R. solani. The identification of the conserved domain and the successful use of dsRNA silencing of the gene containing the conserved domain will offer a new strategy for controlling sheath blight in cereal crops.
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Affiliation(s)
- Yuwei Liu
- State Key Laboratory of North China Crop Improvement and Regulation/Hebei Bioinformatic Utilization and Technological Innovation Center for Agricultural Microbes, Hebei Agricultural University, Hebei 071001, China
| | - Jiayue Liu
- State Key Laboratory of North China Crop Improvement and Regulation/Hebei Bioinformatic Utilization and Technological Innovation Center for Agricultural Microbes, Hebei Agricultural University, Hebei 071001, China
| | - Mingqing Sun
- Shijiazhuang Agricultural Technology Extension Center, Shijiazhuang, 050051, China
| | - Yanan Mao
- State Key Laboratory of North China Crop Improvement and Regulation/Hebei Bioinformatic Utilization and Technological Innovation Center for Agricultural Microbes, Hebei Agricultural University, Hebei 071001, China
| | - Shang Feng
- State Key Laboratory of North China Crop Improvement and Regulation/Hebei Bioinformatic Utilization and Technological Innovation Center for Agricultural Microbes, Hebei Agricultural University, Hebei 071001, China
| | - Shen Shen
- State Key Laboratory of North China Crop Improvement and Regulation/Hebei Bioinformatic Utilization and Technological Innovation Center for Agricultural Microbes, Hebei Agricultural University, Hebei 071001, China
| | - Tingting Liu
- Shijiazhuang Agricultural Technology Extension Center, Shijiazhuang, 050051, China
| | - Zhiyan Cao
- State Key Laboratory of North China Crop Improvement and Regulation/Hebei Bioinformatic Utilization and Technological Innovation Center for Agricultural Microbes, Hebei Agricultural University, Hebei 071001, China; College of Plant Protection/Hebei Key Laboratory of Plant Physiology and Molecular Pathology, Hebei Agricultural University, Baoding, Hebei 071001, China
| | - Zhiyong Li
- Institute of Millet Crops, Hebei Academy of Agriculture and Forestry Sciences/Key Laboratory of Genetic Improvement and Utilization for Featured Coarse Cereals (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs/Key Laboratory of Minor Cereal Crops of Hebei Province, Shijiazhuang, Hebei, 050035, China.
| | - Zhimin Hao
- State Key Laboratory of North China Crop Improvement and Regulation/Hebei Bioinformatic Utilization and Technological Innovation Center for Agricultural Microbes, Hebei Agricultural University, Hebei 071001, China.
| | - Jingao Dong
- State Key Laboratory of North China Crop Improvement and Regulation/Hebei Bioinformatic Utilization and Technological Innovation Center for Agricultural Microbes, Hebei Agricultural University, Hebei 071001, China; College of Plant Protection/Hebei Key Laboratory of Plant Physiology and Molecular Pathology, Hebei Agricultural University, Baoding, Hebei 071001, China.
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21
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Ji J, Gao Y, Xu C, Zhang K, Li D, Li B, Chen L, Gao M, Huangfu N, Elumalai P, Gao X, Zhu X, Wang L, Luo J, Cui J. Chromosome-level genome assembly of marmalade hoverfly Episyrphus balteatus (Diptera: Syrphidae). Sci Data 2024; 11:844. [PMID: 39097648 PMCID: PMC11298007 DOI: 10.1038/s41597-024-03666-6] [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: 02/26/2024] [Accepted: 07/22/2024] [Indexed: 08/05/2024] Open
Abstract
Episyrphus balteatus can provide dual ecosystem services including pest control and pollination, which the larvae are excellent predators of aphid pest whereas adults are efficient pollinator. In this study, we assembled a high-quality genome of E. balteatus from northern China geographical population at the chromosome level by using Illumina, PacBio long reads, and Hi-C technologies. The 467.42 Mb genome was obtained from 723 contigs, with a contig N50 of 9.16 Mb and Scaffold N50 of 118.85 Mb, and 90.25% (431.75 Mb) of the assembly was anchored to 4 pseudo-autosomes and one pseudo-heterosome. In total, 14,848 protein-coding genes were annotated, and 95.14% of genes were fully represented in NR, GO, KEGG databases. Besides, we also obtained the mitochondrial genome of E. balteatus of 16, 837 bp in length with 37 typical mitochondrial genes. Overall, this high-quality genome is valuable for evolutionary and genetic studies of E. balteatus and other Syrphidae hoverfly species.
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Affiliation(s)
- Jichao Ji
- State Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China.
- Zhengzhou Research Base, State Key Laboratory of Cotton Bio-breeding and Integrated Utilization, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450001, China.
- Western Agricultural Research Center, Chinese Academy of Agricultural Sciences, Changji, 831100, China.
| | - Yue Gao
- State Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
- Tianjin Academy of Agricultural Sciences, Tianjin, 300384, China
| | - Chao Xu
- State Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
- Tianjin Academy of Agricultural Sciences, Tianjin, 300384, China
| | - Kaixin Zhang
- State Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
- Western Agricultural Research Center, Chinese Academy of Agricultural Sciences, Changji, 831100, China
| | - Dongyang Li
- State Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
- Western Agricultural Research Center, Chinese Academy of Agricultural Sciences, Changji, 831100, China
| | - Bingbing Li
- Key Laboratory of Plant Stress Biology, College of Life Sciences, Henan University, Kaifeng, 450046, Henan, China
| | - Lulu Chen
- College of Agronomy, Xinjiang Agricultural University, Urumqi, 830052, China
| | - Mengxue Gao
- Key Laboratory of Plant Stress Biology, College of Life Sciences, Henan University, Kaifeng, 450046, Henan, China
| | - Ningbo Huangfu
- State Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
- Tianjin Academy of Agricultural Sciences, Tianjin, 300384, China
| | - Punniyakotti Elumalai
- State Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Xueke Gao
- State Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
- Western Agricultural Research Center, Chinese Academy of Agricultural Sciences, Changji, 831100, China
| | - Xiangzhen Zhu
- State Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China.
- Western Agricultural Research Center, Chinese Academy of Agricultural Sciences, Changji, 831100, China.
| | - Li Wang
- State Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China.
- Western Agricultural Research Center, Chinese Academy of Agricultural Sciences, Changji, 831100, China.
| | - Junyu Luo
- State Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China.
- Western Agricultural Research Center, Chinese Academy of Agricultural Sciences, Changji, 831100, China.
| | - Jinjie Cui
- State Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China.
- Western Agricultural Research Center, Chinese Academy of Agricultural Sciences, Changji, 831100, China.
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Li M, Chen C, Wang H, Qin H, Hou S, Yang X, Jian J, Gao P, Liu M, Mu Z. Telomere-to-telomere genome assembly of sorghum. Sci Data 2024; 11:835. [PMID: 39095379 PMCID: PMC11297213 DOI: 10.1038/s41597-024-03664-8] [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: 11/28/2023] [Accepted: 07/19/2024] [Indexed: 08/04/2024] Open
Abstract
"Cuohu Bazi" (CHBZ) is an ancient sorghum variety collected from the fields of China, known for its agronomic traits like dwarf stature, early maturation. In this study, we present the first telomere-to-telomere (T2T) and gap-free genome assembly of CHBZ using PacBio HiFi reads, Oxford Nanopore Technologies, and Hi-C data. The assembled genome comprises 724.85 Mb, effectively resolving all 3,913 gaps that were present in the previous sorghum BTx623 reference genome. Notably, the T2T assembly captures 10 centromeres and all 20 telomeres, providing strong support for their integrity. This assembly is of high quality in terms of contiguity (contig N50: 71.1 Mb), completeness (BUSCO score: 99.01%, k-mer completeness: 98.88%), and correctness (QV: 61.60). Repetitive sequences accounted for 70.41% of the genome and a total of 32,855 protein-coding genes have been annotated. Furthermore, 161 CHBZ-specific presence/absence variants genes have been identified when comparing to BTx623 genome. This study provides valuable insights for future research on sorghum genetics, genomics, and evolutionary history.
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Affiliation(s)
- Meng Li
- Center for Agricultural Genetic Resources Research, Shanxi Agricultural University, Key Laboratory of Crop Gene Resources and Germplasm Enhancement on Loess Plateau, Ministry of Agriculture and Rural Affairs, Taiyuan, 030031, China.
| | | | - Haigang Wang
- Center for Agricultural Genetic Resources Research, Shanxi Agricultural University, Key Laboratory of Crop Gene Resources and Germplasm Enhancement on Loess Plateau, Ministry of Agriculture and Rural Affairs, Taiyuan, 030031, China
| | - Huibin Qin
- Center for Agricultural Genetic Resources Research, Shanxi Agricultural University, Key Laboratory of Crop Gene Resources and Germplasm Enhancement on Loess Plateau, Ministry of Agriculture and Rural Affairs, Taiyuan, 030031, China
| | - Sen Hou
- Center for Agricultural Genetic Resources Research, Shanxi Agricultural University, Key Laboratory of Crop Gene Resources and Germplasm Enhancement on Loess Plateau, Ministry of Agriculture and Rural Affairs, Taiyuan, 030031, China
| | | | | | | | - Minxuan Liu
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
| | - Zhixin Mu
- Center for Agricultural Genetic Resources Research, Shanxi Agricultural University, Key Laboratory of Crop Gene Resources and Germplasm Enhancement on Loess Plateau, Ministry of Agriculture and Rural Affairs, Taiyuan, 030031, China.
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Zou D, Huang S, Tian S, Kilunda FK, Murphy RW, Dahn HA, Zhou Y, Lee PS, Chen JM. Comparative genomics sheds new light on the convergent evolution of infrared vision in snakes. Proc Biol Sci 2024; 291:20240818. [PMID: 39043244 PMCID: PMC11265913 DOI: 10.1098/rspb.2024.0818] [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: 04/08/2024] [Revised: 05/30/2024] [Accepted: 06/19/2024] [Indexed: 07/25/2024] Open
Abstract
Infrared vision is a highly specialized sensory system that evolved independently in three clades of snakes. Apparently, convergent evolution occurred in the transient receptor potential ankyrin 1 (TRPA1) proteins of infrared-sensing snakes. However, this gene can only explain how infrared signals are received, and not the transduction and processing of those signals. We sequenced the genome of Xenopeltis unicolor, a key outgroup species of pythons, and performed a genome-wide analysis of convergence between two clades of infrared-sensing snakes. Our results revealed pervasive molecular adaptation in pathways associated with neural development and other functions, with parallel selection on loci associated with trigeminal nerve structural organization. In addition, we found evidence of convergent amino acid substitutions in a set of genes, including TRPA1 and TRPM2. The analysis also identified convergent accelerated evolution in non-coding elements near 12 genes involved in facial nerve structural organization and optic nerve development. Thus, convergent evolution occurred across multiple dimensions of infrared vision in vipers and pythons, as well as amino acid substitutions, non-coding elements, genes and functions. These changes enabled independent groups of snakes to develop and use infrared vision.
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Affiliation(s)
- Dahu Zou
- Engineering Research Center of Eco-Environment in Three Gorges Reservoir Region of Ministry of Education, China Three Gorges University, Yichang, Hubei443002, People’s Republic of China
| | - Song Huang
- The Anhui Provincial Key Laboratory of Biodiversity Conservation and Ecological Security in the Yangtze River Basin, College of Life Sciences, Anhui Normal University, Wuhu, Anhui241000, People’s Republic of China
| | - Shilin Tian
- Novogene Bioinformatics Institute, Beijing100000, People’s Republic of China
| | - Felista Kasyoka Kilunda
- Key Laboratory of Genetic Evolution and Animal Models and Yunnan Key Laboratory of Biodiversity and Ecological Conservation of Gaoligong Mountain, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan650223, People’s Republic of China
| | - Robert W. Murphy
- Reptilia Zoo and Education Centre, 2501 Rutherford Road, Vaughan, ONL4K 2N6, Canada
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ONM5S 2C6, Canada
| | - Hollis A. Dahn
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ONM5S 2C6, Canada
| | - Youbing Zhou
- Engineering Research Center of Eco-Environment in Three Gorges Reservoir Region of Ministry of Education, China Three Gorges University, Yichang, Hubei443002, People’s Republic of China
| | - Ping-Shin Lee
- The Anhui Provincial Key Laboratory of Biodiversity Conservation and Ecological Security in the Yangtze River Basin, College of Life Sciences, Anhui Normal University, Wuhu, Anhui241000, People’s Republic of China
| | - Jin-Min Chen
- The Anhui Provincial Key Laboratory of Biodiversity Conservation and Ecological Security in the Yangtze River Basin, College of Life Sciences, Anhui Normal University, Wuhu, Anhui241000, People’s Republic of China
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24
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Wang H, Chen M, Wei X, Xia R, Pei D, Huang X, Han B. Computational tools for plant genomics and breeding. SCIENCE CHINA. LIFE SCIENCES 2024; 67:1579-1590. [PMID: 38676814 DOI: 10.1007/s11427-024-2578-6] [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: 02/05/2024] [Accepted: 03/25/2024] [Indexed: 04/29/2024]
Abstract
Plant genomics and crop breeding are at the intersection of biotechnology and information technology. Driven by a combination of high-throughput sequencing, molecular biology and data science, great advances have been made in omics technologies at every step along the central dogma, especially in genome assembling, genome annotation, epigenomic profiling, and transcriptome profiling. These advances further revolutionized three directions of development. One is genetic dissection of complex traits in crops, along with genomic prediction and selection. The second is comparative genomics and evolution, which open up new opportunities to depict the evolutionary constraints of biological sequences for deleterious variant discovery. The third direction is the development of deep learning approaches for the rational design of biological sequences, especially proteins, for synthetic biology. All three directions of development serve as the foundation for a new era of crop breeding where agronomic traits are enhanced by genome design.
