Black gram (Vigna mungo) is an important short duration grain legume crop. Black gram seeds provide an inexpensive source of dietary protein. Here, we applied the 10X Genomics linked‐read technology to obtain a de novo whole genome assembly of V. mungo cultivated variety Chai Nat 80 (CN80). The preliminary assembly contained 12,228 contigs and had an N50 length of 5.2 Mb. Subsequent scaffolding using the long‐range Chicago and HiC techniques yielded the first high‐quality, chromosome‐level assembly of 499 Mb comprising 11 pseudomolecules. Comparative genomics analyses based on sequence information from single‐copy orthologous genes revealed that black gram and mungbean (Vigna radiata) diverged about 2.7 million years ago . The transversion rate (4DTv) analysis in V. mungo revealed no evidence supporting a recent genome‐wide duplication event observed in the tetraploid créole bean (Vigna reflexo‐pilosa). The proportion of repetitive elements in the black gram genome is slightly lower than the numbers reported for related Vigna species. The majority of long terminal repeat retrotransposons appeared to integrate into the genome within the last five million years. We also examined alternative splicing events in V. mungo using full‐length transcript sequences. While intron retention was the most prevalent mode of alternative splicing in several plant species, alternative 3' acceptor site selection represented the majority of events in black gram. Our high‐quality genome assembly along with the genomic variation information from the germplasm provides valuable resources for accelerating the development of elite varieties through marker‐assisted breeding and for future comparative genomics and phylogenetic studies in legume species.

中文翻译：

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黑革兰 (Vigna mungo) 基因组的染色体规模组装。

黑豆 ( Vigna mungo ) 是一种重要的短期谷物豆类作物。黑克种子提供廉价的膳食蛋白质来源。在这里，我们采用了10X基因组链接阅读技术，以获得一个从头全基因组组装的五蒙哥栽培品种柴纳特80（CN80）。初步组装包含 12,228 个重叠群，N50 长度为 5.2 Mb。随后使用长程芝加哥和 HiC 技术的支架产生了第一个高质量的染色体水平组装，499 Mb，包括 11 个假分子。基于单拷贝直向同源基因序列信息的比较基因组学分析表明，黑豆和绿豆（Vigna radiata) 大约在 270 万年前分化。V. mungo的颠换率 (4DTv) 分析显示没有证据支持最近在四倍体克里奥尔豆 ( Vigna reflexo-pilosa ) 中观察到的全基因组重复事件。黑革兰基因组中重复元件的比例略低于相关豇豆物种报告的数量。大多数长末端重复反转录转座子似乎在过去五百万年内整合到基因组中。我们还检查了V. mungo 中的替代剪接事件使用全长转录序列。虽然内含子保留是几种植物物种中最普遍的选择性剪接模式，但替代性 3' 受体位点选择代表了黑色革兰氏菌中的大多数事件。我们的高质量基因组组装以及来自种质的基因组变异信息为通过标记辅助育种加速优良品种的开发以及未来豆类物种的比较基因组学和系统发育研究提供了宝贵的资源。