Chromosome-length genome assemblies of six legume species provide insights into genome organization, evolution, and agronomic traits for crop improvement

doi:10.1016/j.jare.2021.10.009

KMS > 免疫化学研究所 > 特聘教授组 > Roger D. Kornberg组

	Chromosome-length genome assemblies of six legume species provide insights into genome organization, evolution, and agronomic traits for crop improvement
	Garg, Vanika 1; Dudchenko, Olga 2,3; Wang, Jinpeng 4; Khan, Aamir W.1; Gupta, Saurabh 5; Kaur, Parwinder 6; Han, Kai 7; Saxena, Rachit K.1; Kale, Sandip M.8; Pham, Melanie 2; Yu, Jigao 4; Chitikineni, Annapurna 1; Zhang, Zhikang 4; Fan, Guangyi 7,9; Lui, Christopher 2; Valluri, Vinodkumar 1; Meng, Fanbo 4; Bhandari, Aditi 1; Liu, Xiaochuan 7; Yang, Tao 10; Chen, Hua 11; Valliyodan, Babu 12; Roorkiwal, Manish 1; Shi, Chengcheng 7; Bin Yang, Hong 13; Durand, Neva C.2,3; Pandey, Manish K.1,14; Li, Guowei 15; Barmukh, Rutwik 1; Wang, Xingjun 15; Chen, Xiaoping 13; Lam, Hon-Ming 16,17; Jiang, Huifang 18; Zong, Xuxiao 10; Liang, Xuanqiang 13; Liu, Xin 7,9,19; Liao, Boshou 18; Guo, Baozhu 20; Jackson, Scott 21; Nguyen, Henry T.22,23; Zhuang, Weijian 11; Shubo, Wan 15; Wang, Xiyin 4; Aiden, Erez Lieberman2,3,6,24,25 ; Bennetzen, Jeffrey L.26; Varshney, Rajeev K.1,11,14,27,28
	2022-12-01
发表期刊	JOURNAL OF ADVANCED RESEARCH (IF:11.4[JCR-2023],11.0[5-Year])
ISSN	2090-1232
EISSN	2090-1224
卷号	42
发表状态	已发表
DOI	10.1016/j.jare.2021.10.009
摘要	Introduction: Legume crops are an important source of protein and oil for human health and in fixing atmospheric N2 for soil enrichment. With an objective to accelerate much-needed genetic analyses and breeding applications, draft genome assemblies were generated in several legume crops; many of them are not high quality because they are mainly based on short reads. However, the superior quality of gen-ome assembly is crucial for a detailed understanding of genomic architecture, genome evolution, and crop improvement. Objectives: Present study was undertaken with an objective of developing improved chromosome-length genome assemblies in six different legumes followed by their systematic investigation to unravel differ-ent aspects of genome organization and legume evolution.Methods: We employed in situ Hi-C data to improve the existing draft genomes and performed different evolutionary and comparative analyses using improved genome assemblies.Results: We have developed chromosome-length genome assemblies in chickpea, pigeonpea, soybean, subterranean clover, and two wild progenitor species of cultivated groundnut (A. duranensis and A. ipaen-sis). A comprehensive comparative analysis of these genome assemblies offered improved insights into various evolutionary events that shaped the present-day legume species. We highlighted the expansion of gene families contributing to unique traits such as nodulation in legumes, gravitropism in groundnut, and oil biosynthesis in oilseed legume crops such as groundnut and soybean. As examples, we have demonstrated the utility of improved genome assemblies for enhancing the resolution of "QTL-hotspot" identification for drought tolerance in chickpea and marker-trait associations for agronomic traits in pigeonpea through genome-wide association study. Genomic resources developed in this study are pub-licly available through an online repository, 'Legumepedia'.Conclusion: This study reports chromosome-length genome assemblies of six legume species and demon-strates the utility of these assemblies in crop improvement. The genomic resources developed here will have significant role in accelerating genetic improvement applications of legume crops.(c) 2022 The Authors. Published by Elsevier B.V. on behalf of Cairo University. This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/).