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Affiliation(s)
- Hai Wang
- State Key Laboratory of Maize Bio-breeding, Frontiers Science Center for Molecular Design Breeding, Joint International Research Laboratory of Crop Molecular Breeding, National Maize Improvement Center, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China.
- Sanya Institute of China Agricultural University, Sanya, 572025, China.
- Hainan Yazhou Bay Seed Laboratory, Sanya, 572025, China.
| | - Mengjiao Chen
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of the State Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China
| | - Xin Wei
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, 200234, China
| | - Rui Xia
- College of Horticulture, South China Agricultural University, Guangzhou, 510640, China
| | - Dong Pei
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of the State Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China
| | - Xuehui Huang
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, 200234, China
| | - Bin Han
- National Center for Gene Research, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 200233, China
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25
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Gong S, Gan H, Chu J, Wang Z, Sun J. A chromosome-level genome assembly provides insights into the local adaptation of Tamarix austromongolica in the Yellow River Basin, China. DNA Res 2024; 31:dsae021. [PMID: 38946223 PMCID: PMC11306577 DOI: 10.1093/dnares/dsae021] [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: 02/18/2024] [Revised: 06/06/2024] [Accepted: 06/29/2024] [Indexed: 07/02/2024] Open
Abstract
Tamarix austromongolica is endemic to the Yellow River Basin and has adapted to diverse ecological settings in the region, including the arid areas of northwestern China and the saline soil regions of the Yellow River Delta. However, the genetic basis of its local adaptation remains unclear. We report a chromosome-level assembly of the T. austromongolica genome based on PacBio high-fidelity sequencing and Hi-C technology. The 12 pseudochromosomes cover 98.44% of the 1.32 Gb assembly, with a contig N50 of 52.57 Mb and a BUSCO score of 98.2%. The genome comprises 913.6 Mb (68.83%) of repetitive sequences and 22,374 protein-coding genes. Genome evolution analyses suggest that genes under positive selection and significantly expanded gene families have facilitated T. austromongolica's adaptability to diverse environmental factors and high resistance to diseases. Using genotyping-by-sequencing, we conducted population structure and selection analyses of 114 samples from 15 sites. Two genetic groups were identified, and 114 and 289 candidate genes were assigned to the populations of the northwestern and eastern parts of the Yellow River, respectively. Furthermore, we discovered numerous candidate genes associated with high-altitude adaptability and salt tolerance. This research provides valuable genomic resources for the evolutionary study and genetic breeding of tamarisk.
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Affiliation(s)
- Shuai Gong
- Coastal Forestry Research Center of National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, PR China
| | - Honghao Gan
- Coastal Forestry Research Center of National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, PR China
| | - Jianmin Chu
- Coastal Forestry Research Center of National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, PR China
- Experimental Center of Desert Forestry, Chinese Academy of Forestry, Dengkou 015200, PR China
| | - Zhaoshan Wang
- Coastal Forestry Research Center of National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, PR China
| | - Jia Sun
- Coastal Forestry Research Center of National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, PR China
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26
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Driller M, Brown T, Currie SE, Hiller M, Winkler S, Pippel M, Voigt CC, Fickel J, Mazzoni CJ. A haplotype-resolved reference genome of a long-distance migratory bat, Pipistrellus nathusii (Keyserling & Blasius, 1839). DNA Res 2024; 31:dsae018. [PMID: 38847751 PMCID: PMC11215541 DOI: 10.1093/dnares/dsae018] [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: 02/02/2024] [Revised: 04/18/2024] [Accepted: 06/06/2024] [Indexed: 07/02/2024] Open
Abstract
We present a complete, chromosome-scale reference genome for the long-distance migratory bat Pipistrellus nathusii. The genome encompasses both haplotypic sets of autosomes and the separation of both sex chromosomes by utilizing highly accurate long-reads and preserving long-range phasing information through the use of three-dimensional chromatin conformation capture sequencing (Hi-C). This genome, accompanied by a comprehensive protein-coding sequence annotation, provides a valuable genomic resource for future investigations into the genomic bases of long-distance migratory flight in bats as well as uncovering the genetic architecture, population structure and evolutionary history of Pipistrellus nathusii. The reference-quality genome presented here gives a fundamental resource to further our understanding of bat genetics and evolution, adding to the growing number of high-quality genetic resources in this field. Here, we demonstrate its use in the phylogenetic reconstruction of the order Chiroptera, and in particular, we present the resources to allow detailed investigations into the genetic drivers and adaptations related to long-distance migration.
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Affiliation(s)
- Maximilian Driller
- Berlin Center for Genomics in Biodiversity Research (BeGenDiv), Berlin, Germany
- Evolutionary Genetics Department, Leibniz-Institut für Zoo- und Wildtierforschung (IZW), Berlin, Germany
| | - Thomas Brown
- Berlin Center for Genomics in Biodiversity Research (BeGenDiv), Berlin, Germany
- Evolutionary Genetics Department, Leibniz-Institut für Zoo- und Wildtierforschung (IZW), Berlin, Germany
| | - Shannon E Currie
- Evolutionary Ecology Department, Leibniz-Institut für Zoo- und Wildtierforschung (IZW), Berlin, Germany
- School of Biosciences, University of Melbourne, Parkville, 3010 Victoria, Australia
| | - Michael Hiller
- LOEWE Centre for Translational Biodiversity Genomics, Senckenberganlage 25, 60325 Frankfurt, Germany
- Senckenberg Research Institute, Senckenberganlage 25, 60325 Frankfurt, Germany
- Institute of Cell Biology and Neuroscience, Faculty of Biosciences, Goethe University Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt, Germany
| | - Sylke Winkler
- Sequencing and Genotyping, Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstraße 108, 01307 Dresden, Germany
| | - Martin Pippel
- Sequencing and Genotyping, Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstraße 108, 01307 Dresden, Germany
| | - Christian C Voigt
- Evolutionary Ecology Department, Leibniz-Institut für Zoo- und Wildtierforschung (IZW), Berlin, Germany
| | - Jörns Fickel
- Evolutionary Genetics Department, Leibniz-Institut für Zoo- und Wildtierforschung (IZW), Berlin, Germany
- Institute for Biochemistry and Biology, University of Potsdam, 14476 Potsdam, Germany
| | - Camila J Mazzoni
- Berlin Center for Genomics in Biodiversity Research (BeGenDiv), Berlin, Germany
- Evolutionary Genetics Department, Leibniz-Institut für Zoo- und Wildtierforschung (IZW), Berlin, Germany
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27
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Zhang Y, Zhao M, Tan J, Huang M, Chu X, Li Y, Han X, Fang T, Tian Y, Jarret R, Lu D, Chen Y, Xue L, Li X, Qin G, Li B, Sun Y, Deng XW, Deng Y, Zhang X, He H. Telomere-to-telomere Citrullus super-pangenome provides direction for watermelon breeding. Nat Genet 2024; 56:1750-1761. [PMID: 38977857 PMCID: PMC11319210 DOI: 10.1038/s41588-024-01823-6] [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: 08/26/2023] [Accepted: 06/04/2024] [Indexed: 07/10/2024]
Abstract
To decipher the genetic diversity within the cucurbit genus Citrullus, we generated telomere-to-telomere (T2T) assemblies of 27 distinct genotypes, encompassing all seven Citrullus species. This T2T super-pangenome has expanded the previously published reference genome, T2T-G42, by adding 399.2 Mb and 11,225 genes. Comparative analysis has unveiled gene variants and structural variations (SVs), shedding light on watermelon evolution and domestication processes that enhanced attributes such as bitterness and sugar content while compromising disease resistance. Multidisease-resistant loci from Citrullus amarus and Citrullus mucosospermus were successfully introduced into cultivated Citrullus lanatus. The SVs identified in C. lanatus have not only been inherited from cordophanus but also from C. mucosospermus, suggesting additional ancestors beyond cordophanus in the lineage of cultivated watermelon. Our investigation substantially improves the comprehension of watermelon genome diversity, furnishing comprehensive reference genomes for all Citrullus species. This advancement aids in the exploration and genetic enhancement of watermelon using its wild relatives.
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Affiliation(s)
- Yilin Zhang
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences at Weifang, Weifang, China
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences and School of Life Sciences, Peking University, Beijing, China
| | - Mingxia Zhao
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences at Weifang, Weifang, China
| | - Jingsheng Tan
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences at Weifang, Weifang, China
| | - Minghan Huang
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences and School of Life Sciences, Peking University, Beijing, China
| | - Xiao Chu
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences at Weifang, Weifang, China
| | - Yan Li
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences at Weifang, Weifang, China
| | - Xue Han
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences at Weifang, Weifang, China
| | - Taohong Fang
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences at Weifang, Weifang, China
| | - Yao Tian
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences at Weifang, Weifang, China
| | | | - Dongdong Lu
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences at Weifang, Weifang, China
| | - Yijun Chen
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences at Weifang, Weifang, China
| | - Lifang Xue
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences at Weifang, Weifang, China
| | - Xiaoni Li
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences at Weifang, Weifang, China
| | - Guochen Qin
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences at Weifang, Weifang, China
| | - Bosheng Li
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences at Weifang, Weifang, China
| | - Yudong Sun
- Vegetable Research and Development Center, Huaiyin Institute of Agricultural Sciences of Xuhuai Region in Jiangsu, Huai'an, China
| | - Xing Wang Deng
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences at Weifang, Weifang, China
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences and School of Life Sciences, Peking University, Beijing, China
| | - Yun Deng
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences at Weifang, Weifang, China.
| | - Xingping Zhang
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences at Weifang, Weifang, China.
| | - Hang He
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences at Weifang, Weifang, China.
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences and School of Life Sciences, Peking University, Beijing, China.
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28
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Yoo D, Rhie A, Hebbar P, Antonacci F, Logsdon GA, Solar SJ, Antipov D, Pickett BD, Safonova Y, Montinaro F, Luo Y, Malukiewicz J, Storer JM, Lin J, Sequeira AN, Mangan RJ, Hickey G, Anez GM, Balachandran P, Bankevich A, Beck CR, Biddanda A, Borchers M, Bouffard GG, Brannan E, Brooks SY, Carbone L, Carrel L, Chan AP, Crawford J, Diekhans M, Engelbrecht E, Feschotte C, Formenti G, Garcia GH, de Gennaro L, Gilbert D, Green RE, Guarracino A, Gupta I, Haddad D, Han J, Harris RS, Hartley GA, Harvey WT, Hiller M, Hoekzema K, Houck ML, Jeong H, Kamali K, Kellis M, Kille B, Lee C, Lee Y, Lees W, Lewis AP, Li Q, Loftus M, Loh YHE, Loucks H, Ma J, Mao Y, Martinez JFI, Masterson P, McCoy RC, McGrath B, McKinney S, Meyer BS, Miga KH, Mohanty SK, Munson KM, Pal K, Pennell M, Pevzner PA, Porubsky D, Potapova T, Ringeling FR, Rocha JL, Ryder OA, Sacco S, Saha S, Sasaki T, Schatz MC, Schork NJ, Shanks C, Smeds L, Son DR, Steiner C, Sweeten AP, Tassia MG, Thibaud-Nissen F, Torres-González E, Trivedi M, Wei W, Wertz J, Yang M, Zhang P, Zhang S, Zhang Y, Zhang Z, Zhao SA, Zhu Y, Jarvis ED, Gerton JL, Rivas-González I, Paten B, Szpiech ZA, Huber CD, Lenz TL, Konkel MK, Yi SV, Canzar S, Watson CT, Sudmant PH, Molloy E, Garrison E, Lowe CB, Ventura M, O'Neill RJ, Koren S, Makova KD, Phillippy AM, Eichler EE. Complete sequencing of ape genomes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.31.605654. [PMID: 39131277 PMCID: PMC11312596 DOI: 10.1101/2024.07.31.605654] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 08/13/2024]
Abstract
We present haplotype-resolved reference genomes and comparative analyses of six ape species, namely: chimpanzee, bonobo, gorilla, Bornean orangutan, Sumatran orangutan, and siamang. We achieve chromosome-level contiguity with unparalleled sequence accuracy (<1 error in 500,000 base pairs), completely sequencing 215 gapless chromosomes telomere-to-telomere. We resolve challenging regions, such as the major histocompatibility complex and immunoglobulin loci, providing more in-depth evolutionary insights. Comparative analyses, including human, allow us to investigate the evolution and diversity of regions previously uncharacterized or incompletely studied without bias from mapping to the human reference. This includes newly minted gene families within lineage-specific segmental duplications, centromeric DNA, acrocentric chromosomes, and subterminal heterochromatin. This resource should serve as a definitive baseline for all future evolutionary studies of humans and our closest living ape relatives.
