AUTHOR=Liang Le , Zhang Jianwei , Xiao Jiachang , Li Xiaomei , Xie Yongdong , Tan Huaqiang , Song Xueping , Zhu Li , Xue Xinru , Xu Linyu , Zhou Peihan , Ran Jianzhao , Sun Bo , Huang Zhi , Tang Yi , Lin Lijin , Sun Guochao , Lai Yunsun , Li Huanxiu 

TITLE=Genome and pan-genome assembly of asparagus bean (Vigna unguiculata ssp. sesquipedialis) reveal the genetic basis of cold adaptation

JOURNAL=Frontiers in Plant Science

VOLUME=13

YEAR=2022

URL=https://www.frontiersin.org/journals/plant-science/articles/10.3389/fpls.2022.1059804

DOI=10.3389/fpls.2022.1059804

ISSN=1664-462X

ABSTRACT=<p>Asparagus bean (<italic>Vigna unguiculata</italic> ssp. <italic>sesquipedialis</italic>) is an important cowpea subspecies. We assembled the genomes of Ningjiang 3 (NJ, 550.31 Mb) and Dubai bean (DB, 564.12 Mb) for comparative genomics analysis. The whole-genome duplication events of DB and NJ occurred at 64.55 and 64.81 Mya, respectively, while the divergence between soybean and <italic>Vigna</italic> occurred in the Paleogene period. NJ genes underwent positive selection and amplification in response to temperature and abiotic stress. In species-specific gene families, NJ is mainly enriched in response to abiotic stress, while DB is primarily enriched in respiration and photosynthesis. We established the pan-genomes of four accessions (NJ, DB, IT97K-499-35 and Xiabao II) and identified 20,336 (70.5%) core genes present in all the accessions, 6,507 (55.56%) variable genes in two individuals, and 2,004 (6.95%) unique genes. The final pan genome is 616.35 Mb, and the core genome is 399.78 Mb. The variable genes are manifested mainly in stress response functions, ABC transporters, seed storage, and dormancy control. In the pan-genome sequence variation analysis, genes affected by presence/absence variants were enriched in biological processes associated with defense responses, immune system processes, signal transduction, and agronomic traits. The results of the present study provide genetic data that could facilitate efficient asparagus bean genetic improvement, especially in producing cold-adapted asparagus bean.</p>