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

Garg, V., Dudchenko, O., Wang, J., Khan, A.W., Gupta, S., Kaur, P., Han, K., Saxena, R.K., Kale, S.M., Pham, M., Yu, J., Chitikineni, A., Zhang, Z., Fan, G., Lui, C., Valluri, V., Meng, F., Bhandari, A., Liu, X., Yang, T., Chen, H., Valliyodan, B., Roorkiwal, M., Shi, C., Yang, H.B., Durand, N.C., Pandey, M.K., Li, G., Barmukh, R., Wang, X., Chen, X., Lam, H-M, Jiang, H., Zong, X., Liang, X., Liu, X., Liao, B., Guo, B., Jackson, S., Nguyen, H.T., Zhuang, W., Shubo, W., Wang, X., Aiden, E.L., Bennetzen, J.L. and Varshney, R.K.ORCID: 0000-0002-4562-9131 (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 . In Press.

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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.


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.


We employed in situ Hi-C data to improve the existing draft genomes and performed different evolutionary and comparative analyses using improved genome assemblies.


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’.


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: Journal Article
Murdoch Affiliation(s): Centre for Crop and Food Innovation
Food Futures Institute
Western Australian State Agricultural Biotechnology Centre
Publisher: Elsevier B.V. on behalf of Cairo University
Copyright: © 2021 The Authors.
United Nations SDGs: Goal 12: Responsible Consumption and Production
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