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Affiliation(s)
- DongAhn Yoo
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Arang Rhie
- Genome Informatics Section, Center for Genomics and Data Science Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Prajna Hebbar
- UC Santa Cruz Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95060, USA
| | - Francesca Antonacci
- Department of Biosciences, Biotechnology and Environment, University of Bari, Bari, 70124, Italy
| | - Glennis A Logsdon
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
- Department of Genetics, Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19103, USA
| | - Steven J Solar
- Genome Informatics Section, Center for Genomics and Data Science Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Dmitry Antipov
- Genome Informatics Section, Center for Genomics and Data Science Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Brandon D Pickett
- Genome Informatics Section, Center for Genomics and Data Science Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Yana Safonova
- Computer Science and Engineering Department, Huck Institutes of Life Sciences, Pennsylvania State University, State College, PA 16801, USA
| | - Francesco Montinaro
- Department of Biosciences, Biotechnology and Environment, University of Bari, Bari, 70124, Italy
- Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Yanting Luo
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710, USA
| | - Joanna Malukiewicz
- Research Unit for Evolutionary Immunogenomics, Department of Biology, University of Hamburg, 20146 Hamburg, Germany
| | - Jessica M Storer
- Institute for Systems Genomics, University of Connecticut, Storrs, CT 06269, USA
| | - Jiadong Lin
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Abigail N Sequeira
- Department of Biology, Penn State University, University Park, PA 16802, USA
| | - Riley J Mangan
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Genetics Training Program, Harvard Medical School, Boston, MA 02115, USA
| | - Glenn Hickey
- UC Santa Cruz Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95060, USA
| | | | | | - Anton Bankevich
- Computer Science and Engineering Department, Huck Institutes of Life Sciences, Pennsylvania State University, State College, PA 16801, USA
| | - Christine R Beck
- Institute for Systems Genomics, University of Connecticut, Storrs, CT 06269, USA
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
- Department of Genetics and Genome Sciences, University of Connecticut Health Center, Farmington, CT, USA
| | - Arjun Biddanda
- Department of Biology, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Matthew Borchers
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Gerard G Bouffard
- NIH Intramural Sequencing Center, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Emry Brannan
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, USA
| | - Shelise Y Brooks
- NIH Intramural Sequencing Center, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Lucia Carbone
- Department of Medicine, KCVI, Oregon Health Sciences University, Portland, OR, USA
- Division of Genetics, Oregon National Primate Research Center, Beaverton, OR, USA
| | - Laura Carrel
- PSU Medical School, Penn State University School of Medicine, Hershey, PA, USA
| | - Agnes P Chan
- The Translational Genomics Research Institute, a part of the City of Hope National Medical Center, Phoenix, AZ, USA
| | - Juyun Crawford
- NIH Intramural Sequencing Center, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Mark Diekhans
- UC Santa Cruz Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95060, USA
| | - Eric Engelbrecht
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Louisville, Louisville, KY, USA
| | - Cedric Feschotte
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Giulio Formenti
- Vertebrate Genome Laboratory, The Rockefeller University, New York, NY 10021, USA
| | - Gage H Garcia
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Luciana de Gennaro
- Department of Biosciences, Biotechnology and Environment, University of Bari, Bari, 70124, Italy
| | - David Gilbert
- San Diego Biomedical Research Institute, San Diego, CA, USA
| | | | - Andrea Guarracino
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN 38163, USA
| | - Ishaan Gupta
- Department of Computer Science and Engineering, University of California San Diego, CA, USA
| | - Diana Haddad
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - Junmin Han
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Shanghai Jiao Tong University, Shanghai, China
| | - Robert S Harris
- Department of Biology, Penn State University, University Park, PA 16802, USA
| | - Gabrielle A Hartley
- Institute for Systems Genomics, University of Connecticut, Storrs, CT 06269, USA
| | - William T Harvey
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Michael Hiller
- LOEWE Centre for Translational Biodiversity Genomics, Senckenberg Research Institute, Goethe University, Frankfurt, Germany
| | - Kendra Hoekzema
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Marlys L Houck
- San Diego Zoo Wildlife Alliance, Escondido, CA, 92027-7000, USA
| | - Hyeonsoo Jeong
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA
| | - Kaivan Kamali
- Department of Biology, Penn State University, University Park, PA 16802, USA
| | - Manolis Kellis
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Bryce Kille
- Department of Computer Science, Rice University, Houston, TX 77005, USA
| | - Chul Lee
- Laboratory of Neurogenetics of Language, The Rockefeller University, New York, NY, USA
| | - Youngho Lee
- Laboratory of bioinformatics and population genetics, Interdisciplinary program in bioinformatics, Seoul National University, Republic of Korea
| | - William Lees
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Louisville, Louisville, KY, USA
- Bioengineering Program, Faculty of Engineering, Bar-Ilan University, Ramat Gan, Israel
| | - Alexandra P Lewis
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Qiuhui Li
- Department of Computer Science, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Mark Loftus
- Department of Genetics & Biochemistry, Clemson University, Clemson, SC, USA
- Center for Human Genetics, Clemson University, Greenwood, SC, USA
| | - Yong Hwee Eddie Loh
- Neuroscience Research Institute, University of California, Santa Barbara, CA, USA
| | - Hailey Loucks
- UC Santa Cruz Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95060, USA
| | - Jian Ma
- Ray and Stephanie Lane Computational Biology Department, School of Computer Science, Carnegie Mellon University, PA, USA
| | - Yafei Mao
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Shanghai Jiao Tong University, Shanghai, China
- Center for Genomic Research, International Institutes of Medicine, Fourth Affiliated Hospital, Zhejiang University, Yiwu, Zhejiang, China
- Shanghai Jiao Tong University Chongqing Research Institute, Chongqing, China
| | - Juan F I Martinez
- Computer Science and Engineering Department, Huck Institutes of Life Sciences, Pennsylvania State University, State College, PA 16801, USA
| | - Patrick Masterson
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - Rajiv C McCoy
- Department of Biology, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Barbara McGrath
- Department of Biology, Penn State University, University Park, PA 16802, USA
| | - Sean McKinney
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Britta S Meyer
- Research Unit for Evolutionary Immunogenomics, Department of Biology, University of Hamburg, 20146 Hamburg, Germany
| | - Karen H Miga
- UC Santa Cruz Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95060, USA
| | - Saswat K Mohanty
- Department of Biology, Penn State University, University Park, PA 16802, USA
| | - Katherine M Munson
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Karol Pal
- Department of Biology, Penn State University, University Park, PA 16802, USA
| | - Matt Pennell
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA, USA
| | - Pavel A Pevzner
- Department of Computer Science and Engineering, University of California San Diego, CA, USA
| | - David Porubsky
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Tamara Potapova
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Francisca R Ringeling
- Faculty of Informatics and Data Science, University of Regensburg, 93053 Regensburg, Germany
| | - Joana L Rocha
- Department of Integrative Biology, University of California, Berkeley, Berkeley, USA
| | - Oliver A Ryder
- San Diego Zoo Wildlife Alliance, Escondido, CA, 92027-7000, USA
| | - Samuel Sacco
- University of California Santa Cruz, Santa Cruz, CA, USA
| | - Swati Saha
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Louisville, Louisville, KY, USA
| | - Takayo Sasaki
- San Diego Biomedical Research Institute, San Diego, CA, USA
| | - Michael C Schatz
- Department of Computer Science, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Nicholas J Schork
- The Translational Genomics Research Institute, a part of the City of Hope National Medical Center, Phoenix, AZ, USA
| | - Cole Shanks
- UC Santa Cruz Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95060, USA
| | - Linnéa Smeds
- Department of Biology, Penn State University, University Park, PA 16802, USA
| | - Dongmin R Son
- Department of Ecology, Evolution and Marine Biology, Neuroscience Research Institute, University of California, Santa Barbara, CA, USA
| | - Cynthia Steiner
- San Diego Zoo Wildlife Alliance, Escondido, CA, 92027-7000, USA
| | - Alexander P Sweeten
- Genome Informatics Section, Center for Genomics and Data Science Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Michael G Tassia
- Department of Biology, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Françoise Thibaud-Nissen
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | | | - Mihir Trivedi
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA
| | - Wenjie Wei
- School of Life Sciences, Westlake University, Hangzhou 310024, China
- National Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, 430070, Wuhan, China
| | - Julie Wertz
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Muyu Yang
- Ray and Stephanie Lane Computational Biology Department, School of Computer Science, Carnegie Mellon University, PA, USA
| | - Panpan Zhang
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Shilong Zhang
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Shanghai Jiao Tong University, Shanghai, China
| | - Yang Zhang
- Ray and Stephanie Lane Computational Biology Department, School of Computer Science, Carnegie Mellon University, PA, USA
| | - Zhenmiao Zhang
- Department of Computer Science and Engineering, University of California San Diego, CA, USA
| | - Sarah A Zhao
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Yixin Zhu
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA, USA
| | - Erich D Jarvis
- Laboratory of Neurogenetics of Language, The Rockefeller University, New York, NY, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | | | - Iker Rivas-González
- Department of Primate Behavior and Evolution, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Benedict Paten
- UC Santa Cruz Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95060, USA
| | - Zachary A Szpiech
- Department of Biology, Penn State University, University Park, PA 16802, USA
| | - Christian D Huber
- Department of Biology, Penn State University, University Park, PA 16802, USA
| | - Tobias L Lenz
- Research Unit for Evolutionary Immunogenomics, Department of Biology, University of Hamburg, 20146 Hamburg, Germany
| | - Miriam K Konkel
- Department of Genetics & Biochemistry, Clemson University, Clemson, SC, USA
- Center for Human Genetics, Clemson University, Greenwood, SC, USA
| | - Soojin V Yi
- Department of Ecology, Evolution and Marine Biology, Department of Molecular, Cellular and Developmental Biology, Neuroscience Research Institute, University of California, Santa Barbara, CA, USA
| | - Stefan Canzar
- Faculty of Informatics and Data Science, University of Regensburg, 93053 Regensburg, Germany
| | - Corey T Watson
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Louisville, Louisville, KY, USA
| | - Peter H Sudmant
- Department of Integrative Biology, University of California, Berkeley, Berkeley, USA
- Center for Computational Biology, University of California, Berkeley, Berkeley, USA
| | - Erin Molloy
- Department of Computer Science, University of Maryland, College Park, MD 20742, USA
| | - Erik Garrison
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN 38163, USA
| | - Craig B Lowe
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710, USA
| | - Mario Ventura
- Department of Biosciences, Biotechnology and Environment, University of Bari, Bari, 70124, Italy
| | - Rachel J O'Neill
- Institute for Systems Genomics, University of Connecticut, Storrs, CT 06269, USA
- Department of Genetics and Genome Sciences, University of Connecticut Health Center, Farmington, CT, USA
- Departments of Molecular and Cell Biology, UConn Storrs, CT, USA
| | - Sergey Koren
- Genome Informatics Section, Center for Genomics and Data Science Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Kateryna D Makova
- Department of Biology, Penn State University, University Park, PA 16802, USA
| | - Adam M Phillippy
- Genome Informatics Section, Center for Genomics and Data Science Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Evan E Eichler
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA
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Ye L, Zhang L, Li X, Huang Y, Zhang B, Yang X, Tan W, Li X, Zhang X. De novo genome assembly and functional insights of the first commercial pink Auricularia cornea. Genomics 2024; 116:110902. [PMID: 39053612 DOI: 10.1016/j.ygeno.2024.110902] [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: 06/05/2024] [Revised: 07/08/2024] [Accepted: 07/21/2024] [Indexed: 07/27/2024]
Abstract
A pioneering pink cultivar of Auricularia cornea, first commercially cultivated in 2022, lacks genomic data, hindering research in genetic breeding, gene discovery, and product development. Here, we report the de novo assembly of the pink A. cornea Fen-A1 genome and provide a detailed functional annotation. The genome is 73.17 Mb in size, contains 86 scaffolds (N50 ∼ 5.49 Mb), 59.09% GC content and encodes 19,120 predicted genes with a BUSCO completeness of 92.60%. Comparative genomic analysis reveals the phylogenetic relatedness of Fen-A1 and remarkable gene family dynamics. Putative genes were found mapped to 3 antibiotic-related, 36 light-dependent and 25 terpene metabolites. In addition, 789 CAZymes genes were classified, revealing the dynamics of quality loss due to postharvest refrigeration. Overall, our work is the first report on a pink A. cornea genome and provides a comprehensive insight into its complex functions.
