Browse Articles

Article|01 Dec 2020|OPEN
A chromosome-scale genome assembly of a diploid alfalfa, the progenitor of autotetraploid alfalfa
Ao Li1 , Ai Liu1 , Xin Du1 , Jin-Yuan Chen1 , Mou Yin1 , Hong-Yin Hu1 , Nawal Shrestha1 , Sheng-Dan Wu1 , Hai-Qing Wang2 , Quan-Wen Dou2 , Zhi-Peng Liu3 , Jian-Quan Liu1,4 and Yong-Zhi Yang1 , , Guang-Peng Ren,1 ,
1State Key Laboratory of Grassland Agro-Ecosystems, Institute of Innovation Ecology & School of Life Sciences, Lanzhou University, Lanzhou, China
2Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
3State Key Laboratory of Grassland Agro-Ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
4Key Laboratory of Bio-Resources and Eco-Environment of the Ministry of Education & State Key Lab of Hydraulics & Mountain River Engineering, College of Life Sciences, Sichuan University, Chengdu, China
*Corresponding author. E-mail: yangyongzhi2008@gmail.com,rengp@lzu.edu.cn

Horticulture Research 7,
Article number: 194 (2020)
doi: https://doi.org/10.1038/s41438-020-00417-7
Views: 946

Received: 19 May 2020
Revised: 28 Aug 2020
Accepted: 04 Sep 2020
Published online: 01 Dec 2020

Abstract

Alfalfa (Medicago sativa L.) is one of the most important and widely cultivated forage crops. It is commonly used as a vegetable and medicinal herb because of its excellent nutritional quality and significant economic value. Based on Illumina, Nanopore and Hi-C data, we assembled a chromosome-scale assembly of Medicago sativa spp. caerulea (voucher PI464715), the direct diploid progenitor of autotetraploid alfalfa. The assembled genome comprises 793.2 Mb of genomic sequence and 47,202 annotated protein-coding genes. The contig N50 length is 3.86 Mb. This genome is almost twofold larger and contains more annotated protein-coding genes than that of its close relative, Medicago truncatula (420 Mb and 44,623 genes). The more expanded gene families compared with those in M. truncatula and the expansion of repetitive elements rather than whole-genome duplication (i.e., the two species share the ancestral Papilionoideae whole-genome duplication event) may have contributed to the large genome size of M. sativa spp. caerulea. Comparative and evolutionary analyses revealed that M. sativa spp. caerulea diverged from M. truncatula ~5.2 million years ago, and the chromosomal fissions and fusions detected between the two genomes occurred during the divergence of the two species. In addition, we identified 489 resistance (R) genes and 82 and 85 candidate genes involved in the lignin and cellulose biosynthesis pathways, respectively. The near-complete and accurate diploid alfalfa reference genome obtained herein serves as an important complement to the recently assembled autotetraploid alfalfa genome and will provide valuable genomic resources for investigating the genomic architecture of autotetraploid alfalfa as well as for improving breeding strategies in alfalfa.