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Wu J, Liu F, Jiao J, Luo H, Fan S, Liu J, Wang H, Cui N, Zhao N, Qu Q, Kuraku S, Huang Z, Xu L. Comparative genomics illuminates karyotype and sex chromosome evolution of sharks. CELL GENOMICS 2024; 4:100607. [PMID: 38996479 PMCID: PMC11406177 DOI: 10.1016/j.xgen.2024.100607] [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: 01/15/2024] [Revised: 05/01/2024] [Accepted: 06/19/2024] [Indexed: 07/14/2024]
Abstract
Chondrichthyes is an important lineage to reconstruct the evolutionary history of vertebrates. Here, we analyzed genome synteny for six chondrichthyan chromosome-level genomes. Our comparative analysis reveals a slow evolutionary rate of chromosomal changes, with infrequent but independent fusions observed in sharks, skates, and chimaeras. The chondrichthyan common ancestor had a proto-vertebrate-like karyotype, including the presence of 18 microchromosome pairs. The X chromosome is a conversed microchromosome shared by all sharks, suggesting a likely common origin of the sex chromosome at least 181 million years ago. We characterized the Y chromosomes of two sharks that are highly differentiated from the X except for a small young evolutionary stratum and a small pseudoautosomal region. We found that shark sex chromosomes lack global dosage compensation but that dosage-sensitive genes are locally compensated. Our study on shark chromosome evolution enhances our understanding of shark sex chromosomes and vertebrate chromosome evolution.
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Affiliation(s)
- Jiahong Wu
- Integrative Science Center of Germplasm Creation in Western China (Chongqing) Science City, MOE Key Laboratory of Freshwater Fish Reproduction and Development, School of Life Sciences, Southwest University, Chongqing 400715, China
| | - Fujiang Liu
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, China
| | - Jie Jiao
- Integrative Science Center of Germplasm Creation in Western China (Chongqing) Science City, MOE Key Laboratory of Freshwater Fish Reproduction and Development, School of Life Sciences, Southwest University, Chongqing 400715, China
| | - Haoran Luo
- Integrative Science Center of Germplasm Creation in Western China (Chongqing) Science City, MOE Key Laboratory of Freshwater Fish Reproduction and Development, School of Life Sciences, Southwest University, Chongqing 400715, China; Key Laboratory of Ministry of Education for the Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen 361102, China
| | - Shiyu Fan
- Integrative Science Center of Germplasm Creation in Western China (Chongqing) Science City, MOE Key Laboratory of Freshwater Fish Reproduction and Development, School of Life Sciences, Southwest University, Chongqing 400715, China
| | - Jiao Liu
- Integrative Science Center of Germplasm Creation in Western China (Chongqing) Science City, MOE Key Laboratory of Freshwater Fish Reproduction and Development, School of Life Sciences, Southwest University, Chongqing 400715, China
| | - Hongxiang Wang
- Integrative Science Center of Germplasm Creation in Western China (Chongqing) Science City, MOE Key Laboratory of Freshwater Fish Reproduction and Development, School of Life Sciences, Southwest University, Chongqing 400715, China
| | - Ning Cui
- Integrative Science Center of Germplasm Creation in Western China (Chongqing) Science City, MOE Key Laboratory of Freshwater Fish Reproduction and Development, School of Life Sciences, Southwest University, Chongqing 400715, China
| | - Ning Zhao
- Integrative Science Center of Germplasm Creation in Western China (Chongqing) Science City, MOE Key Laboratory of Freshwater Fish Reproduction and Development, School of Life Sciences, Southwest University, Chongqing 400715, China; Key Laboratory of Animal Genetics and Breeding and Molecular Design of Jiangsu Province, College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
| | - Qingming Qu
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, China
| | - Shigehiro Kuraku
- Molecular Life History Laboratory, Department of Genomics and Evolutionary Biology, National Institute of Genetics, Shizuoka, Japan; Department of Genetics, Sokendai (Graduate University for Advanced Studies), Mishima, Japan
| | - Zhen Huang
- Fujian-Macao Science and Technology Cooperation Base of Traditional Chinese Medicine-Oriented Chronic Disease Prevention and Treatment, Innovation and Transformation Center, Fujian University of Traditional Chinese Medicine, Fuzhou 350108, China
| | - Luohao Xu
- Integrative Science Center of Germplasm Creation in Western China (Chongqing) Science City, MOE Key Laboratory of Freshwater Fish Reproduction and Development, School of Life Sciences, Southwest University, Chongqing 400715, China.
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Zeng X, Yi Z, Zhang X, Du Y, Li Y, Zhou Z, Chen S, Zhao H, Yang S, Wang Y, Chen G. Chromosome-level scaffolding of haplotype-resolved assemblies using Hi-C data without reference genomes. NATURE PLANTS 2024; 10:1184-1200. [PMID: 39103456 DOI: 10.1038/s41477-024-01755-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Accepted: 07/01/2024] [Indexed: 08/07/2024]
Abstract
Scaffolding is crucial for constructing most chromosome-level genomes. The high-throughput chromatin conformation capture (Hi-C) technology has become the primary scaffolding strategy due to its convenience and cost-effectiveness. As sequencing technologies and assembly algorithms advance, constructing haplotype-resolved genomes is increasingly preferred because haplotypes can provide additional genetic information on allelic and non-allelic variations. ALLHiC is a widely used allele-aware scaffolding tool designed for this purpose. However, its dependence on chromosome-level reference genomes and a higher chromosome misassignment rate still impede the unravelling of haplotype-resolved genomes. Here we present HapHiC, a reference-independent allele-aware scaffolding tool with superior performance on chromosome assignment as well as contig ordering and orientation. In addition, we provide new insights into the challenges in allele-aware scaffolding by conducting comprehensive analyses on various adverse factors. Finally, with the help of HapHiC, we constructed the haplotype-resolved allotriploid genome for Miscanthus × giganteus, an important lignocellulosic bioenergy crop.
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Affiliation(s)
- Xiaofei Zeng
- Department of Human Cell Biology and Genetics, Joint Laboratory of Guangdong-Hong Kong Universities for Vascular Homeostasis and Diseases, School of Medicine, Southern University of Science and Technology, Shenzhen, China.
- National Key Laboratory for Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China.
| | - Zili Yi
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, China
- Hunan Engineering Laboratory for Ecological Application of Miscanthus Resources, Changsha, China
| | - Xingtan Zhang
- National Key Laboratory for Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Yuhui Du
- Department of Human Cell Biology and Genetics, Joint Laboratory of Guangdong-Hong Kong Universities for Vascular Homeostasis and Diseases, School of Medicine, Southern University of Science and Technology, Shenzhen, China
| | - Yu Li
- Department of Human Cell Biology and Genetics, Joint Laboratory of Guangdong-Hong Kong Universities for Vascular Homeostasis and Diseases, School of Medicine, Southern University of Science and Technology, Shenzhen, China
| | - Zhiqing Zhou
- Department of Human Cell Biology and Genetics, Joint Laboratory of Guangdong-Hong Kong Universities for Vascular Homeostasis and Diseases, School of Medicine, Southern University of Science and Technology, Shenzhen, China
| | - Sijie Chen
- Department of Human Cell Biology and Genetics, Joint Laboratory of Guangdong-Hong Kong Universities for Vascular Homeostasis and Diseases, School of Medicine, Southern University of Science and Technology, Shenzhen, China
| | - Huijie Zhao
- Department of Human Cell Biology and Genetics, Joint Laboratory of Guangdong-Hong Kong Universities for Vascular Homeostasis and Diseases, School of Medicine, Southern University of Science and Technology, Shenzhen, China
| | - Sai Yang
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, China
- Hunan Engineering Laboratory for Ecological Application of Miscanthus Resources, Changsha, China
| | - Yibin Wang
- National Key Laboratory for Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Guoan Chen
- Department of Human Cell Biology and Genetics, Joint Laboratory of Guangdong-Hong Kong Universities for Vascular Homeostasis and Diseases, School of Medicine, Southern University of Science and Technology, Shenzhen, China.