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Affiliation(s)
- Lei Ye
- College of Resources, Sichuan Agricultural University, Chengdu 611130, China; Sichuan Institute of Edible Fungi, Chengdu 610066, China
| | - Lingzi Zhang
- College of Resources, Sichuan Agricultural University, Chengdu 611130, China
| | - Xin Li
- College of Resources, Sichuan Agricultural University, Chengdu 611130, China
| | - Yu Huang
- Sichuan Institute of Edible Fungi, Chengdu 610066, China; Luzhou Laojiao Co., Ltd, Luzhou 646000, China
| | - Bo Zhang
- Sichuan Institute of Edible Fungi, Chengdu 610066, China
| | - Xuezhen Yang
- Sichuan Institute of Edible Fungi, Chengdu 610066, China
| | - Wei Tan
- Sichuan Institute of Edible Fungi, Chengdu 610066, China
| | - Xiaolin Li
- Sichuan Institute of Edible Fungi, Chengdu 610066, China; Luzhou Laojiao Co., Ltd, Luzhou 646000, China.
| | - Xiaoping Zhang
- College of Resources, Sichuan Agricultural University, Chengdu 611130, China.
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30
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Berasategui A, Salem H, Moller AG, Christopher Y, Vidaurre Montoya Q, Conn C, Read TD, Rodrigues A, Ziemert N, Gerardo N. Genomic insights into the evolution of secondary metabolism of Escovopsis and its allies, specialized fungal symbionts of fungus-farming ants. mSystems 2024; 9:e0057624. [PMID: 38904377 PMCID: PMC11265373 DOI: 10.1128/msystems.00576-24] [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: 04/24/2024] [Accepted: 05/14/2024] [Indexed: 06/22/2024] Open
Abstract
The metabolic intimacy of symbiosis often demands the work of specialists. Natural products and defensive secondary metabolites can drive specificity by ensuring infection and propagation across host generations. But in contrast to bacteria, little is known about the diversity and distribution of natural product biosynthetic pathways among fungi and how they evolve to facilitate symbiosis and adaptation to their host environment. In this study, we define the secondary metabolism of Escovopsis and closely related genera, symbionts in the gardens of fungus-farming ants. We ask how the gain and loss of various biosynthetic pathways correspond to divergent lifestyles. Long-read sequencing allowed us to define the chromosomal features of representative Escovopsis strains, revealing highly reduced genomes composed of seven to eight chromosomes. The genomes are highly syntenic with macrosynteny decreasing with increasing phylogenetic distance, while maintaining a high degree of mesosynteny. An ancestral state reconstruction analysis of biosynthetic pathways revealed that, while many secondary metabolites are shared with non-ant-associated Sordariomycetes, 56 pathways are unique to the symbiotic genera. Reflecting adaptation to diverging ant agricultural systems, we observe that the stepwise acquisition of these pathways mirrors the ecological radiations of attine ants and the dynamic recruitment and replacement of their fungal cultivars. As different clades encode characteristic combinations of biosynthetic gene clusters, these delineating profiles provide important insights into the possible mechanisms underlying specificity between these symbionts and their fungal hosts. Collectively, our findings shed light on the evolutionary dynamic nature of secondary metabolism in Escovopsis and its allies, reflecting adaptation of the symbionts to an ancient agricultural system.IMPORTANCEMicrobial symbionts interact with their hosts and competitors through a remarkable array of secondary metabolites and natural products. Here, we highlight the highly streamlined genomic features of attine-associated fungal symbionts. The genomes of Escovopsis species, as well as species from other symbiont genera, many of which are common with the gardens of fungus-growing ants, are defined by seven chromosomes. Despite a high degree of metabolic conservation, we observe some variation in the symbionts' potential to produce secondary metabolites. As the phylogenetic distribution of the encoding biosynthetic gene clusters coincides with attine transitions in agricultural systems, we highlight the likely role of these metabolites in mediating adaptation by a group of highly specialized symbionts.
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Affiliation(s)
- Aileen Berasategui
- Department of Biology, Emory University, Atlanta, Georgia, USA
- Cluster of Excellence-Controlling Microbes to Fight Infections, University of Tübingen, Tübingen, Germany
- Mutualisms Research Group, Max Planck Institute for Biology, Tübingen, Germany
- Amsterdam Institute for Life and Environment, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
| | - Hassan Salem
- Department of Biology, Emory University, Atlanta, Georgia, USA
- Mutualisms Research Group, Max Planck Institute for Biology, Tübingen, Germany
| | - Abraham G. Moller
- Division of Infectious Diseases, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Yuliana Christopher
- Instituto de Investigaciones Científicas y Servicios de Alta Tecnología, Ciudad del Saber, Panamá City, Panama
| | - Quimi Vidaurre Montoya
- Department of General and Applied Biology, São Paulo State University (UNESP), Institute of Biosciences, Rio Claro, São Paulo, Brazil
| | - Caitlin Conn
- Department of Biology, Emory University, Atlanta, Georgia, USA
- Department of Biology, Berry College, Mount Berry, Georgia, USA
| | - Timothy D. Read
- Division of Infectious Diseases, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Andre Rodrigues
- Department of General and Applied Biology, São Paulo State University (UNESP), Institute of Biosciences, Rio Claro, São Paulo, Brazil
| | - Nadine Ziemert
- Cluster of Excellence-Controlling Microbes to Fight Infections, University of Tübingen, Tübingen, Germany
- Translational Genome Mining for Natural Products, Interfaculty Institute of Microbiology and Infection Medicine Tübingen (IMIT), Interfaculty Institute for Biomedical Informatics (IBMI), University of Tübingen, Tübingen, Germany
| | - Nicole Gerardo
- Department of Biology, Emory University, Atlanta, Georgia, USA
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31
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Xu S, Jiang L, Zou Z, Zou M, Qiao G, Chen J. Two chromosome-level genome assemblies of galling aphids Slavum lentiscoides and Chaetogeoica ovagalla. Sci Data 2024; 11:803. [PMID: 39033163 PMCID: PMC11271456 DOI: 10.1038/s41597-024-03653-x] [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: 04/26/2024] [Accepted: 07/15/2024] [Indexed: 07/23/2024] Open
Abstract
Slavum lentiscoides and Chaetogeoica ovagalla are two aphid species from the subtribe Fordina of Fordini within the subfamily Eriosomatinae, and they produce galls on their primary host plants Pistacia. We assembled chromosome-level genomes of these two species using Nanopore long-read sequencing and Hi-C technology. A 332 Mb genome assembly of S. lentiscoides with a scaffold N50 of 19.77 Mb, including 11,747 genes, and a 289 Mb genome assembly of C. ovagalla with a scaffold N50 of 11.85 Mb, containing 14,492 genes, were obtained. The Benchmarking Universal Single-Copy Orthologs (BUSCO) benchmark of the two genome assemblies reached 93.7% (91.9% single-copy) and 97.0% (95.3% single-copy), respectively. The high-quality genome assemblies in our study provide valuable resources for future genomic research of galling aphids.
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Affiliation(s)
- Shifen Xu
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Liyun Jiang
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Zhengting Zou
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Ming Zou
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Gexia Qiao
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China.
| | - Jing Chen
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.
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32
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Dougan KE, Bellantuono AJ, Kahlke T, Abbriano RM, Chen Y, Shah S, Granados-Cifuentes C, van Oppen MJH, Bhattacharya D, Suggett DJ, Rodriguez-Lanetty M, Chan CX. Whole-genome duplication in an algal symbiont bolsters coral heat tolerance. SCIENCE ADVANCES 2024; 10:eadn2218. [PMID: 39028812 PMCID: PMC11259175 DOI: 10.1126/sciadv.adn2218] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Accepted: 06/14/2024] [Indexed: 07/21/2024]
Abstract
The algal endosymbiont Durusdinium trenchii enhances the resilience of coral reefs under thermal stress. D. trenchii can live freely or in endosymbiosis, and the analysis of genetic markers suggests that this species has undergone whole-genome duplication (WGD). However, the evolutionary mechanisms that underpin the thermotolerance of this species are largely unknown. Here, we present genome assemblies for two D. trenchii isolates, confirm WGD in these taxa, and examine how selection has shaped the duplicated genome regions using gene expression data. We assess how the free-living versus endosymbiotic lifestyles have contributed to the retention and divergence of duplicated genes, and how these processes have enhanced the thermotolerance of D. trenchii. Our combined results suggest that lifestyle is the driver of post-WGD evolution in D. trenchii, with the free-living phase being the most important, followed by endosymbiosis. Adaptations to both lifestyles likely enabled D. trenchii to provide enhanced thermal stress protection to the host coral.
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Affiliation(s)
- Katherine E. Dougan
- School of Chemistry and Molecular Biosciences, Australian Centre for Ecogenomics, The University of Queensland, Brisbane, QLD 4072, Australia
- Department of Biological Sciences, Biomolecular Science Institute, Florida International University, Miami, FL 33099, USA
| | - Anthony J. Bellantuono
- Department of Biological Sciences, Biomolecular Science Institute, Florida International University, Miami, FL 33099, USA
| | - Tim Kahlke
- Climate Change Cluster, University of Technology Sydney, Sydney, NSW 2007, Australia
| | - Raffaela M. Abbriano
- Climate Change Cluster, University of Technology Sydney, Sydney, NSW 2007, Australia
| | - Yibi Chen
- School of Chemistry and Molecular Biosciences, Australian Centre for Ecogenomics, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Sarah Shah
- School of Chemistry and Molecular Biosciences, Australian Centre for Ecogenomics, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Camila Granados-Cifuentes
- Department of Biological Sciences, Biomolecular Science Institute, Florida International University, Miami, FL 33099, USA
| | - Madeleine J. H. van Oppen
- School of Biosciences, The University of Melbourne, Parkville, VIC 3010, Australia
- Australian Institute of Marine Science, Townsville, QLD 4810, Australia
| | - Debashish Bhattacharya
- Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, NJ 08901, USA
| | - David J. Suggett
- Climate Change Cluster, University of Technology Sydney, Sydney, NSW 2007, Australia
- KAUST Reefscape Restoration Initiative (KRRI) and Red Sea Research Center (RSRC), King Abdullah University of Science and Technology, Thuwal 23955, Saudi Arabia
| | - Mauricio Rodriguez-Lanetty
- Department of Biological Sciences, Biomolecular Science Institute, Florida International University, Miami, FL 33099, USA
| | - Cheong Xin Chan
- School of Chemistry and Molecular Biosciences, Australian Centre for Ecogenomics, The University of Queensland, Brisbane, QLD 4072, Australia
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33
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Huang X, Dong G, Fan H, Zhou W, Huang G, Guan D, Zhang D, Wei F. The genome of African manatee Trichechus senegalensis reveals secondary adaptation to the aquatic environment. iScience 2024; 27:110394. [PMID: 39092175 PMCID: PMC11292518 DOI: 10.1016/j.isci.2024.110394] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2024] [Revised: 05/26/2024] [Accepted: 06/25/2024] [Indexed: 08/04/2024] Open
Abstract
Sirenians exhibit unique aquatic adaptations, showcasing both convergent adaptive features shared with cetaceans and unique characteristics such as cold sensitivity and dense bones. Here, we report a chromosome-level genome of the African manatee (Trichechus senegalensis) with high continuity, completeness, and accuracy. We found that genes associated with osteopetrosis have undergone positive selection (CSF1R and LRRK1) or pseudogenized (FAM111A and IGSF23) in the African manatee, potentially contributing to the dense bone formation. The loss of KCNK18 may have increased their sensitivity to cold water temperatures. Moreover, we identified convergent evolutionary signatures in 392 genes among fully aquatic mammals, primarily enriched in skin or skeletal system development and circadian rhythm, which contributed to the transition from terrestrial to fully aquatic lifestyles. The African manatee currently possesses a small effective population size and low genome-wide heterozygosity. Overall, our study provides genetic resources for understanding the evolutionary characteristics and conservation efforts of this species.
