Data_Sheet_3_Genome, Transcriptome, and Germplasm Sequencing Uncovers Functional Variation in the Warm-Season Grain Legume Horsegram Macrotyloma uniflorum (Lam.) Verdc..PDF

Horsegram is a grain legume with excellent nutritional and remedial properties and good climate resilience, able to adapt to harsh environmental conditions. Here, we used a combination of short- and long-read sequencing technologies to generate a genome sequence of 279.12Mb, covering 83.53% of the estimated total size of the horsegram genome, and we annotated 24,521 genes. De novo prediction of DNA repeats showed that approximately 25.04% of the horsegram genome was made up of repetitive sequences, the lowest among the legume genomes sequenced so far. The major transcription factors identified in the horsegram genome were bHLH, ERF, C2H2, WRKY, NAC, MYB, and bZIP, suggesting that horsegram is resistant to drought. Interestingly, the genome is abundant in Bowman–Birk protease inhibitors (BBIs), which can be used as a functional food ingredient. The results of maximum likelihood phylogenetic and estimated synonymous substitution analyses suggested that horsegram is closely related to the common bean and diverged approximately 10.17 million years ago. The double-digested restriction associated DNA (ddRAD) sequencing of 40 germplasms allowed us to identify 3,942 high-quality SNPs in the horsegram genome. A genome-wide association study with powdery mildew identified 10 significant associations similar to the MLO and RPW8.2 genes. The reference genome and other genomic information presented in this study will be of great value to horsegram breeding programs. In addition, keeping the increasing demand for food with nutraceutical values in view, these genomic data provide opportunities to explore the possibility of horsegram for use as a source of food and nutraceuticals.

Horsegram（马豆）作为一种具有卓越营养与药用特性，且对气候适应能力优良的谷物豆科植物，能够适应严酷的生态环境。本研究中，我们运用了短读长与长读长测序技术的结合，成功构建了马豆基因组序列，序列长度达到279.12Mb，覆盖了马豆基因组估计总量的83.53%，并注释了24,521个基因。基于从头预测的DNA重复序列分析显示，马豆基因组中约25.04%由重复序列构成，是目前已测序豆科植物基因组中比例最低的。在马豆基因组中鉴定出的主要转录因子包括bHLH、ERF、C2H2、WRKY、NAC、MYB和bZIP，这表明马豆对干旱具有抗性。有趣的是，马豆基因组富含Bowman–Birk蛋白酶抑制剂（BBIs），这些抑制剂可作为功能性食品成分。最大似然法系统发育分析和同义替换估计分析的结果表明，马豆与普通菜豆亲缘关系密切，约在1017万年前发生分化。对40个种质资源进行双酶切限制性片段长度多态性（ddRAD）测序，使我们能够在马豆基因组中识别出3,942个高质量的单核苷酸多态性（SNPs）。与白粉病进行的全基因组关联分析鉴定出与MLO和RPW8.2基因相似的10个显著关联。本研究中提供的参考基因组及其他基因组信息将对马豆育种计划具有极大的价值。此外，鉴于对富含营养价值的食品需求日益增长，这些基因组数据为探索马豆作为食品和功能性食品来源的可能性提供了机遇。