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Nie B, Chen X, Hou Z, Guo M, Li C, Sun W, Ji J, Zang L, Yang S, Fan P, Zhang W, Li H, Tan Y, Li W, Wang L. Haplotype-phased genome unveils the butylphthalide biosynthesis and homoploid hybrid origin of Ligusticum chuanxiong. SCIENCE ADVANCES 2024; 10:eadj6547. [PMID: 38324681 PMCID: PMC10849598 DOI: 10.1126/sciadv.adj6547] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2023] [Accepted: 01/05/2024] [Indexed: 02/09/2024]
Abstract
Butylphthalide is one of the first-line drugs for ischemic stroke therapy, while no biosynthetic enzyme for butylphthalide has been reported. Here, we present a haplotype-resolved genome of Ligusticum chuanxiong, a long-cultivated and phthalide-rich medicinal plant in Apiaceae. On the basis of comprehensive screening, four Fe(II)- and 2-oxoglutarate-dependent dioxygenases and two CYPs were mined and further biochemically verified as phthalide C-4/C-5 desaturases (P4,5Ds) that effectively promoted the forming of (S)-3-n-butylphthalide and butylidenephthalide. The substrate promiscuity and functional redundancy featured for P4,5Ds may contribute to the high phthalide diversity in L. chuanxiong. Notably, comparative genomic evidence supported L. chuanxiong as a homoploid hybrid with Ligusticum sinense as a potential parent. The two haplotypes demonstrated exceptional structure variance and diverged around 3.42 million years ago. Our study is an icebreaker for the dissection of phthalide biosynthetic pathway and reveals the hybrid origin of L. chuanxiong, which will facilitate the metabolic engineering for (S)-3-n-butylphthalide production and breeding for L. chuanxiong.
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Affiliation(s)
- Bao Nie
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Xueqing Chen
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Zhuangwei Hou
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Miaoxian Guo
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Cheng Li
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Wenkai Sun
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Jiaojiao Ji
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Lanlan Zang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Song Yang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Pengxiang Fan
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310063, China
| | - Wenhao Zhang
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Hang Li
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Yuzhu Tan
- State Key Laboratory of Southwestern Chinese Medicine Resources, Pharmacy College, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
| | - Wei Li
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Li Wang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
- Key Laboratory for Quality Ensurance and Sustainable Use of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
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Nestor BJ, Bayer PE, Fernandez CGT, Edwards D, Finnegan PM. Approaches to increase the validity of gene family identification using manual homology search tools. Genetica 2023; 151:325-338. [PMID: 37817002 PMCID: PMC10692271 DOI: 10.1007/s10709-023-00196-8] [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: 06/07/2023] [Accepted: 10/01/2023] [Indexed: 10/12/2023]
Abstract
Identifying homologs is an important process in the analysis of genetic patterns underlying traits and evolutionary relationships among species. Analysis of gene families is often used to form and support hypotheses on genetic patterns such as gene presence, absence, or functional divergence which underlie traits examined in functional studies. These analyses often require precise identification of all members in a targeted gene family. Manual pipelines where homology search and orthology assignment tools are used separately are the most common approach for identifying small gene families where accurate identification of all members is important. The ability to curate sequences between steps in manual pipelines allows for simple and precise identification of all possible gene family members. However, the validity of such manual pipeline analyses is often decreased by inappropriate approaches to homology searches including too relaxed or stringent statistical thresholds, inappropriate query sequences, homology classification based on sequence similarity alone, and low-quality proteome or genome sequences. In this article, we propose several approaches to mitigate these issues and allow for precise identification of gene family members and support for hypotheses linking genetic patterns to functional traits.
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Affiliation(s)
- Benjamin J Nestor
- School of Biological Sciences, University of Western Australia, Perth, WA, 6009, Australia.
- Centre for Applied Bioinformatics, University of Western Australia, Perth, WA, 6009, Australia.
| | - Philipp E Bayer
- School of Biological Sciences, University of Western Australia, Perth, WA, 6009, Australia
- Centre for Applied Bioinformatics, University of Western Australia, Perth, WA, 6009, Australia
| | - Cassandria G Tay Fernandez
- School of Biological Sciences, University of Western Australia, Perth, WA, 6009, Australia
- Centre for Applied Bioinformatics, University of Western Australia, Perth, WA, 6009, Australia
| | - David Edwards
- School of Biological Sciences, University of Western Australia, Perth, WA, 6009, Australia
- Centre for Applied Bioinformatics, University of Western Australia, Perth, WA, 6009, Australia
| | - Patrick M Finnegan
- School of Biological Sciences, University of Western Australia, Perth, WA, 6009, Australia
- Centre for Applied Bioinformatics, University of Western Australia, Perth, WA, 6009, Australia
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5
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Colbert JB, Coleman HD. Functional Diversification and the Plant Secondary Cell Wall. J Mol Evol 2023; 91:761-772. [PMID: 37979044 DOI: 10.1007/s00239-023-10145-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: 05/25/2023] [Accepted: 11/09/2023] [Indexed: 11/19/2023]
Abstract
Much evidence exists suggesting the presence of genetic functional diversification in plants, though literature associated with the role of functional diversification in the evolution of the plant secondary cell wall (SCW) has sparsely been compiled and reviewed in a recent context. This review aims to elucidate, through the examination of gene phylogenies associated with its biosynthesis and maintenance, the role of functional diversification in shaping the critical, dynamic, and characteristic organelle, the secondary cell wall. It will be asserted that gene families resulting from gene duplication and subsequent functional divergence are present and are heavily involved in SCW biosynthesis and maintenance. Furthermore, diversification will be presented as a significant driver behind the evolution of the many functional characteristics of the SCW. The structure and function of the plant cell wall and its constituents will first be explored, followed by a discussion on the phenomenon of gene duplication and the resulting genetic functional divergence that can emerge. Finally, the major constituents of the SCW and their individual relationships with duplication and divergence will be reviewed to the extent of current knowledge on the subject.
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Affiliation(s)
- Joseph B Colbert
- Biology Department, Syracuse University, 107 College Place, Syracuse, NY, 13244, USA
| | - Heather D Coleman
- Biology Department, Syracuse University, 107 College Place, Syracuse, NY, 13244, USA.
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6
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Zhang Y, Lu HW, Ruan J. GAEP: a comprehensive genome assembly evaluating pipeline. J Genet Genomics 2023; 50:747-754. [PMID: 37245652 DOI: 10.1016/j.jgg.2023.05.009] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Revised: 05/19/2023] [Accepted: 05/23/2023] [Indexed: 05/30/2023]
Abstract
With the rapid development of sequencing technologies, especially the maturity of third-generation sequencing technologies, there has been a significant increase in the number and quality of published genome assemblies. The emergence of these high-quality genomes has raised higher requirements for genome evaluation. Although numerous computational methods have been developed to evaluate assembly quality from various perspectives, the selective use of these evaluation methods can be arbitrary and inconvenient for fairly comparing the assembly quality. To address this issue, we have developed the Genome Assembly Evaluating Pipeline (GAEP), which provides a comprehensive assessment pipeline for evaluating genome quality from multiple perspectives, including continuity, completeness, and correctness. Additionally, GAEP includes new functions for detecting misassemblies and evaluating the assembly redundancy, which performs well in our testing. GAEP is publicly available at https://github.com/zy-optimistic/GAEP under the GPL3.0 License. With GAEP, users can quickly obtain accurate and reliable evaluation results, facilitating the comparison and selection of high-quality genome assemblies.