关键词	Evolution Plant genomes GWAS Nodulation QTL Legumes
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收录类别	SCI
语种	英语
WOS研究方向	Science & Technology - Other Topics
WOS类目	Multidisciplinary Sciences
WOS记录号	WOS:000906397900001
出版者	ELSEVIER
引用统计	正在获取...
文献类型	期刊论文
条目标识符	https://kms.shanghaitech.edu.cn/handle/2MSLDSTB/272828
专题	免疫化学研究所_特聘教授组_结构生物化学实验室
通讯作者	Shubo, Wan; Wang, Xiyin; Aiden, Erez Lieberman; Bennetzen, Jeffrey L.; Varshney, Rajeev K.
作者单位	1.Int Crops Res Inst Semi Arid Trop, Ctr Excellence Genom & Syst Biol, Hyderabad, India 2.Baylor Coll Med, Dept Mol & Human Genet, Ctr Genome Architecture, Houston, TX 77030 USA 3.Rice Univ, Ctr Theoret Biol Phys, Houston, TX USA 4.North China Univ Sci & Technol, Sch Life Sci, Tangshan, Peoples R China 5.Max Planck Inst Mol Plant Physiol, Potsdam, Germany 6.Univ Western Australia, UWA Sch Agr & Environm, Perth, WA, Australia 7.BGI Shenzhen, BGI Qingdao, Qingdao 266555, Peoples R China 8.Leibniz Inst Plant Genet & Crop Plant Res IPK, Gatersleben, Germany 9.BGI Shenzhen, Shenzhen 518083, Peoples R China 10.Chinese Acad Agr Sci, Natl Key Facil Crop Gene Resources & Genet Improv, Inst Crop Sci, Beijing 100081, Peoples R China 11.Fujian Agr & Forestry Univ, Ctr Legume Oil Crop Genet & Syst Biol, Inst Oil Crops, Fuzhou, Peoples R China 12.Lincoln Univ, Dept Agr & Environm Sci, Jefferson City, MO USA 13.Guangdong Acad Agr Sci, Crops Res Inst, Guangzhou, Peoples R China 14.Shandong Acad Agr Sci, Shandong Peanut Res Inst, Qingdao, Peoples R China 15.Shandong Acad Agr Sci, Biotechnol Res Ctr, Shandong Prov Key Lab Crop Genet Improvement Ecol, Jinan, Peoples R China 16.Chinese Univ Hong Kong, Ctr Soybean Res, State Key Lab Agrobiotechnol, Hong Kong, Peoples R China 17.Chinese Univ Hong Kong, Sch Life Sci, Hong Kong, Peoples R China 18.Chinese Acad Agr Sci, Key Lab Biol & Genet Improvement Oil Crops, Minist Agr & Rural Affairs, Oil Crops Res Inst, Wuhan, Peoples R China 19.BGI Shenzhen, China Natl GeneBank, Shenzhen 518120, Peoples R China 20.USDA ARS, Crop Genet & Breeding Res Unit, Tifton, GA 31793 USA 21.Bayer Crop Sci, Chesterfield, MO USA 22.Univ Missouri, Div Plant Sci, Columbia, MO USA 23.Univ Missouri, Natl Ctr Soybean Biotechnol, Columbia, MO USA 24.ShanghaiTech, Shanghai Inst Adv Immunochem Studies, Pudong, Peoples R China 25.Broad Inst MIT & Harvard, Cambridge, MA 02142 USA 26.Univ Georgia, Dept Genet, Athens, GA 30602 USA 27.Murdoch Univ, State Agr Biotechnol Ctr, Ctr Crop & Food Innovat, Food Futures Inst, Murdoch, WA, Australia 28.Univ Western Australia, UWA Inst Agr, Perth, WA, Australia
通讯作者单位	免疫化学研究所
推荐引用方式 GB/T 7714	Garg, Vanika,Dudchenko, Olga,Wang, Jinpeng,et al. Chromosome-length genome assemblies of six legume species provide insights into genome organization, evolution, and agronomic traits for crop improvement[J]. JOURNAL OF ADVANCED RESEARCH,2022,42.
APA	Garg, Vanika.,Dudchenko, Olga.,Wang, Jinpeng.,Khan, Aamir W..,Gupta, Saurabh.,...&Varshney, Rajeev K..(2022).Chromosome-length genome assemblies of six legume species provide insights into genome organization, evolution, and agronomic traits for crop improvement.JOURNAL OF ADVANCED RESEARCH,42.
MLA	Garg, Vanika,et al."Chromosome-length genome assemblies of six legume species provide insights into genome organization, evolution, and agronomic traits for crop improvement".JOURNAL OF ADVANCED RESEARCH 42(2022).