Table_1_Genome and pan-genome assembly of asparagus bean (Vigna unguiculata ssp. sesquipedialis) reveal the genetic basis of cold adaptation.xlsx

Asparagus bean (Vigna unguiculata ssp. sesquipedialis) 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 Vigna 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.

长豇豆（Vigna unguiculata ssp. sesquipedialis）是一类重要的豇豆亚种。本研究对宁豇3号（简称NJ，基因组组装大小550.31 Mb）与迪拜豆（简称DB，基因组组装大小564.12 Mb）进行了全基因组组装，以开展比较基因组学分析。DB与NJ的全基因组复制事件分别发生于64.55百万年前（Mya）与64.81百万年前，而大豆与豇豆属（Vigna）物种的分化发生在古近纪（Paleogene）时期。宁豇3号的基因在应对温度与非生物胁迫的过程中经历了正向选择与基因扩增事件。在物种特异性基因家族中，NJ的基因主要富集于非生物胁迫响应通路，而DB的基因则主要富集于呼吸作用与光合作用通路。本研究构建了4份种质材料（NJ、DB、IT97K-499-35及夏宝II号）的泛基因组（pan-genome），共鉴定出20336个核心基因（占全部基因的70.5%，存在于所有供试种质中）、6507个变异基因（占比55.56%，存在于2份材料中）以及2004个特有基因（占比6.95%）。最终构建的泛基因组总长度为616.35 Mb，核心基因组（core genome）总长度为399.78 Mb。变异基因主要富集于胁迫响应功能、ABC转运蛋白（ABC transporters）、种子储存与休眠调控相关通路。在泛基因组序列变异分析中，受存在/缺失变异影响的基因显著富集于防御响应、免疫系统进程、信号转导以及农艺性状相关的生物学过程。本研究结果可为长豇豆的高效遗传改良提供宝贵的遗传数据支撑，尤其有助于培育耐低温长豇豆品种。