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Affiliation(s)
- Yong Zhang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong 518120, China
| | - Hong-Wei Lu
- State Key Laboratory of Rice Biology and Breeding, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou, Zhejiang 311401, China
| | - Jue Ruan
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong 518120, China.
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Xing L, Wang M, He Q, Zhang H, Liang H, Zhou Q, Liu Y, Liu Z, Wang Y, Du C, Xiao Y, Liu J, Li W, Liu G, Du H. Differential subgenome expression underlies biomass accumulation in allotetraploid Pennisetum giganteum. BMC Biol 2023; 21:161. [PMID: 37480118 PMCID: PMC10362693 DOI: 10.1186/s12915-023-01643-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: 01/11/2023] [Accepted: 06/06/2023] [Indexed: 07/23/2023] Open
Abstract
BACKGROUND Pennisetum giganteum (AABB, 2n = 4x = 28) is a C4 plant in the genus Pennisetum with origin in Africa but currently also grown in Asia and America. It is a crucial forage and potential energy grass with significant advantages in yield, stress resistance, and environmental adaptation. However, the mechanisms underlying these advantageous traits remain largely unexplored. Here, we present a high-quality genome assembly of the allotetraploid P. giganteum aiming at providing insights into biomass accumulation. RESULTS Our assembly has a genome size 2.03 Gb and contig N50 of 88.47 Mb that was further divided into A and B subgenomes. Genome evolution analysis revealed the evolutionary relationships across the Panicoideae subfamily lineages and identified numerous genome rearrangements that had occurred in P. giganteum. Comparative genomic analysis showed functional differentiation between the subgenomes. Transcriptome analysis found no subgenome dominance at the overall gene expression level; however, differentially expressed homoeologous genes and homoeolog-specific expressed genes between the two subgenomes were identified, suggesting that complementary effects between the A and B subgenomes contributed to biomass accumulation of P. giganteum. Besides, C4 photosynthesis-related genes were significantly expanded in P. giganteum and their sequences and expression patterns were highly conserved between the two subgenomes, implying that both subgenomes contributed greatly and almost equally to the highly efficient C4 photosynthesis in P. giganteum. We also identified key candidate genes in the C4 photosynthesis pathway that showed sustained high expression across all developmental stages of P. giganteum. CONCLUSIONS Our study provides important genomic resources for elucidating the genetic basis of advantageous traits in polyploid species, and facilitates further functional genomics research and genetic improvement of P. giganteum.
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Affiliation(s)
- Longsheng Xing
- College of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding, 071000, China
- Hebei Basic Science Center for Biotic Interaction, Baoding, 071000, China
| | - Meijia Wang
- College of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding, 071000, China
| | - Qiang He
- College of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding, 071000, China
- Hebei Basic Science Center for Biotic Interaction, Baoding, 071000, China
| | - Hongyu Zhang
- College of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding, 071000, China
| | - Hanfei Liang
- College of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding, 071000, China
| | - Qinghong Zhou
- College of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding, 071000, China
| | - Yu Liu
- College of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding, 071000, China
| | - Ze Liu
- College of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding, 071000, China
| | - Yu Wang
- College of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding, 071000, China
| | - Cailian Du
- College of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding, 071000, China
| | - Yao Xiao
- College of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding, 071000, China
| | - Jianan Liu
- College of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding, 071000, China
| | - Wei Li
- College of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding, 071000, China
- Hebei Basic Science Center for Biotic Interaction, Baoding, 071000, China
| | - Guixia Liu
- College of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding, 071000, China.
- Hebei Basic Science Center for Biotic Interaction, Baoding, 071000, China.
| | - Huilong Du
- College of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding, 071000, China.
- Hebei Basic Science Center for Biotic Interaction, Baoding, 071000, China.
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8
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Xu L, Wang Y, Dong J, Zhang W, Tang M, Zhang W, Wang K, Chen Y, Zhang X, He Q, Zhang X, Wang K, Wang L, Ma Y, Xia K, Liu L. A chromosome-level genome assembly of radish (Raphanus sativus L.) reveals insights into genome adaptation and differential bolting regulation. PLANT BIOTECHNOLOGY JOURNAL 2023; 21:990-1004. [PMID: 36648398 PMCID: PMC10106849 DOI: 10.1111/pbi.14011] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Revised: 11/29/2022] [Accepted: 01/03/2023] [Indexed: 05/04/2023]
Abstract
High-quality radish (Raphanus sativus) genome represents a valuable resource for agronomical trait improvements and understanding genome evolution among Brassicaceae species. However, existing radish genome assembly remains fragmentary, which greatly hampered functional genomics research and genome-assisted breeding. Here, using a NAU-LB radish inbred line, we generated a reference genome of 476.32 Mb with a scaffold N50 of 56.88 Mb by incorporating Illumina, PacBio and BioNano optical mapping techniques. Utilizing Hi-C data, 448.12 Mb (94.08%) of the assembled sequences were anchored to nine radish chromosomes with 40 306 protein-coding genes annotated. In total, 249.14 Mb (52.31%) comprised the repetitive sequences, among which long terminal repeats (LTRs, 30.31%) were the most abundant class. Beyond confirming the whole-genome triplication (WGT) event in R. sativus lineage, we found several tandem arrayed genes were involved in stress response process, which may account for the distinctive phenotype of high disease resistance in R. sativus. By comparing against the existing Xin-li-mei radish genome, a total of 2 108 573 SNPs, 7740 large insertions, 7757 deletions and 84 inversions were identified. Interestingly, a 647-bp insertion in the promoter of RsVRN1 gene can be directly bound by the DOF transcription repressor RsCDF3, resulting into its low promoter activity and late-bolting phenotype of NAU-LB cultivar. Importantly, introgression of this 647-bp insertion allele, RsVRN1In-536 , into early-bolting genotype could contribute to delayed bolting time, indicating that it is a potential genetic resource for radish late-bolting breeding. Together, this genome resource provides valuable information to facilitate comparative genomic analysis and accelerate genome-guided breeding and improvement in radish.
