Assembly and comparative analysis of the mitochondrial genome in diploid potatoes.

IF 5.3 2区 生物学 Q1 PLANT SCIENCES Plant Cell Reports Pub Date : 2024-10-02 DOI:10.1007/s00299-024-03326-4
Qun Lian, Shuo Zhang, Zhiqiang Wu, Chunzhi Zhang, Sónia Negrão
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Abstract

Key message: We report the mitochondrial genome of 39 diploid potatoes and identify a candidate ORF potentially linked to cytoplasmic male sterility in potatoes. Potato (Solanum tuberosum L.) holds a critical position as the foremost non-grain food crop, playing a pivotal role in ensuring global food security. Diploid potatoes constitute a vital genetic resource pool, harboring the potential to revolutionize modern potato breeding. Nevertheless, diploid potatoes are relatively understudied, and mitochondrial DNA can provide valuable insights into key potato breeding traits such as CMS. In this study, we examine and assemble the mitochondrial genome evolution and diversity of 39 accessions of diploid potatoes using high-fidelity (HiFi) sequencing. We annotated 54 genes for all the investigated accessions, comprising 34 protein-coding genes, 3 rRNA genes, and 17 tRNA genes. Our analyses revealed differences in repeats sequences between wild and cultivated landraces. To understand the evolution of diploid maternal lineage inheritance, we conducted phylogenetic analysis, which clearly distinguished mitochondrial from nuclear gene trees, further supporting the evidence-based of clustering between wild and cultivated landraces accessions. Our study discovers new candidate ORFs associated with CMS in potatoes, including ORF137, which is homologous to other CMS in Solanaceae. Ultimately, this work bridges the gap in mitochondrial genome research for diploid potatoes, providing a steppingstone into evolutionary studies and potato breeding.

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二倍体马铃薯线粒体基因组的组装和比较分析。
关键信息:我们报告了 39 个二倍体马铃薯的线粒体基因组,并鉴定了一个可能与马铃薯细胞质雄性不育有关的候选 ORF。马铃薯(Solanum tuberosum L.)作为最重要的非粮食作物,在确保全球粮食安全方面发挥着关键作用。二倍体马铃薯是重要的遗传资源库,具有彻底改变现代马铃薯育种的潜力。然而,对二倍体马铃薯的研究相对不足,而线粒体 DNA 可以为 CMS 等关键马铃薯育种性状提供有价值的见解。在本研究中,我们利用高保真(HiFi)测序技术研究并组装了 39 个二倍体马铃薯品种的线粒体基因组进化和多样性。我们注释了所有调查品种的 54 个基因,包括 34 个蛋白质编码基因、3 个 rRNA 基因和 17 个 tRNA 基因。我们的分析揭示了野生种和栽培种之间重复序列的差异。为了了解二倍体母系遗传的进化过程,我们进行了系统进化分析,结果明确区分了线粒体基因树与核基因树,进一步支持了野生和栽培陆地栽培品种之间的聚类证据。我们的研究发现了与马铃薯CMS相关的新候选ORF,包括与茄科植物中其他CMS同源的ORF137。最终,这项工作弥补了二倍体马铃薯线粒体基因组研究的空白,为进化研究和马铃薯育种提供了一个平台。
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来源期刊
Plant Cell Reports
Plant Cell Reports 生物-植物科学
CiteScore
10.80
自引率
1.60%
发文量
135
审稿时长
3.2 months
期刊介绍: Plant Cell Reports publishes original, peer-reviewed articles on new advances in all aspects of plant cell science, plant genetics and molecular biology. Papers selected for publication contribute significant new advances to clearly identified technological problems and/or biological questions. The articles will prove relevant beyond the narrow topic of interest to a readership with broad scientific background. The coverage includes such topics as: - genomics and genetics - metabolism - cell biology - abiotic and biotic stress - phytopathology - gene transfer and expression - molecular pharming - systems biology - nanobiotechnology - genome editing - phenomics and synthetic biology The journal also publishes opinion papers, review and focus articles on the latest developments and new advances in research and technology in plant molecular biology and biotechnology.
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