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Affiliation(s)
- Xin Huang
- Center for Evolution and Conservation Biology, Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Guixin Dong
- Guangdong Chimelong Group, Co., Ltd., Guangzhou 511400, China
| | - Huizhong Fan
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Wenliang Zhou
- Center for Evolution and Conservation Biology, Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China
| | - Guangping Huang
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- Jiangxi Provincial Key Laboratory of Conservation Biology, College of Forestry, Jiangxi Agricultural University, Nanchang 330045, China
| | - Dengfeng Guan
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Delu Zhang
- Chimelong Ocean Kingdom, Zhuhai 519000, China
| | - Fuwen Wei
- Center for Evolution and Conservation Biology, Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Jiangxi Provincial Key Laboratory of Conservation Biology, College of Forestry, Jiangxi Agricultural University, Nanchang 330045, China
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34
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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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35
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Conlan S, Subramanian P, Plata Barril B, Youn JH, Thomas PJ, Koren S, Dotson GA, Park M, Rhie A, Segre JA, Dekker JP, Zelazny AM. Whole-genome sequence of Mucor velutinosus NIH1002, a strain associated with disseminated disease. Microbiol Resour Announc 2024; 13:e0006224. [PMID: 38899875 PMCID: PMC11256851 DOI: 10.1128/mra.00062-24] [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: 01/23/2024] [Accepted: 05/28/2024] [Indexed: 06/21/2024] Open
Abstract
The draft genome of Mucor velutinosus NIH1002, a 2011 isolate from a case of disseminated disease, was sequenced using PacBio long-read and HiSeq short-read technologies. The genome has 43 contigs, an N50 of 2.65 Mb, and 13,295 protein-coding genes. It is the most complete M. velutinosus genome to date.
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Affiliation(s)
- Sean Conlan
- National Human Genome Research Institute, NIH, Bethesda, Maryland, USA
| | - Poorani Subramanian
- National Institute of Allergy and Infectious Diseases, NIH, Bethesda, Maryland, USA
| | | | - Jung-Ho Youn
- National Institutes of Health Clinical Center, NIH, Bethesda, Maryland, USA
| | - Pamela J. Thomas
- NIH Intramural Sequencing Center, NHGRI, NIH, Rockville, Maryland, USA
| | - Sergey Koren
- National Human Genome Research Institute, NIH, Bethesda, Maryland, USA
| | | | - Morgan Park
- NIH Intramural Sequencing Center, NHGRI, NIH, Rockville, Maryland, USA
| | - Arang Rhie
- National Human Genome Research Institute, NIH, Bethesda, Maryland, USA
| | - Julie A. Segre
- National Human Genome Research Institute, NIH, Bethesda, Maryland, USA
| | - John P. Dekker
- National Institute of Allergy and Infectious Diseases, NIH, Bethesda, Maryland, USA
- National Institutes of Health Clinical Center, NIH, Bethesda, Maryland, USA
| | - Adrian M. Zelazny
- National Institutes of Health Clinical Center, NIH, Bethesda, Maryland, USA
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36
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Shekhar MS, Katneni VK, Jangam AK, Krishnan K, Prabhudas SK, Jayaraman R, Angel JRJ, Kailasam M. Genome assembly, Full-length transcriptome, and isoform diversity of Red Snapper, Lutjanus argentimaculatus. Sci Data 2024; 11:796. [PMID: 39025998 PMCID: PMC11258364 DOI: 10.1038/s41597-024-03633-1] [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: 01/30/2024] [Accepted: 07/10/2024] [Indexed: 07/20/2024] Open
Abstract
The mangrove red snapper, Lutjanus argentimaculatus, is a marine food fish of economic and aquaculture importance. The application of genomic selection-based breeding programs for this species is limited by the absence of a reference genome and transcriptome profiles. The current study attempted to fill this void by generating genomic and transcriptomic resources for red snapper. Using PacBio long reads, and Arima Hi-C linked reads, a scaffold-level genome assembly was generated for L. argentimaculatus. The assembly is of 1.03 Gb comprising of 400 scaffolds with N50 of 33.8 Mb and was assessed to be 97.2% complete upon benchmarking with BUSCO. Full-length transcriptome generated with PacBio Iso-Sequencing strategy using six tissues (muscle, gills, liver, kidney, stomach, and gonad) contained 56,515 isoforms belonging to 18,108 unique genes with N50 length of 3,973 bp. The resources generated will have potential applications in the functional studies, conservation, broodstock management and selective breeding programmes of L. argentimaculatus.
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Affiliation(s)
- Mudagandur S Shekhar
- Centre for Bioinformatics, ICAR-Central Institute of Brackishwater Aquaculture, No 75, Santhome High Road, MRC Nagar, Chennai, 600028, Tamil Nadu, India
| | - Vinaya Kumar Katneni
- Centre for Bioinformatics, ICAR-Central Institute of Brackishwater Aquaculture, No 75, Santhome High Road, MRC Nagar, Chennai, 600028, Tamil Nadu, India.
| | - Ashok Kumar Jangam
- Centre for Bioinformatics, ICAR-Central Institute of Brackishwater Aquaculture, No 75, Santhome High Road, MRC Nagar, Chennai, 600028, Tamil Nadu, India
| | - Karthic Krishnan
- Centre for Bioinformatics, ICAR-Central Institute of Brackishwater Aquaculture, No 75, Santhome High Road, MRC Nagar, Chennai, 600028, Tamil Nadu, India
| | - Sudheesh K Prabhudas
- Centre for Bioinformatics, ICAR-Central Institute of Brackishwater Aquaculture, No 75, Santhome High Road, MRC Nagar, Chennai, 600028, Tamil Nadu, India
| | - Roja Jayaraman
- Centre for Bioinformatics, ICAR-Central Institute of Brackishwater Aquaculture, No 75, Santhome High Road, MRC Nagar, Chennai, 600028, Tamil Nadu, India
| | - Jesudhas Raymond Jani Angel
- Crustacean Culture Division, ICAR-Central Institute of Brackishwater Aquaculture, No 75, Santhome High Road, MRC Nagar, Chennai, 600028, Tamil Nadu, India
| | - Muniyandi Kailasam
- Finfish Culture Division, ICAR-Central Institute of Brackishwater Aquaculture, No 75, Santhome High Road, MRC Nagar, Chennai, 600028, Tamil Nadu, India
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Cao LJ, Guan TB, Chen JC, Yang F, Liu JX, Jin FL, Wei SJ. Chromosome-level genome assembly of the two-spotted spider mite Tetranychus urticae. Sci Data 2024; 11:798. [PMID: 39025916 PMCID: PMC11258348 DOI: 10.1038/s41597-024-03640-2] [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: 03/08/2024] [Accepted: 07/11/2024] [Indexed: 07/20/2024] Open
Abstract
The two-spotted spider mite, Tetranychus urticae Koch (Acari: Tetranychidae), is a notorious pest in agriculture that has developed resistance to almost all chemical types used for its control. Here, we assembled a chromosome-level genome for the TSSM using Illumina, Nanopore, and Hi-C sequencing technologies. The assembled contigs had a total length of 103.94 Mb with an N50 of 3.46 Mb, with 87.7 Mb of 34 contigs anchored to three chromosomes. The chromosome-level genome assembly had a BUSCO completeness of 94.8%. We identified 15,604 protein-coding genes, with 11,435 genes that could be functionally annotated. The high-quality genome provides invaluable resources for the genetic and evolutionary study of TSSM.
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Affiliation(s)
- Li-Jun Cao
- College of Plant Protection, South China Agricultural University, Guangzhou, China
- Institute of Plant Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Tian-Bo Guan
- College of Plant Protection, South China Agricultural University, Guangzhou, China
- Institute of Plant Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Jin-Cui Chen
- Institute of Plant Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Fangyuan Yang
- Institute of Plant Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Jing-Xian Liu
- College of Plant Protection, South China Agricultural University, Guangzhou, China
| | - Feng-Liang Jin
- College of Plant Protection, South China Agricultural University, Guangzhou, China.
| | - Shu-Jun Wei
- Institute of Plant Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China.
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Ong CT, Mody KT, Cavallaro AS, Yan Y, Nguyen LT, Shao R, Mitter N, Mahony TJ, Ross EM. Chromosome-Scale Genome Assembly of the Sheep-Biting Louse Bovicola ovis Using Nanopore Sequencing Data and Pore-C Analysis. Int J Mol Sci 2024; 25:7824. [PMID: 39063065 PMCID: PMC11276745 DOI: 10.3390/ijms25147824] [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: 06/10/2024] [Revised: 07/15/2024] [Accepted: 07/15/2024] [Indexed: 07/28/2024] Open
Abstract
Bovicola ovis, commonly known as the sheep-biting louse, is an ectoparasite that adversely affects the sheep industry. Sheep louse infestation lowers the quality of products, including wool and leather, causing a loss of approximately AUD 123M per annum in Australia alone. The lack of a high-quality genome assembly for the sheep-biting louse, as well as any closely related livestock lice, has hindered the development of louse research and management control tools. In this study, we present the assembly of B. ovis with a genome size of ~123 Mbp based on a nanopore long-read sequencing library and Illumina RNA sequencing, complemented with a chromosome-level scaffolding using the Pore-C multiway chromatin contact dataset. Combining multiple alignment and gene prediction tools, a comprehensive annotation on the assembled B. ovis genome was conducted and recalled 11,810 genes as well as other genomic features including orf, ssr, rRNA and tRNA. A manual curation using alignment with the available closely related louse species, Pediculus humanus, increased the number of annotated genes to 16,024. Overall, this study reported critical genetic resources and biological insights for the advancement of sheep louse research and the development of sustainable control strategies in the sheep industry.
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Affiliation(s)
- Chian Teng Ong
- Centre for Animal Science, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, QLD 4072, Australia; (C.T.O.); (A.S.C.); (Y.Y.); (L.T.N.); (N.M.); (T.J.M.)
| | - Karishma T. Mody
- Centre for Animal Science, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, QLD 4072, Australia; (C.T.O.); (A.S.C.); (Y.Y.); (L.T.N.); (N.M.); (T.J.M.)
| | - Antonino S. Cavallaro
- Centre for Animal Science, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, QLD 4072, Australia; (C.T.O.); (A.S.C.); (Y.Y.); (L.T.N.); (N.M.); (T.J.M.)
| | - Yakun Yan
- Centre for Animal Science, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, QLD 4072, Australia; (C.T.O.); (A.S.C.); (Y.Y.); (L.T.N.); (N.M.); (T.J.M.)
| | - Loan T. Nguyen
- Centre for Animal Science, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, QLD 4072, Australia; (C.T.O.); (A.S.C.); (Y.Y.); (L.T.N.); (N.M.); (T.J.M.)
| | - Renfu Shao
- Centre for Bioinnovation, University of the Sunshine Coast, Sippy Downs, QLD 4556, Australia;
- School of Science, Technology and Engineering, University of the Sunshine Coast, Sippy Downs, QLD 4556, Australia
| | - Neena Mitter
- Centre for Animal Science, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, QLD 4072, Australia; (C.T.O.); (A.S.C.); (Y.Y.); (L.T.N.); (N.M.); (T.J.M.)
| | - Timothy J. Mahony
- Centre for Animal Science, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, QLD 4072, Australia; (C.T.O.); (A.S.C.); (Y.Y.); (L.T.N.); (N.M.); (T.J.M.)
| | - Elizabeth M. Ross
- Centre for Animal Science, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, QLD 4072, Australia; (C.T.O.); (A.S.C.); (Y.Y.); (L.T.N.); (N.M.); (T.J.M.)