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Affiliation(s)
- Liang Xu
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Horticultural Crop Biology and Genetic Improvement (East China) of MOAR, College of HorticultureNanjing Agricultural UniversityNanjingChina
| | - Yan Wang
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Horticultural Crop Biology and Genetic Improvement (East China) of MOAR, College of HorticultureNanjing Agricultural UniversityNanjingChina
| | - Junhui Dong
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Horticultural Crop Biology and Genetic Improvement (East China) of MOAR, College of HorticultureNanjing Agricultural UniversityNanjingChina
| | - Wei Zhang
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Horticultural Crop Biology and Genetic Improvement (East China) of MOAR, College of HorticultureNanjing Agricultural UniversityNanjingChina
- College of Horticulture and Landscape ArchitectureYangzhou UniversityYangzhouChina
| | - Mingjia Tang
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Horticultural Crop Biology and Genetic Improvement (East China) of MOAR, College of HorticultureNanjing Agricultural UniversityNanjingChina
| | - Weilan Zhang
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Horticultural Crop Biology and Genetic Improvement (East China) of MOAR, College of HorticultureNanjing Agricultural UniversityNanjingChina
| | - Kai Wang
- School of Life SciencesNantong UniversityNantongChina
| | - Yinglong Chen
- The UWA Institute of Agriculture, and School of Agriculture and EnvironmentThe University of Western AustraliaPerthWAAustralia
| | - Xiaoli Zhang
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Horticultural Crop Biology and Genetic Improvement (East China) of MOAR, College of HorticultureNanjing Agricultural UniversityNanjingChina
| | - Qing He
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Horticultural Crop Biology and Genetic Improvement (East China) of MOAR, College of HorticultureNanjing Agricultural UniversityNanjingChina
| | - Xinyu Zhang
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Horticultural Crop Biology and Genetic Improvement (East China) of MOAR, College of HorticultureNanjing Agricultural UniversityNanjingChina
| | - Kai Wang
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Horticultural Crop Biology and Genetic Improvement (East China) of MOAR, College of HorticultureNanjing Agricultural UniversityNanjingChina
| | - Lun Wang
- College of Horticulture and Landscape ArchitectureYangzhou UniversityYangzhouChina
| | - Yinbo Ma
- College of Horticulture and Landscape ArchitectureYangzhou UniversityYangzhouChina
| | - Kai Xia
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Horticultural Crop Biology and Genetic Improvement (East China) of MOAR, College of HorticultureNanjing Agricultural UniversityNanjingChina
| | - Liwang Liu
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Horticultural Crop Biology and Genetic Improvement (East China) of MOAR, College of HorticultureNanjing Agricultural UniversityNanjingChina
- College of Horticulture and Landscape ArchitectureYangzhou UniversityYangzhouChina
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9
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Kui L, Majeed A, Wang X, Yang Z, Chen J, He L, Di Y, Li X, Qian Z, Jiao Y, Wang G, Liu L, Xu R, Gu S, Yang Q, Chen S, Lou H, Meng Y, Xie L, Xu F, Shen Q, Singh A, Gruber K, Pan Y, Hao T, Dong Y, Li F. A chromosome-level genome assembly for Erianthus fulvus provides insights into its biofuel potential and facilitates breeding for improvement of sugarcane. PLANT COMMUNICATIONS 2023:100562. [PMID: 36814384 PMCID: PMC10363513 DOI: 10.1016/j.xplc.2023.100562] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Revised: 12/21/2022] [Accepted: 02/16/2023] [Indexed: 06/18/2023]
Abstract
Erianthus produces substantial biomass, exhibits a good Brix value, and shows wide environmental adaptability, making it a potential biofuel plant. In contrast to closely related sorghum and sugarcane, Erianthus can grow in degraded soils, thus releasing pressure on agricultural lands used for biofuel production. However, the lack of genomic resources for Erianthus hinders its genetic improvement, thus limiting its potential for biofuel production. In the present study, we generated a chromosome-scale reference genome for Erianthus fulvus Nees. The genome size estimated by flow cytometry was 937 Mb, and the assembled genome size was 902 Mb, covering 96.26% of the estimated genome size. A total of 35 065 protein-coding genes were predicted, and 67.89% of the genome was found to be repetitive. A recent whole-genome duplication occurred approximately 74.10 million years ago in the E. fulvus genome. Phylogenetic analysis showed that E. fulvus is evolutionarily closer to S. spontaneum and diverged after S. bicolor. Three of the 10 chromosomes of E. fulvus formed through rearrangements of ancestral chromosomes. Phylogenetic reconstruction of the Saccharum complex revealed a polyphyletic origin of the complex and a sister relationship of E. fulvus with Saccharum sp., excluding S. arundinaceum. On the basis of the four amino acid residues that provide substrate specificity, the E. fulvus SWEET proteins were classified as mono- and disaccharide sugar transporters. Ortho-QTL genes identified for 10 biofuel-related traits may aid in the rapid screening of E. fulvus populations to enhance breeding programs for improved biofuel production. The results of this study provide valuable insights for breeding programs aimed at improving biofuel production in E. fulvus and enhancing sugarcane introgression programs.
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Affiliation(s)
- Ling Kui
- Sugarcane Research Institute of Yunnan Agricultural University, Kunming, Yunnan 650201, China; Shenzhen Qianhai Shekou Free Trade Zone Hospital, Shenzhen 518067, China
| | - Aasim Majeed
- Plant Molecular Genetics Laboratory, School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, India
| | - Xianhong Wang
- Sugarcane Research Institute of Yunnan Agricultural University, Kunming, Yunnan 650201, China; College of Agronomy and Biotechnology of Yunnan Agricultural University, Kunming, Yunnan 650201, China; The Key Laboratory of Crop Production and Smart Agriculture of Yunnan Province, Kunming, Yunnan 650201, China
| | - Zijiang Yang
- College of Agronomy and Biotechnology of Yunnan Agricultural University, Kunming, Yunnan 650201, China
| | - Jian Chen
- International Genome Center, Jiangsu University, Zhenjiang, Jiangsu 212013, China
| | - Lilian He
- Sugarcane Research Institute of Yunnan Agricultural University, Kunming, Yunnan 650201, China; College of Agronomy and Biotechnology of Yunnan Agricultural University, Kunming, Yunnan 650201, China
| | - Yining Di
- College of Agronomy and Biotechnology of Yunnan Agricultural University, Kunming, Yunnan 650201, China
| | - Xuzhen Li
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, Yunnan 650201, China; Yunnan Plateau Characteristic Agriculture Industry Research Institute, Kunming, Yunnan 650201, China
| | - Zhenfeng Qian
- College of Agronomy and Biotechnology of Yunnan Agricultural University, Kunming, Yunnan 650201, China
| | - Yinming Jiao
- Shenzhen Qianhai Shekou Free Trade Zone Hospital, Shenzhen 518067, China
| | - Guoyun Wang
- Shenzhen Qianhai Shekou Free Trade Zone Hospital, Shenzhen 518067, China
| | - Lufeng Liu
- Sugarcane Research Institute of Yunnan Agricultural University, Kunming, Yunnan 650201, China; The Key Laboratory of Crop Production and Smart Agriculture of Yunnan Province, Kunming, Yunnan 650201, China
| | - Rong Xu
- College of Agronomy and Biotechnology of Yunnan Agricultural University, Kunming, Yunnan 650201, China
| | - Shujie Gu
- College of Agronomy and Biotechnology of Yunnan Agricultural University, Kunming, Yunnan 650201, China
| | - Qinghui Yang
- Sugarcane Research Institute of Yunnan Agricultural University, Kunming, Yunnan 650201, China; College of Agronomy and Biotechnology of Yunnan Agricultural University, Kunming, Yunnan 650201, China
| | - Shuying Chen
- Sugarcane Research Institute of Yunnan Agricultural University, Kunming, Yunnan 650201, China; College of Agronomy and Biotechnology of Yunnan Agricultural University, Kunming, Yunnan 650201, China
| | - Hongbo Lou
- Sugarcane Research Institute of Yunnan Agricultural University, Kunming, Yunnan 650201, China; College of Agronomy and Biotechnology of Yunnan Agricultural University, Kunming, Yunnan 650201, China
| | - Yu Meng
- College of Agronomy and Biotechnology of Yunnan Agricultural University, Kunming, Yunnan 650201, China
| | - Linyan Xie
- College of Agronomy and Biotechnology of Yunnan Agricultural University, Kunming, Yunnan 650201, China
| | - Fu Xu
- College of Agronomy and Biotechnology of Yunnan Agricultural University, Kunming, Yunnan 650201, China
| | - Qingqing Shen
- College of Agronomy and Biotechnology of Yunnan Agricultural University, Kunming, Yunnan 650201, China
| | - Amit Singh
- Institute of Molecular Biosciences, University of Graz, 8010 Graz, Austria
| | - Karl Gruber
- Institute of Molecular Biosciences, University of Graz, 8010 Graz, Austria
| | - Yunbing Pan
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, Yunnan 650201, China; Yunnan Plateau Characteristic Agriculture Industry Research Institute, Kunming, Yunnan 650201, China
| | - Tingting Hao
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, Yunnan 650201, China; Yunnan Plateau Characteristic Agriculture Industry Research Institute, Kunming, Yunnan 650201, China
| | - Yang Dong
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, Yunnan 650201, China; Yunnan Plateau Characteristic Agriculture Industry Research Institute, Kunming, Yunnan 650201, China.
| | - Fusheng Li
- Sugarcane Research Institute of Yunnan Agricultural University, Kunming, Yunnan 650201, China; College of Agronomy and Biotechnology of Yunnan Agricultural University, Kunming, Yunnan 650201, China; The Key Laboratory of Crop Production and Smart Agriculture of Yunnan Province, Kunming, Yunnan 650201, China.
