De novo assembly of the complete mitochondrial genome of pepino (Solanum muricatum) using PacBio HiFi sequencing: insights into structure, phylogenetic implications, and RNA editing

文献类型： 外文期刊

第一作者： Li, Ziwei

作者： Li, Ziwei;Guo, Yanbing;Wu, Hongzhi;Jin, Shoulin;Liu, Jiaxun;Liang, Mingtai;Chen, Xia

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关键词： Solanum muricatum; HiFi sequencing; Mitochondrial genome; Phylogenetic relationship; RNA editing

期刊名称：BMC PLANT BIOLOGY （ 影响因子：5.3； 五年影响因子：5.9 ）

ISSN： 1471-2229

年卷期： 2024 年 24 卷 1 期

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收录情况： SCI

摘要： Background Solanum muricatum is an emerging horticultural fruit crop with rich nutritional and antioxidant properties. Although the chromosome-scale genome of this species has been sequenced, its mitochondrial genome sequence has not been reported to date. Results PacBio HiFi sequencing was used to assemble the circular mitogenome of S. muricatum, which was 433,466 bp in length. In total, 38 protein-coding, 19 tRNA, and 3 rRNA genes were annotated. The reticulate mitochondrial conformations with multiple junctions were verified by polymerase chain reaction, and codon usage, sequence repeats, and gene migration from chloroplast to mitochondrial genome were determined. A collinearity analysis of eight Solanum mitogenomes revealed high structural variability. Overall, 585 RNA editing sites in protein coding genes were identified based on RNA-seq data. Among them, mttB was the most frequently edited (52 times), followed by ccmB (46 times). A phylogenetic analysis based on the S. muricatum mitogenome and those of 39 other taxa (including 25 Solanaceae species) revealed the evolutionary and taxonomic status of S. muricatum. Conclusions We provide the first report of the assembled and annotated S. muricatum mitogenome. This information will help to lay the groundwork for future research on the evolutionary biology of Solanaceae species. Furthermore, the results will assist the development of molecular breeding strategies for S. muricatum based on the most beneficial agronomic traits of this species.

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