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Mpeyako LA, Hart AJ, Bailey NP, Carlton JM, Henrissat B, Sullivan SA, Hirt RP. Comparative genomics between Trichomonas tenax and Trichomonas vaginalis: CAZymes and candidate virulence factors. Front Microbiol 2024; 15:1437572. [PMID: 39086644 PMCID: PMC11288935 DOI: 10.3389/fmicb.2024.1437572] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2024] [Accepted: 06/28/2024] [Indexed: 08/02/2024] Open
Abstract
Introduction The oral trichomonad Trichomonas tenax is increasingly appreciated as a likely contributor to periodontitis, a chronic inflammatory disease induced by dysbiotic microbiota, in humans and domestic animals and is strongly associated with its worst prognosis. Our current understanding of the molecular basis of T. tenax interactions with host cells and the microbiota of the oral cavity are still rather limited. One laboratory strain of T. tenax (Hs-4:NIH/ATCC 30207) can be grown axenically and two draft genome assemblies have been published for that strain, although the structural and functional annotation of these genomes is not available. Methods GenSAS and Galaxy were used to annotate two publicly available draft genomes for T. tenax, with a focus on protein-coding genes. A custom pipeline was used to annotate the CAZymes for T. tenax and the human sexually transmitted parasite Trichomonas vaginalis, the most well-characterized trichomonad. A combination of bioinformatics analyses was used to screen for homologs of T. vaginalis virulence and colonization factors within the T. tenax annotated proteins. Results Our annotation of the two T. tenax draft genome sequences and their comparison with T. vaginalis proteins provide evidence for several candidate virulence factors. These include candidate surface proteins, secreted proteins and enzymes mediating potential interactions with host cells and/or members of the oral microbiota. The CAZymes annotation identified a broad range of glycoside hydrolase (GH) families, with the majority of these being shared between the two Trichomonas species. Discussion The presence of candidate T. tenax virulence genes supports the hypothesis that this species is associated with periodontitis through direct and indirect mechanisms. Notably, several GH proteins could represent potential new virulence factors for both Trichomonas species. These data support a model where T. tenax interactions with host cells and members of the oral microbiota could synergistically contribute to the damaging inflammation characteristic of periodontitis, supporting a causal link between T. tenax and periodontitis.
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Affiliation(s)
- Lenshina A. Mpeyako
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Adam J. Hart
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Nicholas P. Bailey
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Jane M. Carlton
- Department of Biology, Center for Genomics and Systems Biology, New York University, New York, NY, United States
- Department of Molecular Microbiology and Immunology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, United States
| | - Bernard Henrissat
- Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
- Department of Biotechnology and Biomedicine (DTU Bioengineering), Technical University of Denmark, Lyngby, Denmark
| | - Steven A. Sullivan
- Department of Biology, Center for Genomics and Systems Biology, New York University, New York, NY, United States
- Department of Molecular Microbiology and Immunology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, United States
| | - Robert P. Hirt
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
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Dong Z, Wang F, Liu Y, Li Y, Yu H, Peng S, Sun T, Qu M, Sun K, Wang L, Ma Y, Chen K, Zhao J, Lin Q. Genomic and single-cell analyses reveal genetic signatures of swimming pattern and diapause strategy in jellyfish. Nat Commun 2024; 15:5936. [PMID: 39009560 PMCID: PMC11250803 DOI: 10.1038/s41467-024-49848-z] [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: 10/18/2023] [Accepted: 06/21/2024] [Indexed: 07/17/2024] Open
Abstract
Jellyfish exhibit innovative swimming patterns that contribute to exploring the origins of animal locomotion. However, the genetic and cellular basis of these patterns remains unclear. Herein, we generated chromosome-level genome assemblies of two jellyfish species, Turritopsis rubra and Aurelia coerulea, which exhibit straight and free-swimming patterns, respectively. We observe positive selection of numerous genes involved in statolith formation, hair cell ciliogenesis, ciliary motility, and motor neuron function. The lineage-specific absence of otolith morphogenesis- and ciliary movement-related genes in T. rubra may be associated with homeostatic structural statocyst loss and straight swimming pattern. Notably, single-cell transcriptomic analyses covering key developmental stages reveal the enrichment of diapause-related genes in the cyst during reverse development, suggesting that the sustained diapause state favours the development of new polyps under favourable conditions. This study highlights the complex relationship between genetics, locomotion patterns and survival strategies in jellyfish, thereby providing valuable insights into the evolutionary lineages of movement and adaptation in the animal kingdom.
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Affiliation(s)
- Zhijun Dong
- CAS Key Laboratory of Coastal Environmental Processes and Ecological Remediation, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, Shandong, 264003, China.
- University of Chinese Academy of Sciences, Beijing, 100101, China.
| | - Fanghan Wang
- CAS Key Laboratory of Coastal Environmental Processes and Ecological Remediation, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, Shandong, 264003, China
- University of Chinese Academy of Sciences, Beijing, 100101, China
| | - Yali Liu
- University of Chinese Academy of Sciences, Beijing, 100101, China
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China
- Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China
| | - Yongxue Li
- CAS Key Laboratory of Coastal Environmental Processes and Ecological Remediation, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, Shandong, 264003, China
- University of Chinese Academy of Sciences, Beijing, 100101, China
| | - Haiyan Yu
- College of the Environment and Ecology, Xiamen University, Xiamen, 361102, China
| | - Saijun Peng
- CAS Key Laboratory of Coastal Environmental Processes and Ecological Remediation, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, Shandong, 264003, China
- University of Chinese Academy of Sciences, Beijing, 100101, China
| | - Tingting Sun
- CAS Key Laboratory of Coastal Environmental Processes and Ecological Remediation, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, Shandong, 264003, China
- University of Chinese Academy of Sciences, Beijing, 100101, China
| | - Meng Qu
- University of Chinese Academy of Sciences, Beijing, 100101, China
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China
- Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China
| | - Ke Sun
- State Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, Yunnan, 650500, China
| | - Lei Wang
- CAS Key Laboratory of Coastal Environmental Processes and Ecological Remediation, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, Shandong, 264003, China
- University of Chinese Academy of Sciences, Beijing, 100101, China
| | - Yuanqing Ma
- Shandong Key Laboratory of Marine Ecological Restoration, Shandong Marine Resource and Environment Research Institute, Yantai, Shandong, 264006, China
| | - Kai Chen
- State Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, Yunnan, 650500, China
| | - Jianmin Zhao
- CAS Key Laboratory of Coastal Environmental Processes and Ecological Remediation, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, Shandong, 264003, China.
- University of Chinese Academy of Sciences, Beijing, 100101, China.
| | - Qiang Lin
- University of Chinese Academy of Sciences, Beijing, 100101, China.
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China.
- Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China.
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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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Yang X, Luo S, Yang S, Duoji C, Wang Q, Chen Z, Yang D, Yang T, Wan X, Yang Y, Liu T, Yang Y. Chromosome-level genome assembly of Hippophae rhamnoides variety. Sci Data 2024; 11:776. [PMID: 39003298 PMCID: PMC11246439 DOI: 10.1038/s41597-024-03549-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: 01/02/2024] [Accepted: 06/19/2024] [Indexed: 07/15/2024] Open
Abstract
Fructus hippophae (Hippophae rhamnoides spp. mongolica×Hippophae rhamnoides sinensis), a hybrid variety of sea buckthorn that Hippophae rhamnoides spp. mongolica serves as the female parent and Hippophae rhamnoides sinensis serves as the male parent, is a traditional plant with great potentials of economic and medical values. Herein, we gained a chromosome-level genome of Fructus hippophae about 918.59 Mb, with the scaffolds N50 reaching 83.65 Mb. Then, we anchored 440 contigs with 97.17% of the total genome sequences onto 12 pseudochromosomes. Next, de-novo, homology and transcriptome assembly strategies were adopted for gene structure prediction. This predicted 36475 protein-coding genes, of which 36226 genes could be functionally annotated. Simultaneously, various strategies were used for quality assessment, both the complete BUSCO value (98.80%) and the mapping rate indicated the high assembly quality. Repetitive elements, which occupied 63.68% of the genome, and 1483600 bp of non-coding RNA were annotated. Here, we provide genomic information on female plants of a popular variety, which can provide data for pan-genomic construction of sea buckthorn and for the resolution of the mechanism of sex differentiation.
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Grants
- This research was supported by Regional Science and Technology Collaborative Innovation Project of Shigatse Bureau of Science and Technology(QYXTZX-RKZ2021-01 and QYXTZX-RKZ2021-07)
- the Second Tibetan Plateau Scientific Expedition and Research (STEP) program (2019QZKK0502),the Major Program of National Natural Science Foundation of China (31590820, 31590823), the National Natural Science Foundation of China (31601999 and 41771123), and the 13th Five-year Informatization Plan of Chinese Academy of Sciences,Grant No. XXH13506.
- This research was supported by Regional Science and Technology Collaborative Innovation Project of Shigatse Bureau of Science and Technology(QYXTZX-RKZ2021-01 and QYXTZX-RKZ2021-07), the Second Tibetan Plateau Scientific Expedition and Research (STEP) program (2019QZKK0502), Yunling Scholar Project to Yang Yongping, Regional Science and Technology Collaborative Innovation Project of Shigatse Bureau of Science and Technology(QYXTZX-RKZ2022-01), the Major Program of National Natural Science Foundation of China (31590820, 31590823), the National Natural Science Foundation of China (31601999 and 41771123), and the 13th Five-year Informatization Plan of Chinese Academy of Sciences,Grant No. XXH13506.
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Affiliation(s)
- Xingyu Yang
- Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, kunming, 650000, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Shujie Luo
- Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, kunming, 650000, China
- Dali University, Dali, 671000, China
| | - Shihai Yang
- Yunwang Industrial Corporation, Ltd, Tibet, 850000, China
| | - Ciren Duoji
- Service Center for Forestry and Grassland Bureau of Sangzhuzi District in Xizang, Xizang, 850000, China
| | - Qianwen Wang
- Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, kunming, 650000, China
| | - Zhiyu Chen
- University of Chinese Academy of Sciences, Beijing, 100049, China
- Plant Germplasm and Genomics Center, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
- Institute of Tibetan Plateau Research at Kunming, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
| | - Danni Yang
- Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, kunming, 650000, China
| | - Tianyu Yang
- University of Chinese Academy of Sciences, Beijing, 100049, China
- Plant Germplasm and Genomics Center, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
- Institute of Tibetan Plateau Research at Kunming, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
| | - Xi Wan
- Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, kunming, 650000, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yunqiang Yang
- Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, kunming, 650000, China
- Plant Germplasm and Genomics Center, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
- Institute of Tibetan Plateau Research at Kunming, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
| | | | - Yongping Yang
- Plant Germplasm and Genomics Center, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China.
- Institute of Tibetan Plateau Research at Kunming, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China.
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Kitchen SA, Naragon TH, Brückner A, Ladinsky MS, Quinodoz SA, Badroos JM, Viliunas JW, Kishi Y, Wagner JM, Miller DR, Yousefelahiyeh M, Antoshechkin IA, Eldredge KT, Pirro S, Guttman M, Davis SR, Aardema ML, Parker J. The genomic and cellular basis of biosynthetic innovation in rove beetles. Cell 2024; 187:3563-3584.e26. [PMID: 38889727 PMCID: PMC11246231 DOI: 10.1016/j.cell.2024.05.012] [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: 06/07/2023] [Revised: 02/29/2024] [Accepted: 05/06/2024] [Indexed: 06/20/2024]
Abstract
How evolution at the cellular level potentiates macroevolutionary change is central to understanding biological diversification. The >66,000 rove beetle species (Staphylinidae) form the largest metazoan family. Combining genomic and cell type transcriptomic insights spanning the largest clade, Aleocharinae, we retrace evolution of two cell types comprising a defensive gland-a putative catalyst behind staphylinid megadiversity. We identify molecular evolutionary steps leading to benzoquinone production by one cell type via a mechanism convergent with plant toxin release systems, and synthesis by the second cell type of a solvent that weaponizes the total secretion. This cooperative system has been conserved since the Early Cretaceous as Aleocharinae radiated into tens of thousands of lineages. Reprogramming each cell type yielded biochemical novelties enabling ecological specialization-most dramatically in symbionts that infiltrate social insect colonies via host-manipulating secretions. Our findings uncover cell type evolutionary processes underlying the origin and evolvability of a beetle chemical innovation.
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Affiliation(s)
- Sheila A Kitchen
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Thomas H Naragon
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Adrian Brückner
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Mark S Ladinsky
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Sofia A Quinodoz
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Jean M Badroos
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Joani W Viliunas
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Yuriko Kishi
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Julian M Wagner
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - David R Miller
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Mina Yousefelahiyeh
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Igor A Antoshechkin
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - K Taro Eldredge
- Museum of Zoology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Stacy Pirro
- Iridian Genomes, 613 Quaint Acres Dr., Silver Spring, MD 20904, USA
| | - Mitchell Guttman
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Steven R Davis
- Division of Invertebrate Zoology, American Museum of Natural History, New York, NY 10024, USA
| | - Matthew L Aardema
- Department of Biology, Montclair State University, Montclair, NJ 07043, USA
| | - Joseph Parker
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA.