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10
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Genome-Wide Characterization and Expression Profiling of the GRAS Gene Family in Salt and Alkali Stresses in Miscanthus sinensis. Int J Mol Sci 2022; 23:ijms232314521. [PMID: 36498850 PMCID: PMC9737823 DOI: 10.3390/ijms232314521] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 11/10/2022] [Accepted: 11/17/2022] [Indexed: 11/23/2022] Open
Abstract
The GRAS family genes encode plant-specific transcription factors that play important roles in a diverse range of developmental processes and abiotic stress responses. However, the information of GRAS gene family in the bioenergy crop Miscanthus has not been available. Here, we report the genome-wide identification of GRAS gene family in Micanthus sinensis. A total of 123 MsGRAS genes were identified, which were divided into ten subfamilies based on the phylogenetic analysis. The co-linearity analysis revealed that 59 MsGRAS genes experienced segmental duplication, forming 35 paralogous pairs. The expression of six MsGRAS genes in responding to salt, alkali, and mixed salt-alkali stresses was analyzed by transcriptome and real-time quantitative PCR (RT-qPCR) assays. Furthermore, the role of MsGRAS60 in salt and alkali stress response was characterized in transgenic Arabidopsis. The MsGRAS60 overexpression lines exhibited hyposensitivity to abscisic acid (ABA) treatment and resulted in compromised tolerance to salt and alkali stresses, suggesting that MsGRAS60 is a negative regulator of salt and alkali tolerance via an ABA-dependent signaling pathway. The salt and alkali stress-inducible MsGRAS genes identified serve as candidates for the improvement of abiotic stress tolerance in Miscanthus.
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11
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Su X, Liu T, Liu YP, Harris AJ, Chen JY. Adaptive radiation in Orinus, an endemic alpine grass of the Qinghai-Tibet Plateau, based on comparative transcriptomic analysis. JOURNAL OF PLANT PHYSIOLOGY 2022; 277:153786. [PMID: 35963042 DOI: 10.1016/j.jplph.2022.153786] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 07/20/2022] [Accepted: 07/20/2022] [Indexed: 06/15/2023]
Abstract
The species of Orinus (Poaceae) are important alpine plants with a variety of phenotypic traits and potential usages in molecular breeding toward drought-tolerant forage crops. However, the genetic basis of evolutionary adaption and diversification in the genus is still unclear. In the present study, we obtained transcriptomes for the two most divergent species, O. thoroldii and O. kokonoricus, using the Illumina platform and de novo assembly. In total, we generated 23,029 and 24,086 unigenes with N50 values of 1188 and 1203 for O. thoroldii and O. kokonoricus respectively, and identified 19,005 pairs of putative orthologs between the two species of Orinus. For these orthologs, estimations of non-synonymous/synonymous substitution rate ratios indicated that 568 pairs may be under strongly positive selection (Ka/Ks > 1), and Gene Ontogeny (GO) enrichment analysis revealed that significantly enriched pathways were in DNA repair and resistance to abiotic stress. Meanwhile, the divergence times of species between O. thoroldii and O. kokonoricus occurred 3.2 million years ago (Mya), and the recent evolutionary branch is an allotetraploid species, Cleistogenes songorica. We also detected a Ks peak of ∼0.60 for Orinus. Additionally, we identified 188 pairs of differentially expressed genes (DEGs) between the two species of Orinus, which were significantly enrich in stress resistance and lateral root development. Thus, we considered that the species diversification and evolutionary adaption of this genus was initiated by environmental selection, followed by phenotypic differentiation, finally leading to niche separation in the Qinghai-Tibet Plateau.
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Affiliation(s)
- Xu Su
- School of Life Sciences, Qinghai Normal University, Xining, 810008, China; Academy of Plateau Science and Sustainability, Qinghai Normal University, Xining, 810016, China; Key Laboratory of Medicinal Animal and Plant Resources of the Qinghai-Tibet Plateau in Qinghai Province, Qinghai Normal University, Xining, 810008, China; Key Laboratory of Land Surface Processes and Ecological Conservation of the Qinghai-Tibet Plateau, The Ministry of Education, Qinghai Normal University, Xining, 810008, China
| | - Tao Liu
- School of Life Sciences, Qinghai Normal University, Xining, 810008, China; School of Geographical Science, Qinghai Normal University, Xining, 810008, China
| | - Yu Ping Liu
- School of Life Sciences, Qinghai Normal University, Xining, 810008, China; Key Laboratory of Medicinal Animal and Plant Resources of the Qinghai-Tibet Plateau in Qinghai Province, Qinghai Normal University, Xining, 810008, China.
| | - A J Harris
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China.
| | - Jin Yuan Chen
- School of Life Sciences, Qinghai Normal University, Xining, 810008, China; Key Laboratory of Medicinal Animal and Plant Resources of the Qinghai-Tibet Plateau in Qinghai Province, Qinghai Normal University, Xining, 810008, China
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12
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He M, He Y, Zhang K, Lu X, Zhang X, Gao B, Fan Y, Zhao H, Jha R, Huda MN, Tang Y, Wang J, Yang W, Yan M, Cheng J, Ruan J, Dulloo E, Zhang Z, Georgiev MI, Chapman MA, Zhou M. Comparison of buckwheat genomes reveals the genetic basis of metabolomic divergence and ecotype differentiation. THE NEW PHYTOLOGIST 2022; 235:1927-1943. [PMID: 35701896 DOI: 10.1111/nph.18306] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Accepted: 05/22/2022] [Indexed: 05/09/2023]
Abstract
Golden buckwheat (Fagopyrum dibotrys or Fagopyrum cymosum) and Tartary buckwheat (Fagopyrum tataricum) belong to the Polygonaceae and the Fagopyrum genus is rich in flavonoids. Golden buckwheat is a wild relative of Tartary buckwheat, yet golden buckwheat is a traditional Chinese herbal medicine and Tartary buckwheat is a food crop. The genetic basis of adaptive divergence between these two buckwheats is poorly understood. Here, we assembled a high-quality chromosome-level genome of golden buckwheat and found a one-to-one syntenic relationship with the chromosomes of Tartary buckwheat. Two large inversions were identified that differentiate golden buckwheat and Tartary buckwheat. Metabolomic and genetic comparisons of golden buckwheat and Tartary buckwheat indicate an amplified copy number of FdCHI, FdF3H, FdDFR, and FdLAR gene families in golden buckwheat, and a parallel increase in medicinal flavonoid content. Resequencing of 34 wild golden buckwheat accessions across the two morphologically distinct ecotypes identified candidate genes, including FdMYB44 and FdCRF4, putatively involved in flavonoid accumulation and differentiation of plant architecture, respectively. Our comparative genomic study provides abundant genomic resources of genomic divergent variation to improve buckwheat with excellent nutritional and medicinal value.
