Characterization of the complete mitochondrial genome of the rice bean (Vigna umbellata).

IF 4.3 2区 生物学 Q1 PLANT SCIENCES
Yuqing Wu, Kai Zhang, Boyang Zhang, Yuqian Li, Guiming Liu, Zhen Liang, Jiewei Zhang
{"title":"Characterization of the complete mitochondrial genome of the rice bean (Vigna umbellata).","authors":"Yuqing Wu, Kai Zhang, Boyang Zhang, Yuqian Li, Guiming Liu, Zhen Liang, Jiewei Zhang","doi":"10.1186/s12870-024-05963-z","DOIUrl":null,"url":null,"abstract":"<p><strong>Background: </strong>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.</p><p><strong>Results: </strong>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.</p><p><strong>Conclusions: </strong>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.</p>","PeriodicalId":9198,"journal":{"name":"BMC Plant Biology","volume":"24 1","pages":"1239"},"PeriodicalIF":4.3000,"publicationDate":"2024-12-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11664933/pdf/","citationCount":"0","resultStr":null,"platform":"Semanticscholar","paperid":null,"PeriodicalName":"BMC Plant Biology","FirstCategoryId":"99","ListUrlMain":"https://doi.org/10.1186/s12870-024-05963-z","RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q1","JCRName":"PLANT SCIENCES","Score":null,"Total":0}
引用次数: 0

Abstract

Background: 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.

Results: 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.

Conclusions: 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.

稻豆(Vigna umellata)线粒体全基因组的鉴定。
背景:豆荚(Vigna umellata)是一种被低估的豆科作物,对土壤肥力较差具有较强的适应性,具有增强全球粮食安全的巨大潜力。由于其高蛋白含量、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。虽然已获得高质量的稻豆基因组,但其线粒体基因组(mitogenome)序列尚未报道。结果:首次利用PacBio HiFi测序和Geseq软件对水稻豆有丝分裂基因组进行了组装和注释。有丝分裂基因组是一个长度为404493 bp的圆形分子,包含32个蛋白质编码基因,17个trna和3个rrna。密码子使用和序列重复也被测定。在水稻豆中检测到6个从叶绿体到有丝分裂基因组的基因迁移事件。通过对稻豆有丝分裂基因组和其他25个分类群(其中23个属Fabales种)的系统发育分析,阐明了稻豆的进化和分类地位。此外,7个Fabales有丝分裂基因组的共线性分析显示了高度的结构变异性。总共鉴定出473个蛋白质编码基因中的RNA编辑位点。结论:本研究首次完成了水稻豆有丝分裂基因组的测序、组装、注释和分析,为了解该物种的进化提供了有价值的背景信息。这些发现为未来的遗传研究和改良水稻豆的分子育种工作奠定了基础。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
求助全文
约1分钟内获得全文 求助全文
来源期刊
BMC Plant Biology
BMC Plant Biology 生物-植物科学
CiteScore
8.40
自引率
3.80%
发文量
539
审稿时长
3.8 months
期刊介绍: BMC Plant Biology is an open access, peer-reviewed journal that considers articles on all aspects of plant biology, including molecular, cellular, tissue, organ and whole organism research.
×
引用
GB/T 7714-2015
复制
MLA
复制
APA
复制
导出至
BibTeX EndNote RefMan NoteFirst NoteExpress
×
提示
您的信息不完整,为了账户安全,请先补充。
现在去补充
×
提示
您因"违规操作"
具体请查看互助需知
我知道了
×
提示
确定
请完成安全验证×
copy
已复制链接
快去分享给好友吧!
我知道了
右上角分享
点击右上角分享
0
联系我们:info@booksci.cn Book学术提供免费学术资源搜索服务,方便国内外学者检索中英文文献。致力于提供最便捷和优质的服务体验。 Copyright © 2023 布克学术 All rights reserved.
京ICP备2023020795号-1
ghs 京公网安备 11010802042870号
Book学术文献互助
Book学术文献互助群
群 号:604180095
Book学术官方微信