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Hatmaker EA, Barber AE, Drott MT, Sauters TJC, Alastruey-Izquierdo A, Garcia-Hermoso D, Kurzai O, Rokas A. Pathogenicity is associated with population structure in a fungal pathogen of humans. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.05.602241. [PMID: 39026826 PMCID: PMC11257439 DOI: 10.1101/2024.07.05.602241] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/20/2024]
Abstract
Aspergillus flavus is a clinically and agriculturally important saprotrophic fungus responsible for severe human infections and extensive crop losses. We analyzed genomic data from 250 (95 clinical and 155 environmental) A. flavus isolates from 9 countries, including 70 newly sequenced clinical isolates, to examine population and pan-genome structure and their relationship to pathogenicity. We identified five A. flavus populations, including a new population, D, corresponding to distinct clades in the genome-wide phylogeny. Strikingly, > 75% of clinical isolates were from population D. Accessory genes, including genes within biosynthetic gene clusters, were significantly more common in some populations but rare in others. Population D was enriched for genes associated with zinc ion binding, lipid metabolism, and certain types of hydrolase activity. In contrast to the major human pathogen Aspergillus fumigatus, A. flavus pathogenicity in humans is strongly associated with population structure, making it a great system for investigating how population-specific genes contribute to pathogenicity.
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Affiliation(s)
- E. Anne Hatmaker
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA
- Evolutionary Studies Initiative, Vanderbilt University, Nashville, TN, USA
| | - Amelia E. Barber
- Institute for Microbiology, Friedrich Schiller University, Jena, Germany
| | - Milton T. Drott
- Cereal Disease Laboratory, Agricultural Research Service, USDA, Saint Paul, MN, USA
| | - Thomas J. C. Sauters
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA
- Evolutionary Studies Initiative, Vanderbilt University, Nashville, TN, USA
| | - Ana Alastruey-Izquierdo
- Mycology Reference Laboratory, National Center for Microbiology, Instituto de Salud Carlos III, Madrid, Spain
- Center for Biomedical Research in Network in Infectious Diseases (CIBERINFEC), Carlos III Heath Institute, Madrid, Spain
| | - Dea Garcia-Hermoso
- Institut Pasteur, Université Paris Cité, National Reference Center for Invasive Mycoses and Antifungals, Translational Mycology Research Group, Mycology Department, Paris, France
| | - Oliver Kurzai
- National Reference Center for Invasive Fungal Infections NRZMyk, Leibniz Institute for Natural Product Research and Infection Biology – Hans-Knoell-Institute, Jena, Germany
- Institute for Hygiene and Microbiology, University of Würzburg. Würzburg, Germany
| | - Antonis Rokas
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA
- Evolutionary Studies Initiative, Vanderbilt University, Nashville, TN, USA
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Liu J, Zhou SZ, Liu YL, Zhao BY, Yu D, Zhong MC, Jiang XD, Cui WH, Zhao JX, Qiu J, Liu LM, Guo ZH, Li HT, Tan DY, Hu JY, Li DZ. Genomes of Meniocus linifolius and Tetracme quadricornis reveal the ancestral karyotype and genomic features of core Brassicaceae. PLANT COMMUNICATIONS 2024; 5:100878. [PMID: 38475995 PMCID: PMC11287156 DOI: 10.1016/j.xplc.2024.100878] [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: 03/20/2023] [Revised: 03/03/2024] [Accepted: 03/11/2024] [Indexed: 03/14/2024]
Abstract
Brassicaceae represents an important plant family from both a scientific and economic perspective. However, genomic features related to the early diversification of this family have not been fully characterized, especially upon the uplift of the Tibetan Plateau, which was followed by increasing aridity in the Asian interior, intensifying monsoons in Eastern Asia, and significantly fluctuating daily temperatures. Here, we reveal the genomic architecture that accompanied early Brassicaceae diversification by analyzing two high-quality chromosome-level genomes for Meniocus linifolius (Arabodae; clade D) and Tetracme quadricornis (Hesperodae; clade E), together with genomes representing all major Brassicaceae clades and the basal Aethionemeae. We reconstructed an ancestral core Brassicaceae karyotype (CBK) containing 9 pseudochromosomes with 65 conserved syntenic genomic blocks and identified 9702 conserved genes in Brassicaceae. We detected pervasive conflicting phylogenomic signals accompanied by widespread ancient hybridization events, which correlate well with the early divergence of core Brassicaceae. We identified a successive Brassicaceae-specific expansion of the class I TREHALOSE-6-PHOSPHATE SYNTHASE 1 (TPS1) gene family, which encodes enzymes with essential regulatory roles in flowering time and embryo development. The TPS1s were mainly randomly amplified, followed by expression divergence. Our results provide fresh insights into historical genomic features coupled with Brassicaceae evolution and offer a potential model for broad-scale studies of adaptive radiation under an ever-changing environment.
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Affiliation(s)
- Jie Liu
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia & Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shi-Zhao Zhou
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia & Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yun-Long Liu
- Germplasm Bank of Wild Species & Yunnan Key Laboratory for Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
| | - Bin-Yan Zhao
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia & Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Dongmei Yu
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia & Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
| | - Mi-Cai Zhong
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia & Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
| | - Xiao-Dong Jiang
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia & Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
| | - Wei-Hua Cui
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia & Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
| | - Jiu-Xia Zhao
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia & Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Juan Qiu
- College of Life Sciences, Xinjiang Agricultural University, Ürümqi 830052, China
| | - Liang-Min Liu
- Germplasm Bank of Wild Species & Yunnan Key Laboratory for Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhen-Hua Guo
- Germplasm Bank of Wild Species & Yunnan Key Laboratory for Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
| | - Hong-Tao Li
- Germplasm Bank of Wild Species & Yunnan Key Laboratory for Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
| | - Dun-Yan Tan
- College of Life Sciences, Xinjiang Agricultural University, Ürümqi 830052, China
| | - Jin-Yong Hu
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia & Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China.
| | - De-Zhu Li
- Germplasm Bank of Wild Species & Yunnan Key Laboratory for Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China.
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46
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Feng L, Teng F, Li N, Zhang JC, Zhang BJ, Tsai SN, Yue XL, Gu LF, Meng GH, Deng TQ, Tong SW, Wang CM, Li Y, Shi W, Zeng YL, Jiang YM, Yu W, Ngai SM, An LZ, Lam HM, He JX. A reference-grade genome of the xerophyte Ammopiptanthus mongolicus sheds light on its evolution history in legumes and drought-tolerance mechanisms. PLANT COMMUNICATIONS 2024; 5:100891. [PMID: 38561965 PMCID: PMC11287142 DOI: 10.1016/j.xplc.2024.100891] [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: 09/02/2023] [Revised: 02/26/2024] [Accepted: 03/29/2024] [Indexed: 04/04/2024]
Abstract
Plants that grow in extreme environments represent unique sources of stress-resistance genes and mechanisms. Ammopiptanthus mongolicus (Leguminosae) is a xerophytic evergreen broadleaf shrub native to semi-arid and desert regions; however, its drought-tolerance mechanisms remain poorly understood. Here, we report the assembly of a reference-grade genome for A. mongolicus, describe its evolutionary history within the legume family, and examine its drought-tolerance mechanisms. The assembled genome is 843.07 Mb in length, with 98.7% of the sequences successfully anchored to the nine chromosomes of A. mongolicus. The genome is predicted to contain 47 611 protein-coding genes, and 70.71% of the genome is composed of repetitive sequences; these are dominated by transposable elements, particularly long-terminal-repeat retrotransposons. Evolutionary analyses revealed two whole-genome duplication (WGD) events at 130 and 58 million years ago (mya) that are shared by the genus Ammopiptanthus and other legumes, but no species-specific WGDs were found within this genus. Ancestral genome reconstruction revealed that the A. mongolicus genome has undergone fewer rearrangements than other genomes in the legume family, confirming its status as a "relict plant". Transcriptomic analyses demonstrated that genes involved in cuticular wax biosynthesis and transport are highly expressed, both under normal conditions and in response to polyethylene glycol-induced dehydration. Significant induction of genes related to ethylene biosynthesis and signaling was also observed in leaves under dehydration stress, suggesting that enhanced ethylene response and formation of thick waxy cuticles are two major mechanisms of drought tolerance in A. mongolicus. Ectopic expression of AmERF2, an ethylene response factor unique to A. mongolicus, can markedly increase the drought tolerance of transgenic Arabidopsis thaliana plants, demonstrating the potential for application of A. mongolicus genes in crop improvement.
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Affiliation(s)
- Lei Feng
- School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Sha Tin, New Territories, Hong Kong, China; Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou 510631, China
| | - Fei Teng
- BGI-Shenzhen Tech Co., Ltd., Beishan Industrial Zone, Yantian District, Shenzhen 518083, China
| | - Na Li
- School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Sha Tin, New Territories, Hong Kong, China
| | - Jia-Cheng Zhang
- School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Sha Tin, New Territories, Hong Kong, China
| | - Bian-Jiang Zhang
- School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Sha Tin, New Territories, Hong Kong, China
| | - Sau-Na Tsai
- School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Sha Tin, New Territories, Hong Kong, China
| | - Xiu-Le Yue
- School of Life Sciences and Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, Lanzhou University, Lanzhou 730030, China
| | - Li-Fei Gu
- School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Sha Tin, New Territories, Hong Kong, China
| | - Guang-Hua Meng
- School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Sha Tin, New Territories, Hong Kong, China
| | - Tian-Quan Deng
- BGI-Shenzhen Tech Co., Ltd., Beishan Industrial Zone, Yantian District, Shenzhen 518083, China
| | - Suk-Wah Tong
- School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Sha Tin, New Territories, Hong Kong, China
| | - Chun-Ming Wang
- School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Sha Tin, New Territories, Hong Kong, China
| | - Yan Li
- State Key Laboratory of Subtropical Silviculture, Zhejiang Agriculture and Forestry University, Hangzhou 311300, China
| | - Wei Shi
- BGI-Shenzhen Tech Co., Ltd., Beishan Industrial Zone, Yantian District, Shenzhen 518083, China
| | - Yong-Lun Zeng
- State Key Laboratory of Plant Diversity and Specialty Crops, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
| | - Yue-Ming Jiang
- Guangdong Provincial Key Laboratory of Applied Botany & Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
| | - Weichang Yu
- College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, China
| | - Sai-Ming Ngai
- School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Sha Tin, New Territories, Hong Kong, China
| | - Li-Zhe An
- School of Life Sciences and Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, Lanzhou University, Lanzhou 730030, China; State Key Laboratory of Efficient Production of Forest Resources, Beijing Forestry University, Beijing 100083, China.
| | - Hon-Ming Lam
- School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Sha Tin, New Territories, Hong Kong, China.
| | - Jun-Xian He
- School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Sha Tin, New Territories, Hong Kong, China.
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Wei X, Chen M, Zhang Q, Gong J, Liu J, Yong K, Wang Q, Fan J, Chen S, Hua H, Luo Z, Zhao X, Wang X, Li W, Cong J, Yu X, Wang Z, Huang R, Chen J, Zhou X, Qiu J, Xu P, Murray J, Wang H, Xu Y, Xu C, Xu G, Yang J, Han B, Huang X. Genomic investigation of 18,421 lines reveals the genetic architecture of rice. Science 2024; 385:eadm8762. [PMID: 38963845 DOI: 10.1126/science.adm8762] [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: 11/10/2023] [Accepted: 04/29/2024] [Indexed: 07/06/2024]
Abstract
Understanding how numerous quantitative trait loci (QTL) shape phenotypic variation is an important question in genetics. To address this, we established a permanent population of 18,421 (18K) rice lines with reduced population structure. We generated reference-level genome assemblies of the founders and genotyped all 18K-rice lines through whole-genome sequencing. Through high-resolution mapping, 96 high-quality candidate genes contributing to variation in 16 traits were identified, including OsMADS22 and OsFTL1 verified as causal genes for panicle number and heading date, respectively. We identified epistatic QTL pairs and constructed a genetic interaction network with 19 genes serving as hubs. Overall, 170 masking epistasis pairs were characterized, serving as an important factor contributing to genetic background effects across diverse varieties. The work provides a basis to guide grain yield and quality improvements in rice.