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Affiliation(s)
- Ming He
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, National Crop Genebank Building, Zhongguancun South Street no. 12, Haidian District, Beijing, 100081, China
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Yuqi He
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, National Crop Genebank Building, Zhongguancun South Street no. 12, Haidian District, Beijing, 100081, China
| | - Kaixuan Zhang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, National Crop Genebank Building, Zhongguancun South Street no. 12, Haidian District, Beijing, 100081, China
| | - Xiang Lu
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, National Crop Genebank Building, Zhongguancun South Street no. 12, Haidian District, Beijing, 100081, China
- College of Agriculture, Guizhou University, Guiyang, 550025, China
| | - Xuemei Zhang
- Annoroad Gene Technology (Beijing) Co. Ltd, Beijing, 100176, China
| | - Bin Gao
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, National Crop Genebank Building, Zhongguancun South Street no. 12, Haidian District, Beijing, 100081, China
| | - Yu Fan
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, National Crop Genebank Building, Zhongguancun South Street no. 12, Haidian District, Beijing, 100081, China
- College of Agriculture, Guizhou University, Guiyang, 550025, China
| | - Hui Zhao
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, National Crop Genebank Building, Zhongguancun South Street no. 12, Haidian District, Beijing, 100081, China
| | - Rintu Jha
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, National Crop Genebank Building, Zhongguancun South Street no. 12, Haidian District, Beijing, 100081, China
| | - Md Nurul Huda
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, National Crop Genebank Building, Zhongguancun South Street no. 12, Haidian District, Beijing, 100081, China
| | - Yu Tang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, National Crop Genebank Building, Zhongguancun South Street no. 12, Haidian District, Beijing, 100081, China
| | - Junzhen Wang
- Research Station of Alpine Crop, Xichang Institute of Agricultural Sciences, Liangshan, 616150, Sichuan, China
| | - Weifei Yang
- Annoroad Gene Technology (Beijing) Co. Ltd, Beijing, 100176, China
| | - Mingli Yan
- Crop Research Institute, Hunan Academy of Agricultural Sciences, Changsha, 410125, China
| | - Jianping Cheng
- College of Agriculture, Guizhou University, Guiyang, 550025, China
| | - Jingjun Ruan
- College of Agriculture, Guizhou University, Guiyang, 550025, China
| | - Ehsan Dulloo
- The Alliance of Bioversity International and CIAT, Via di San Domenico, 100153, Rome, Italy
| | - Zongwen Zhang
- The Alliance of Bioversity International and CIAT, Via di San Domenico, 100153, Rome, Italy
| | - Milen I Georgiev
- Group of Plant Cell Biotechnology and Metabolomics, The Stephan Angeloff Institute of Microbiology, Bulgarian Academy of Sciences, 4002, Plovdiv, Bulgaria
- Center of Plant Systems Biology and Biotechnology, 4002, Plovdiv, Bulgaria
| | - Mark A Chapman
- Biological Sciences, University of Southampton, Life Sciences Building 85, Highfield Campus, Southampton, SO17 1BJ, UK
| | - Meiliang Zhou
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, National Crop Genebank Building, Zhongguancun South Street no. 12, Haidian District, Beijing, 100081, China
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13
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Zeng P, Tian Z, Han Y, Zhang W, Zhou T, Peng Y, Hu H, Cai J. Comparison of ONT and CCS sequencing technologies on the polyploid genome of a medicinal plant showed that high error rate of ONT reads are not suitable for self-correction. Chin Med 2022; 17:94. [PMID: 35945546 PMCID: PMC9364492 DOI: 10.1186/s13020-022-00644-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Accepted: 07/19/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Many medicinal plants are known for their complex genomes with high ploidy, heterozygosity, and repetitive content which pose severe challenges for genome sequencing of those species. Long reads from Oxford nanopore sequencing technology (ONT) or Pacific Biosciences Single Molecule, Real-Time (SMRT) sequencing offer great advantages in de novo genome assembly, especially for complex genomes with high heterozygosity and repetitive content. Currently, multiple allotetraploid species have sequenced their genomes by long-read sequencing. However, we found that a considerable proportion of these genomes (7.9% on average, maximum 23.7%) could not be covered by NGS (Next Generation Sequencing) reads (uncovered region by NGS reads, UCR) suggesting the questionable and low-quality of those area or genomic areas that can't be sequenced by NGS due to sequencing bias. The underlying causes of those UCR in the genome assembly and solutions to this problem have never been studied. METHODS In the study, we sequenced the tetraploid genome of Veratrum dahuricum (Turcz.) O. Loes (VDL), a Chinese medicinal plant, with ONT platform and assembled the genome with three strategies in parallel. We compared the qualities, coverage, and heterozygosity of the three ONT assemblies with another released assembly of the same individual using reads from PacBio circular consensus sequencing (CCS) technology, to explore the cause of the UCR. RESULTS By mapping the NGS reads against the three ONT assemblies and the CCS assembly, we found that the coverage of those ONT assemblies by NGS reads ranged from 49.15 to 76.31%, much smaller than that of the CCS assembly (99.53%). And alignment between ONT assemblies and CCS assembly showed that most UCR can be aligned with CCS assembly. So, we conclude that the UCRs in ONT assembly are low-quality sequences with a high error rate that can't be aligned with short reads, rather than genomic regions that can't be sequenced by NGS. Further comparison among the intermediate versions of ONT assemblies showed that the most probable origin of those errors is a combination of artificial errors introduced by "self-correction" and initial sequencing error in long reads. We also found that polishing the ONT assembly with CCS reads can correct those errors efficiently. CONCLUSIONS Through analyzing genome features and reads alignment, we have found the causes for the high proportion of UCR in ONT assembly of VDL are sequencing errors and additional errors introduced by self-correction. The high error rates of ONT-raw reads make them not suitable for self-correction prior to allotetraploid genome assembly, as the self-correction will introduce artificial errors to > 5% of the UCR sequences. We suggest high-precision CCS reads be used to polish the assembly to correct those errors effectively for polyploid genomes.
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Affiliation(s)
- Peng Zeng
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macau, China
| | - Zunzhe Tian
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, China
| | - Yuwei Han
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, China
| | - Weixiong Zhang
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macau, China
| | - Tinggan Zhou
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, China
| | - Yingmei Peng
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, China
| | - Hao Hu
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macau, China.
| | - Jing Cai
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, China.
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14
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Wang W, Shao A, Xu X, Fan S, Fu J. Comparative genomics reveals the molecular mechanism of salt adaptation for zoysiagrasses. BMC PLANT BIOLOGY 2022; 22:355. [PMID: 35864464 PMCID: PMC9306052 DOI: 10.1186/s12870-022-03752-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Accepted: 07/13/2022] [Indexed: 06/15/2023]
Abstract
BACKGROUND Zoysiagrass (Zoysia spp.) is a warm-season turfgrass. It is widely used as turfgrasses throughout the world, offers good turf qualities, including salt tolerance, resistance to drought and heat. However, the underlying genetic mechanism of zoysiagrass responsive to salt stress remains largely unexplored. RESULTS In present study, we performed a whole-genome comparative analysis for ten plant genomes. Evolutionary analysis revealed that Chloridoideae diverged from Panicoideae approximately 33.7 million years ago (Mya), and the phylogenetic relationship among three zoysiagrasses species suggested that Zoysia matrella may represent an interspecific hybrid between Zoysia japonica and Zoysia pacifica. Genomic synteny indicated that Zoysia underwent a genus-specific whole-genome duplication (WGD) event approximately 20.8 Mya. The expression bais of homologous genes between the two subgenomes suggested that the B subgenome of Z. japonica contributes to salt tolerance. In additon, comparative genomic analyses revealed that the salt adaptation of Zoysia is likely attributable to the expanded cytochrome P450 and ABA biosynthetic gene families. Furthermore, we further found that many duplicated genes from the extra WGD event exhibited distinct functional divergence in response to salt stress using transcriptomic analysis, suggesting that this WGD event contributed to strong resistance to salt stress. CONCLUSIONS Here, our results revealed that expanded cytochrome P450 and ABA biosynthetic gene families, and many of those duplicated genes from recent zoysia-specific WGD event contributed to salt adaptation of zoysiagrass, which provided insight into the genetic underpinning of salt adaptation and valuable information for further studies on salt stress-related traits in Zoysia.
