Wu Yuqing, Zhang Kai, Zhang Boyang, Li Yuqian, Liu Guiming, Liang Zhen, Zhang Jiewei
School of Life Science, Shanxi University, Taiyuan, Shanxi, 030006, China.
Beijing Key Laboratory of Agricultural Genetic Resources and Biotechnology, Beijing Academy of Agricultural and Forestry Sciences, Beijing, 100097, China.
BMC Plant Biol. 2024 Dec 23;24(1):1239. doi: 10.1186/s12870-024-05963-z.
Rice bean (Vigna umbellata), an underrated legume crop, demonstrates strong adaptability to poor soil fertility and has significant potential to enhance global food security. It is valuable both as a vegetable and fodder crop due to its high protein content, essential fatty acids, and micronutrients. Despite the sequencing of a high-quality genome of rice bean, its mitochondrial genome (mitogenome) sequence has not yet been reported.
For the first time, the rice bean mitogenome was assembled and annotated using PacBio HiFi sequencing and Geseq software. The mitogenome is a circular molecule with a length of 404,493 bp, containing 32 protein-coding genes, 17 tRNAs, and 3 rRNAs. Codon usage and sequence repeats were also determined. Six gene migration events from the chloroplast to the mitogenome were detected in rice bean. A phylogenetic analysis, including the rice bean mitogenome and 25 other taxa (23 of which are Fabales species), clarified the evolutionary and taxonomic status of rice bean. Additionally, a collinearity analysis of seven Fabales mitogenomes revealed high structural variability. In total, 473 RNA editing sites in protein-coding genes were identified.
This study presents the first sequencing, assembly, annotation, and analysis of the rice bean mitogenome, providing valuable background information for understanding the evolution of this species. These findings lay the groundwork for future genetic studies and molecular breeding efforts aimed at improving rice bean.
饭豆（Vigna umbellata）是一种未得到充分重视的豆类作物，对土壤肥力贫瘠具有很强的适应性，在增强全球粮食安全方面具有巨大潜力。因其高蛋白含量、必需脂肪酸和微量营养素，它作为蔬菜和饲料作物都很有价值。尽管已经对饭豆的高质量基因组进行了测序，但其线粒体基因组（mitogenome）序列尚未见报道。
首次利用PacBio HiFi测序和Geseq软件组装并注释了饭豆的线粒体基因组。该线粒体基因组是一个长度为404,493 bp的环状分子，包含32个蛋白质编码基因、17个tRNA和3个rRNA。还确定了密码子使用情况和序列重复情况。在饭豆中检测到6个从叶绿体到线粒体基因组的基因迁移事件。一项系统发育分析，包括饭豆线粒体基因组和其他25个分类单元（其中23个是豆目物种），阐明了饭豆的进化和分类地位。此外，对7个豆目线粒体基因组的共线性分析揭示了高度的结构变异性。总共在蛋白质编码基因中鉴定出473个RNA编辑位点。
本研究首次对饭豆线粒体基因组进行了测序、组装、注释和分析，为理解该物种的进化提供了有价值的背景信息。这些发现为未来旨在改良饭豆的遗传研究和分子育种工作奠定了基础。