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Affiliation(s)
- Xin Wei
- Shanghai Key Laboratory of Plant Molecular Sciences, Development Center of Plant Germplasm Resources, College of Life Sciences, Shanghai Normal University, Shanghai 200234, China
| | - Mengjiao Chen
- Shanghai Key Laboratory of Plant Molecular Sciences, Development Center of Plant Germplasm Resources, College of Life Sciences, Shanghai Normal University, Shanghai 200234, China
| | - Qi Zhang
- Shanghai Key Laboratory of Plant Molecular Sciences, Development Center of Plant Germplasm Resources, College of Life Sciences, Shanghai Normal University, Shanghai 200234, China
| | - Junyi Gong
- State Key Laboratory of Rice Biology and Breeding, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou 310006, China
| | - Jie Liu
- Shanghai Key Laboratory of Plant Molecular Sciences, Development Center of Plant Germplasm Resources, College of Life Sciences, Shanghai Normal University, Shanghai 200234, China
| | - Kaicheng Yong
- Shanghai Key Laboratory of Plant Molecular Sciences, Development Center of Plant Germplasm Resources, College of Life Sciences, Shanghai Normal University, Shanghai 200234, China
| | - Qin Wang
- Shanghai Key Laboratory of Plant Molecular Sciences, Development Center of Plant Germplasm Resources, College of Life Sciences, Shanghai Normal University, Shanghai 200234, China
| | - Jiongjiong Fan
- State Key Laboratory of Rice Biology and Breeding, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou 310006, China
| | - Suhui Chen
- Shanghai Key Laboratory of Plant Molecular Sciences, Development Center of Plant Germplasm Resources, College of Life Sciences, Shanghai Normal University, Shanghai 200234, China
| | - Hua Hua
- Shanghai Key Laboratory of Plant Molecular Sciences, Development Center of Plant Germplasm Resources, College of Life Sciences, Shanghai Normal University, Shanghai 200234, China
| | - Zhaowei Luo
- Shanghai Key Laboratory of Plant Molecular Sciences, Development Center of Plant Germplasm Resources, College of Life Sciences, Shanghai Normal University, Shanghai 200234, China
| | - Xiaoyan Zhao
- Shanghai Key Laboratory of Plant Molecular Sciences, Development Center of Plant Germplasm Resources, College of Life Sciences, Shanghai Normal University, Shanghai 200234, China
| | - Xuan Wang
- Shanghai Key Laboratory of Plant Molecular Sciences, Development Center of Plant Germplasm Resources, College of Life Sciences, Shanghai Normal University, Shanghai 200234, China
| | - Wei Li
- Shanghai Key Laboratory of Plant Molecular Sciences, Development Center of Plant Germplasm Resources, College of Life Sciences, Shanghai Normal University, Shanghai 200234, China
| | - Jia Cong
- Shanghai Key Laboratory of Plant Molecular Sciences, Development Center of Plant Germplasm Resources, College of Life Sciences, Shanghai Normal University, Shanghai 200234, China
| | - Xiting Yu
- Shanghai Key Laboratory of Plant Molecular Sciences, Development Center of Plant Germplasm Resources, College of Life Sciences, Shanghai Normal University, Shanghai 200234, China
| | - Zhihan Wang
- Shanghai Key Laboratory of Plant Molecular Sciences, Development Center of Plant Germplasm Resources, College of Life Sciences, Shanghai Normal University, Shanghai 200234, China
| | - Ruipeng Huang
- Shanghai Key Laboratory of Plant Molecular Sciences, Development Center of Plant Germplasm Resources, College of Life Sciences, Shanghai Normal University, Shanghai 200234, China
| | - Jiaxin Chen
- Shanghai Key Laboratory of Plant Molecular Sciences, Development Center of Plant Germplasm Resources, College of Life Sciences, Shanghai Normal University, Shanghai 200234, China
| | - Xiaoyi Zhou
- Shanghai Key Laboratory of Plant Molecular Sciences, Development Center of Plant Germplasm Resources, College of Life Sciences, Shanghai Normal University, Shanghai 200234, China
| | - Jie Qiu
- Shanghai Key Laboratory of Plant Molecular Sciences, Development Center of Plant Germplasm Resources, College of Life Sciences, Shanghai Normal University, Shanghai 200234, China
| | - Ping Xu
- Shanghai Key Laboratory of Plant Molecular Sciences, Development Center of Plant Germplasm Resources, College of Life Sciences, Shanghai Normal University, Shanghai 200234, China
| | - Jeremy Murray
- CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200233, China
| | - Hai Wang
- State Key Laboratory of Plant Physiology and Biochemistry, College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
| | - Yang Xu
- Key Laboratory of Plant Functional Genomics of Ministry of Education, College of Agriculture, Yangzhou University, Yangzhou 225009, China
| | - Chenwu Xu
- Key Laboratory of Plant Functional Genomics of Ministry of Education, College of Agriculture, Yangzhou University, Yangzhou 225009, China
| | - Gen Xu
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE 68583, USA
| | - Jinliang Yang
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE 68583, USA
| | - Bin Han
- CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200233, China
| | - Xuehui Huang
- Shanghai Key Laboratory of Plant Molecular Sciences, Development Center of Plant Germplasm Resources, College of Life Sciences, Shanghai Normal University, Shanghai 200234, China
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48
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Zhang ZX, Shang YX, Zhang MY, Zhang JJ, Geng Y, Xia JW, Zhang XG. Phylogenomics, taxonomy and morphological characters of the Microdochiaceae (Xylariales, Sordariomycetes). MycoKeys 2024; 106:303-325. [PMID: 38993357 PMCID: PMC11237568 DOI: 10.3897/mycokeys.106.127355] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2024] [Accepted: 06/20/2024] [Indexed: 07/13/2024] Open
Abstract
Species of the family Microdochiaceae (Xylariales, Sordariomycetes) have been reported from worldwide, and collected from different plant hosts. The proposed new genus and two new species, viz., Macroidriella gen. nov., M.bambusae sp. nov. and Microdochiumaustrale sp. nov., are based on multi-locus phylogenies from a combined dataset of ITS rDNA, LSU, RPB2 and TUB2 with morphological characteristics. Microdochiumsinense has been collected from diseased leaves of Phragmitesaustralis and this is the first report of the fungus on this host plant. Simultaneously, we annotated 10,372 to 11,863 genes, identified 4,909 single-copy orthologous genes, and conducted phylogenomic analysis based on genomic data. A gene family analysis was performed and it will expand the understanding of the evolutionary history and biodiversity of the Microdochiaceae. The detailed descriptions and illustrations of species are provided.
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Affiliation(s)
- Zhao-Xue Zhang
- Shandong Provincial Key Laboratory for Biology of Vegetable Diseases and Insect Pests, College of Plant Protection, Shandong Agricultural University, Taian, 271018, ChinaShandong Agricultural UniversityTaianChina
| | - Yu-Xin Shang
- Shandong Provincial Key Laboratory for Biology of Vegetable Diseases and Insect Pests, College of Plant Protection, Shandong Agricultural University, Taian, 271018, ChinaShandong Agricultural UniversityTaianChina
| | - Meng-Yuan Zhang
- Shandong Provincial Key Laboratory for Biology of Vegetable Diseases and Insect Pests, College of Plant Protection, Shandong Agricultural University, Taian, 271018, ChinaShandong Agricultural UniversityTaianChina
| | - Jin-Jia Zhang
- Shandong Provincial Key Laboratory for Biology of Vegetable Diseases and Insect Pests, College of Plant Protection, Shandong Agricultural University, Taian, 271018, ChinaShandong Agricultural UniversityTaianChina
| | - Yun Geng
- Institute of Crop Germplasm Resources, Shandong Academy of Agricultural Sciences, Jinan, 250100, ChinaShandong Academy of Agricultural SciencesJinanChina
| | - Ji-Wen Xia
- Shandong Provincial Key Laboratory for Biology of Vegetable Diseases and Insect Pests, College of Plant Protection, Shandong Agricultural University, Taian, 271018, ChinaShandong Agricultural UniversityTaianChina
| | - Xiu-Guo Zhang
- Shandong Provincial Key Laboratory for Biology of Vegetable Diseases and Insect Pests, College of Plant Protection, Shandong Agricultural University, Taian, 271018, ChinaShandong Agricultural UniversityTaianChina
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49
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Occean JR, Yang N, Sun Y, Dawkins MS, Munk R, Belair C, Dar S, Anerillas C, Wang L, Shi C, Dunn C, Bernier M, Price NL, Kim JS, Cui CY, Fan J, Bhattacharyya M, De S, Maragkakis M, deCabo R, Sidoli S, Sen P. Gene body DNA hydroxymethylation restricts the magnitude of transcriptional changes during aging. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.02.15.528714. [PMID: 36824863 PMCID: PMC9949049 DOI: 10.1101/2023.02.15.528714] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/17/2023]
Abstract
DNA hydroxymethylation (5hmC), the most abundant oxidative derivative of DNA methylation, is typically enriched at enhancers and gene bodies of transcriptionally active and tissue-specific genes. Although aberrant genomic 5hmC has been implicated in age-related diseases, its functional role in aging remains unknown. Here, using mouse liver and cerebellum as model organs, we show that 5hmC accumulates in gene bodies associated with tissue-specific function and restricts the magnitude of gene expression changes with age. Mechanistically, 5hmC decreases the binding of splicing associated factors and correlates with age-related alternative splicing events. We found that various age-related contexts, such as prolonged quiescence and senescence, drive the accumulation of 5hmC with age. We provide evidence that this age-related transcriptionally restrictive function is conserved in mouse and human tissues. Our findings reveal that 5hmC regulates tissue-specific function and may play a role in longevity.
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50
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Li Z, Chen F, Chen L, Liu J, Tseng D, Hadi F, Omarjee S, Kishore K, Kent J, Kirkpatrick J, D’Santos C, Lawson M, Gertz J, Sikora MJ, McDonnell DP, Carroll JS, Polyak K, Oesterreich S, Lee AV. EstroGene2.0: A multi-omic database of response to estrogens, ER-modulators, and resistance to endocrine therapies in breast cancer. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.28.601163. [PMID: 39005294 PMCID: PMC11244912 DOI: 10.1101/2024.06.28.601163] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/16/2024]
Abstract
Endocrine therapies targeting the estrogen receptor (ER/ESR1) are the cornerstone to treat ER-positive breast cancers patients, but resistance often limits their effectiveness. Understanding the molecular mechanisms is thus key to optimize the existing drugs and to develop new ER-modulators. Notable progress has been made although the fragmented way data is reported has reduced their potential impact. Here, we introduce EstroGene2.0, an expanded database of its precursor 1.0 version. EstroGene2.0 focusses on response and resistance to endocrine therapies in breast cancer models. Incorporating multi-omic profiling of 361 experiments from 212 studies across 28 cell lines, a user-friendly browser offers comprehensive data visualization and metadata mining capabilities (https://estrogeneii.web.app/). Taking advantage of the harmonized data collection, our follow-up meta-analysis revealed substantial diversity in response to different classes of ER-modulators including SERMs, SERDs, SERCA and LDD/PROTAC. Notably, endocrine resistant models exhibit a spectrum of transcriptomic alterations including a contra-directional shift in ER and interferon signaling, which is recapitulated clinically. Furthermore, dissecting multiple ESR1-mutant cell models revealed the different clinical relevance of genome-edited versus ectopic overexpression model engineering and identified high-confidence mutant-ER targets, such as NPY1R. These examples demonstrate how EstroGene2.0 helps investigate breast cancer's response to endocrine therapies and explore resistance mechanisms.
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Affiliation(s)
- Zheqi Li
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Fangyuan Chen
- School of Medicine, Tsinghua University, Beijing, China
- Women’s Cancer Research Center, UPMC Hillman Cancer Center, Pittsburgh PA, USA
| | - Li Chen
- Computational Biology Department, Carnegie Mellon University, Pittsburgh PA, USA
| | - Jiebin Liu
- Women’s Cancer Research Center, UPMC Hillman Cancer Center, Pittsburgh PA, USA
- Medical Scientist Training Program, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Danielle Tseng
- Women’s Cancer Research Center, UPMC Hillman Cancer Center, Pittsburgh PA, USA
| | | | - Soleilmane Omarjee
- Cancer Research UK, Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Kamal Kishore
- Cancer Research UK, Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Joshua Kent
- Cancer Research UK, Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Joanna Kirkpatrick
- Cancer Research UK, Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Clive D’Santos
- Cancer Research UK, Cambridge Institute, University of Cambridge, Cambridge, UK
| | | | - Jason Gertz
- Department of Oncological Sciences, University of Utah, Salt Lake City, UT, USA
| | - Matthew J. Sikora
- Department of Pathology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Donald P. McDonnell
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, NC, USA
| | - Jason S. Carroll
- Cancer Research UK, Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Kornelia Polyak
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Steffi Oesterreich
- Women’s Cancer Research Center, UPMC Hillman Cancer Center, Pittsburgh PA, USA
- Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh PA, USA
| | - Adrian V. Lee
- Women’s Cancer Research Center, UPMC Hillman Cancer Center, Pittsburgh PA, USA
- Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh PA, USA
- Institute for Precision Medicine, University of Pittsburgh, Pittsburgh, PA, USA
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