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Affiliation(s)
- Wei Wang
- Coastal Salinity Tolerant Grass Engineering and Technology Research Center, Ludong University, Yantai, Shandong, China
| | - An Shao
- Coastal Salinity Tolerant Grass Engineering and Technology Research Center, Ludong University, Yantai, Shandong, China
| | - Xiao Xu
- Coastal Salinity Tolerant Grass Engineering and Technology Research Center, Ludong University, Yantai, Shandong, China
| | - Shugao Fan
- Coastal Salinity Tolerant Grass Engineering and Technology Research Center, Ludong University, Yantai, Shandong, China
| | - Jinmin Fu
- Coastal Salinity Tolerant Grass Engineering and Technology Research Center, Ludong University, Yantai, Shandong, China.
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15
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Lin T, Xu X, Du H, Fan X, Chen Q, Hai C, Zhou Z, Su X, Kou L, Gao Q, Deng L, Jiang J, You H, Ma Y, Cheng Z, Wang G, Liang C, Zhang G, Yu H, Li J. Extensive sequence divergence between the reference genomes of Taraxacum kok-saghyz and Taraxacum mongolicum. SCIENCE CHINA. LIFE SCIENCES 2022; 65:515-528. [PMID: 34939160 DOI: 10.1007/s11427-021-2033-2] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Accepted: 11/25/2021] [Indexed: 12/15/2022]
Abstract
Plants belonging to the genus Taraxacum are widespread all over the world, which contain rubber-producing and non-rubber-producing species. However, the genomic basis underlying natural rubber (NR) biosynthesis still needs more investigation. Here, we presented high-quality genome assemblies of rubber-producing T. kok-saghyz TK1151 and non-rubber-producing T. mongolicum TM5. Comparative analyses uncovered a large number of genetic variations, including inversions, translocations, presence/absence variations, as well as considerable protein divergences between the two species. Two gene duplication events were found in these two Taraxacum species, including one common ancestral whole-genome triplication and one subsequent round of gene amplification. In genomes of both TK1151 and TM5, we identified the genes encoding for each step in the NR biosynthesis pathway and found that the SRPP and CPT gene families have experienced a more obvious expansion in TK1151 compared to TM5. This study will have large-ranging implications for the mechanism of NR biosynthesis and genetic improvement of NR-producing crops.
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Affiliation(s)
- Tao Lin
- State Key Laboratory of Plant Genomics, National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, 100101, China.,State Key Laboratory of Agrobiotechnology, College of Horticulture, China Agricultural University, Beijing, 100193, China
| | - Xia Xu
- State Key Laboratory of Plant Genomics, National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
| | - Huilong Du
- State Key Laboratory of Plant Genomics, National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, 100101, China.,School of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding, 071002, China
| | - Xiuli Fan
- State Key Laboratory of Plant Genomics, National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, 100101, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Qingwen Chen
- State Key Laboratory of Plant Genomics, National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, 100101, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Chunyan Hai
- State Key Laboratory of Plant Genomics, National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, 100101, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zijian Zhou
- State Key Laboratory of Agrobiotechnology, College of Horticulture, China Agricultural University, Beijing, 100193, China
| | - Xiao Su
- State Key Laboratory of Agrobiotechnology, College of Horticulture, China Agricultural University, Beijing, 100193, China
| | - Liquan Kou
- State Key Laboratory of Plant Genomics, National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
| | - Qiang Gao
- Genomics and Genetic Engineering Laboratory of Ornamental Plants, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Lingwei Deng
- Biotechnology Research Institute, Heilongjiang Academy of Agricultural Sciences, Harbin, 150086, China
| | - Jinsheng Jiang
- Biotechnology Research Institute, Heilongjiang Academy of Agricultural Sciences, Harbin, 150086, China
| | - Hanli You
- State Key Laboratory of Plant Genomics, National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, 100101, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yihua Ma
- State Key Laboratory of Plant Genomics, National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, 100101, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zhukuan Cheng
- State Key Laboratory of Plant Genomics, National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
| | - Guodong Wang
- State Key Laboratory of Plant Genomics, National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
| | - Chengzhi Liang
- State Key Laboratory of Plant Genomics, National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, 100101, China. .,University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Guomin Zhang
- Biotechnology Research Institute, Heilongjiang Academy of Agricultural Sciences, Harbin, 150086, China.
| | - Hong Yu
- State Key Laboratory of Plant Genomics, National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, 100101, China.
| | - Jiayang Li
- State Key Laboratory of Plant Genomics, National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, 100101, China.,University of Chinese Academy of Sciences, Beijing, 100049, China.,Guangdong Laboratory of Lingnan Modern Agriculture, Guangzhou, 510642, China
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16
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Yu F, Zhao X, Chai J, Ding X, Li X, Huang Y, Wang X, Wu J, Zhang M, Yang Q, Deng Z, Jiang J. Chromosome-specific painting unveils chromosomal fusions and distinct allopolyploid species in the Saccharum complex. THE NEW PHYTOLOGIST 2022; 233:1953-1965. [PMID: 34874076 DOI: 10.1111/nph.17905] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Accepted: 11/29/2021] [Indexed: 06/13/2023]
Abstract
Karyotypes provide key cytogenetic information on the phylogenetic relationships and evolutionary origins in related eukaryotic species. Despite our knowledge of the chromosome numbers of sugarcane and its wild relatives, the chromosome composition and evolution among the species in the Saccharum complex have been elusive owing to the complex polyploidy and the large numbers of chromosomes of these species. Oligonucleotide-based chromosome painting has become a powerful tool of cytogenetic studies especially for plant species with large numbers of chromosomes. We developed oligo-based chromosome painting probes for all 10 chromosomes in Saccharum officinarum (2n = 8x = 80). The 10 painting probes generated robust fluorescence in situ hybridization signals in all plant species within the Saccharum complex, including species in the genera Saccharum, Miscanthus, Narenga and Erianthus. We conducted comparative chromosome analysis using the same set of probes among species from four different genera within the Saccharum complex. Excitingly, we discovered several novel cytotypes and chromosome rearrangements in these species. We discovered that fusion from two different chromosomes is a common type of chromosome rearrangement associated with the species in the Saccharum complex. Such fusion events changed the basic chromosome number and resulted in distinct allopolyploids in the Saccharum complex.
