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

Garg, V and Dudchenko, O and Wang, J and Khan, A W and Gupta, S and Kaur, P and Han, K and Saxena, R K and Kale, S M and Pham, M and Yu, J and Chitikineni, A and Zhang, Z and Fan, G and Lui, C and Valluri, V K and Meng, F and Bhandari, A and Liu, X and Yang, T and Chen, H and Valliyodan, B and Roorkiwal, M and Shi, C and Yang, H B and Durand, N C and Pandey, M K and Li, G and Barmukh, R and Wang, X and Chen, X and Lam, H M and Jiang, H and Zong, X and Liang, X and Liu, X and Liao, B and Guo, B and Jackson, S and Nguyen, H T and Zhuang, W and Shubo, W and Wang, X and Aiden, E L and Bennetzen, J L and Varshney, R K (2021) 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. pp. 315-329. ISSN 2090-1224

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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 genome 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 different 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. ipaensis). 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 publicly available through an online repository, ‘Legumepedia’. Conclusion: This study reports chromosome-length genome assemblies of six legume species and demonstrates 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.

Item Type: Article
Divisions: Center of Excellence in Genomics and Systems Biology
Uncontrolled Keywords: Evolution, Plant genomes, GWAS, Nodulation, QTL, Legumes
Subjects: Others > Plant Genetics
Others > Legume Crops
Depositing User: Mr Nagaraju T
Date Deposited: 22 Sep 2023 11:23
Last Modified: 22 Sep 2023 11:23
Official URL:
Acknowledgement: R.K.V. acknowledges funding support in parts from Bill and Melinda Gates Foundation (USA), Department of Agriculture and Cooperation, Ministry of Agriculture and Farmers Welfare, and Department of Biotechnology, Ministry of Science & Technology of Government of India. Hi-C data were created in collaboration with the DNA Zoo Consortium ( DNA Zoo sequencing effort is supported by Illumina, Inc., IBM, and the Pawsey Supercomputing Center. E.L.A. was supported by the Welch Foundation (Q-1866), a McNair Medical Institute Scholar Award, an NIH Encyclopedia of DNA Elements Mapping Center Award (UM1HG009375), a US-Israel Binational Science Foundation Award (2019276), the Behavioral Plasticity Research Institute (NSF DBI-2021795), NSF Physics Frontiers Center Award (NSF PHY-2019745), and an NIH CEGS (RM1HG011016-01A1). Xiyin W. acknowledges funding support from China Natural Science Foundation Grant (#32070669). P.K. was supported by the University of Western Australia with additional computational resources and support from the Pawsey Supercomputing Centre with funding from the Australian Government and the Government of Western Australia. B.V. acknowledges the United States Department of Agriculture-National Institute of Food and Agriculture (USDANIFA), Evans Allen funding support (Project #1020002). W.Z. acknowledges Natural Science Foundation, China for funding support (#U1705233). H.-M.L was supported by Hong Kong Research Grants Council Area of Excellence Scheme (AoE/M-403/16). Thanks are also due to Dr. Mahendar Thudi, Dr. Himabindu Kudapa, Dr. Lekha Pazhamala and Mr. Prasad Bajaj from ICRISAT for useful discussions and support while analysing data and preparing the manuscript.
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