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

Authors: GARG, VANIKA - International Crops Research Institute For Semi-Arid Tropics (ICRISAT) - India; DUDCHENKO, OLGA - Baylor College Of Medicine; WANG, JINPENG - North China University Of Science And Technology; KHAN, AAMIR - International Crops Research Institute For Semi-Arid Tropics (ICRISAT) - India; GUPTA, SAURABH - Max Planck Institute Of Molecular Plant Physiology; KAUR, PARWINDER - University Of Western Australia; HAN, KAI - Bgi Shenzhen; SAXENA, RACHIT - International Crops Research Institute For Semi-Arid Tropics (ICRISAT) - India; KALE, SANDIP - Leibniz Institute Of Plant Genetics And Crop Plant Research; PHAM, MELANIE - Baylor College Of Medicine; YU, JIGAO - North China University Of Science And Technology; CHITIKINENI, ANNAPURNA - International Crops Research Institute For Semi-Arid Tropics (ICRISAT) - India; ZHANG, ZHIKANG - North China University Of Science And Technology; FAN, GUANGYI - Bgi Shenzhen; LUI, CHRISTOPHER - Baylor College Of Medicine; VALLURI, VINODKUMAR - International Crops Research Institute For Semi-Arid Tropics (ICRISAT) - India; MENG, FANBO - North China University Of Science And Technology; BHANDARI, ADITI - International Crops Research Institute For Semi-Arid Tropics (ICRISAT) - India; LIU, XIAOCHUAN - Bgi Shenzhen; YANG, TAO - Chinese Academy Of Agricultural Sciences; CHEN, HUA - Fujian Agricultural & Forestry University; VALLIYODAN, BABU - Lincoln University Of Missouri; ROORKIWAL, MANISH - International Crops Research Institute For Semi-Arid Tropics (ICRISAT) - India; SHI, CHENGCHENG - Bgi Shenzhen; YANG, HONG BIN - Guangdong Academy Of Agricultural Sciences; DURAND, NEVA - Baylor College Of Medicine; PANDEY, MANISH - International Crops Research Institute For Semi-Arid Tropics (ICRISAT) - India; LI, GUOWEI - Shandong Academy Of Agricultural Sciences; BARMUKH, RUTWIK - International Crops Research Institute For Semi-Arid Tropics (ICRISAT) - India; WANG, XINGJUN - Shandong Academy Of Agricultural Sciences; CHEN, XIAOPING - Guangdong Academy Of Agricultural Sciences; LAM, HON-MING - The Chinese University Of Hong Kong (CUHK); JIANG, HUIFANG - Chinese Academy Of Agricultural Sciences; ZONG, XUXIAO - Chinese Academy Of Agricultural Sciences; LIANG, XUANQIANG - Guangdong Academy Of Agricultural Sciences; LIU, XIN - Bgi Shenzhen; LIAO, BOSHOU - Chinese Academy Of Agricultural Sciences; Guo, Baozhu; JACKSON, SCOTT - Bayer Corporation; NGUYEN, HENRY - University Of Missouri; ZHUANG, WEIJIAN - Fujian Agriculture And Forest University; WAN, SHUBO - Shandong Academy Of Agricultural Sciences; WANG, XIYIN - North China University Of Science And Technology; AIDEN, EREZ - Baylor College Of Medicine; BENNETZEN, JEFFREY - University Of Georgia; VARSHNEY, RAJEEV - International Crops Research Institute For Semi-Arid Tropics (ICRISAT) - India

Submitted to: Journal of Advanced Research
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 10/24/2021
Publication Date: 11/3/2021
Citation: 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., Durand, N.C., Pandey, M.K., Li, G., Barmukh, R., Wang, X., Chen, X., Lam, H., Jiang, H., Zong, X., Liang, X., Liu, X., Liao, B., Guo, B., Jackson, S., Nguyen, H.T., Zhuang, W., Wan, S., Wang, X., Aiden, E.L., Bennetzen, J.L., 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. 42:315-329. https://doi.org/10.1016/j.jare.2021.10.009.
DOI: https://doi.org/10.1016/j.jare.2021.10.009

Interpretive Summary: A high-quality reference genome is pre-requisite to understand genome organization, to describe evolutionary events and to precisely identify genomic regions and genes associated with agronomically important traits. Therefore, in this study, we used in-situ Hi-C data to develop improved chromosome-length genome assemblies of chickpea, pigeonpea, soybean, wild peanut Arachis duranensis and A. ipaensis, and subterranean clover. 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 such unique legume traits as nodulation in legumes, gravitropism in peanut, and oil biosynthesis in oilseed legume crops such as peanut and soybean. We have also demonstrated the utility of improved genome assemblies for genetic analysis and breeding applications for crop improvement.

Technical Abstract: Legume crops are an important source of protein for human health and in fixing atmospheric N2 for soil enrichment. Although draft genome assemblies were generated in several legume crops, many of them are not high quality because they are mainly based on short reads. Here, we present improved chromosome-length genome assemblies of six legume species: chickpea, pigeonpea, soybean, subterranean clover and two wild progenitor species (Arachis duranensis and A. ipaensis) of cultivated groundnut, using in situ Hi-C analysis. 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 such unique legume traits as nodulation in legumes, gravitropism in groundnut, and oil biosynthesis in oilseed legume crops such as groundnut and soybean. We have also demonstrated the utility of improved genome assemblies for genetic analysis and breeding applications for crop improvement.