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Affiliation(s)
- Fan Yu
- National Engineering Research Center for Sugarcane, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
- State Key Laboratory for Protection and Utilization of Subtropical Agro-bioresources, Guangxi University, Nanning, 530004, China
| | - Xinwang Zhao
- National Engineering Research Center for Sugarcane, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
| | - Jin Chai
- National Engineering Research Center for Sugarcane, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
| | - Xueer Ding
- National Engineering Research Center for Sugarcane, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
| | - Xueting Li
- National Engineering Research Center for Sugarcane, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
| | - Yongji Huang
- Marine and Agricultural Biotechnology Laboratory, Fuzhou Institute of Oceanography, Minjiang University, Fuzhou, 350108, China
| | - Xianhong Wang
- College of Agriculture, Yunnan Agricultural University, Kunming, 650201, Yunnan, China
| | - Jiayun Wu
- National Engineering Research Center for Sugarcane, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
- Institute of Nanfan & Seed Industry, Guangdong Academy of Sciences, Guangzhou, 510316, China
| | - Muqing Zhang
- State Key Laboratory for Protection and Utilization of Subtropical Agro-bioresources, Guangxi University, Nanning, 530004, China
| | - Qinghui Yang
- College of Agriculture, Yunnan Agricultural University, Kunming, 650201, Yunnan, China
| | - Zuhu Deng
- National Engineering Research Center for Sugarcane, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
- State Key Laboratory for Protection and Utilization of Subtropical Agro-bioresources, Guangxi University, Nanning, 530004, China
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
| | - Jiming Jiang
- Department of Plant Biology, Department of Horticulture, MSU AgBioResearch, Michigan State University, East Lansing, MI, 48824, USA
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17
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Chen Z, He Y, Iqbal Y, Shi Y, Huang H, Yi Z. Investigation of genetic relationships within three Miscanthus species using SNP markers identified with SLAF-seq. BMC Genomics 2022; 23:43. [PMID: 35012465 PMCID: PMC8751252 DOI: 10.1186/s12864-021-08277-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Accepted: 12/22/2021] [Indexed: 01/31/2023] Open
Abstract
BACKGROUND Miscanthus, which is a leading dedicated-energy grass in Europe and in parts of Asia, is expected to play a key role in the development of the future bioeconomy. However, due to its complex genetic background, it is difficult to investigate phylogenetic relationships in this genus. Here, we investigated 50 Miscanthus germplasms: 1 female parent (M. lutarioriparius), 30 candidate male parents (M. lutarioriparius, M. sinensis, and M. sacchariflorus), and 19 offspring. We used high-throughput Specific-Locus Amplified Fragment sequencing (SLAF-seq) to identify informative single nucleotide polymorphisms (SNPs) in all germplasms. RESULTS We identified 257,889 SLAF tags, of which 87,162 were polymorphic. Each tag was 264-364 bp long. The obtained 724,773 population SNPs were used to investigate genetic relationships within three species of Miscanthus. We constructed a phylogenetic tree of the 50 germplasms using the obtained SNPs and grouped them into two clades: one clade comprised of M. sinensis alone and the other one included the offspring, M. lutarioriparius, and M. sacchariflorus. Genetic cluster analysis had revealed that M. lutarioriparius germplasm C3 was the most likely male parent of the offspring. CONCLUSIONS As a high-throughput sequencing method, SLAF-seq can be used to identify informative SNPs in Miscanthus germplasms and to rapidly characterize genetic relationships within this genus. Our results will support the development of breeding programs with the focus on utilizing Miscanthus cultivars with elite biomass- or fiber-production potential for the developing bioeconomy.
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Affiliation(s)
- Zhiyong Chen
- College of Bioscience & Biotechnology, Hunan Agricultural University, Changsha, 410128, PR China. .,Hunan Engineering Laboratory of Miscanthus Ecological Applications, Hunan Agricultural University, Changsha, 410128, PR China.
| | - Yancen He
- College of Bioscience & Biotechnology, Hunan Agricultural University, Changsha, 410128, PR China.,Hunan Engineering Laboratory of Miscanthus Ecological Applications, Hunan Agricultural University, Changsha, 410128, PR China
| | - Yasir Iqbal
- College of Bioscience & Biotechnology, Hunan Agricultural University, Changsha, 410128, PR China.,Hunan Engineering Laboratory of Miscanthus Ecological Applications, Hunan Agricultural University, Changsha, 410128, PR China
| | - Yanlan Shi
- College of Bioscience & Biotechnology, Hunan Agricultural University, Changsha, 410128, PR China.,Hunan Engineering Laboratory of Miscanthus Ecological Applications, Hunan Agricultural University, Changsha, 410128, PR China
| | - Hongmei Huang
- College of Bioscience & Biotechnology, Hunan Agricultural University, Changsha, 410128, PR China. .,Hunan Engineering Laboratory of Miscanthus Ecological Applications, Hunan Agricultural University, Changsha, 410128, PR China.
| | - Zili Yi
- College of Bioscience & Biotechnology, Hunan Agricultural University, Changsha, 410128, PR China. .,Hunan Engineering Laboratory of Miscanthus Ecological Applications, Hunan Agricultural University, Changsha, 410128, PR China.
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18
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Nie G, Yang Z, He J, Liu A, Chen J, Wang S, Wang X, Feng G, Li D, Peng Y, Huang L, Zhang X. Genome-Wide Investigation of the NAC Transcription Factor Family in Miscanthus sinensis and Expression Analysis Under Various Abiotic Stress. FRONTIERS IN PLANT SCIENCE 2021; 12:766550. [PMID: 34804100 PMCID: PMC8600139 DOI: 10.3389/fpls.2021.766550] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/29/2021] [Accepted: 10/11/2021] [Indexed: 06/13/2023]
Abstract
The NAC transcription factor family is deemed to be a large plant-specific gene family that plays important roles in plant development and stress response. Miscanthus sinensis is commonly planted in vast marginal land as forage, ornamental grass, or bioenergy crop which demand a relatively high resistance to abiotic stresses. The recent release of a draft chromosome-scale assembly genome of M. sinensis provided a basic platform for the genome-wide investigation of NAC proteins. In this study, a total of 261 M. sinensis NAC genes were identified and a complete overview of the gene family was presented, including gene structure, conserved motif compositions, chromosomal distribution, and gene duplications. Results showed that gene length, molecular weights (MW), and theoretical isoelectric points (pI) of NAC family were varied, while gene structure and motifs were relatively conserved. Chromosomal mapping analysis found that the M. sinensis NAC genes were unevenly distributed on 19 M. sinensis chromosomes, and the interchromosomal evolutionary analysis showed that nine pairs of tandem duplicates genes and 121 segmental duplications were identified, suggesting that gene duplication, especially segmental duplication, is possibly associated with the amplification of M. sinensis NAC gene family. The expression patterns of 14 genes from M. sinensis SNAC subgroup were analyzed under high salinity, PEG, and heavy metals, and multiple NAC genes could be induced by the treatment. These results will provide a very useful reference for follow-up study of the functional characteristics of NAC genes in the mechanism of stress-responsive and potential roles in the development of M. sinensis.
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19
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Wu S, Li Y. A Unique Sulfotransferase-Involving Strigolactone Biosynthetic Route in Sorghum. FRONTIERS IN PLANT SCIENCE 2021; 12:793459. [PMID: 34970291 PMCID: PMC8713700 DOI: 10.3389/fpls.2021.793459] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Accepted: 11/08/2021] [Indexed: 05/17/2023]
Abstract
LOW GERMINATION STIMULANT 1 (LGS1) plays an important role in strigolactones (SLs) biosynthesis and Striga resistance in sorghum, but the catalytic function remains unclear. Using the recently developed SL-producing microbial consortia, we examined the activities of sorghum MORE AXILLARY GROWTH1 (MAX1) analogs and LGS1. Surprisingly, SbMAX1a (cytochrome P450 711A enzyme in sorghum) synthesized 18-hydroxy-carlactonoic acid (18-hydroxy-CLA) directly from carlactone (CL) through four-step oxidations. The further oxidated product orobanchol (OB) was also detected in the microbial consortium. Further addition of LGS1 led to the synthesis of both 5-deoxystrigol (5DS) and 4-deoxyorobanchol (4DO). Further biochemical characterization found that LGS1 functions after SbMAX1a by converting 18-hydroxy-CLA to 5DS and 4DO possibly through a sulfonation-mediated pathway. The unique functions of SbMAX1 and LGS1 imply a previously unknown synthetic route toward SLs.
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