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Main Conclusion <p>In the present research, the mitogenome of V. philippica—a perennial herbaceous plant with medicinal, ornamental, and edible value—was sequenced, assembled, and annotated using Illumina and Nanopore sequencing technologies. The complete mitogenome is 446,926 bp in length with a GC content of 44.31%, containing 38 protein‑coding genes (including all core subunits), 23 tRNA genes, and 3 rRNA genes. The genome features 143 dispersed repeats and 96 SSRs, and exhibits a strong codon usage bias toward A/T‑ending codons. A total of 400 potential RNA‑editing sites were predicted, predominantly in ccmB and nad4, with leucine showing the highest substitution frequency. We also identified 22,495 bp of chloroplast‑derived DNA, mainly comprising tRNA genes, underscoring the evolutionary conservation of tRNAs. Phylogenetic analysis firmly places V. philippica within Violaceae, closely related to Salicaceae and Passifloraceae. This comprehensive characterization provides crucial insights into the genetic architecture, evolutionary dynamics, and phylogenetic relationships of the V. philippica mitogenome, offering a valuable resource for future genetic studies, conservation strategies, and broader investigations into plant mitogenome evolution.</p> Abstract <p>We sequenced, assembled, and annotated the mitochondrial genome of <i>Viola philippica</i>, a medicinal herb used for treating infections and inflammation. <i>V. philippica</i> has a circular mitogenome with a total length of 446,926&#xa0;bp, a GC content of 44.31%, and contains 38 protein-coding genes (PCGs), 23 tRNA genes, and 3 rRNA genes. A total of 143 dispersed repeat sequences and 96 simple-sequence repeats (SSRs) were identified in the genome, with tetranucleotide repeats accounting for the highest proportion (38.55%). Codon preference analysis showed that <i>V. philippica</i> prefers codons ending in A/T, accounting for 86.66% of high-frequency codons. Four hundred RNA-editing sites were predicted, mainly distributed in <i>ccmB</i> and <i>nad4</i> genes, with leucine showing the highest conversion frequency after editing (43.75%). In addition, the mitogenome contained a 22,495&#xa0;bp sequence homologous to the chloroplast genome, mainly comprising tRNA genes. Phylogenetic analysis showed that <i>V. philippica</i> belongs to the family Violaceae and has a close relationship with Salicaceae and Passifloraceae. This study presents the first complete <i>V. philippica</i> mitogenome, providing insights into its genetic evolution and a scientific basis for elucidating the species’ phylogenetic relationships and genetic diversity. It expands our understanding of Violaceae genomic evolution and supports the conservation and utilization of this medicinal plant’s germplasm resources.</p>

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Assembly and comparative analysis of the complete mitochondrial genome of Viola philippica (Malpighiales, Violaceae)

  • 期刊论文

  • 发表日期：

    2026年7月4日

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  • Tao Wang,
  • Chunyu Tian,
  • Yanting Yang,
  • Zhiyong Li,
  • Wenlong Gong,
  • Lemeng Liu,
  • Yumei Feng,
  • Liqing Zhao,
  • Zinian Wu

摘要

Main Conclusion

In the present research, the mitogenome of V. philippica—a perennial herbaceous plant with medicinal, ornamental, and edible value—was sequenced, assembled, and annotated using Illumina and Nanopore sequencing technologies. The complete mitogenome is 446,926 bp in length with a GC content of 44.31%, containing 38 protein‑coding genes (including all core subunits), 23 tRNA genes, and 3 rRNA genes. The genome features 143 dispersed repeats and 96 SSRs, and exhibits a strong codon usage bias toward A/T‑ending codons. A total of 400 potential RNA‑editing sites were predicted, predominantly in ccmB and nad4, with leucine showing the highest substitution frequency. We also identified 22,495 bp of chloroplast‑derived DNA, mainly comprising tRNA genes, underscoring the evolutionary conservation of tRNAs. Phylogenetic analysis firmly places V. philippica within Violaceae, closely related to Salicaceae and Passifloraceae. This comprehensive characterization provides crucial insights into the genetic architecture, evolutionary dynamics, and phylogenetic relationships of the V. philippica mitogenome, offering a valuable resource for future genetic studies, conservation strategies, and broader investigations into plant mitogenome evolution.

Abstract

We sequenced, assembled, and annotated the mitochondrial genome of Viola philippica, a medicinal herb used for treating infections and inflammation. V. philippica has a circular mitogenome with a total length of 446,926 bp, a GC content of 44.31%, and contains 38 protein-coding genes (PCGs), 23 tRNA genes, and 3 rRNA genes. A total of 143 dispersed repeat sequences and 96 simple-sequence repeats (SSRs) were identified in the genome, with tetranucleotide repeats accounting for the highest proportion (38.55%). Codon preference analysis showed that V. philippica prefers codons ending in A/T, accounting for 86.66% of high-frequency codons. Four hundred RNA-editing sites were predicted, mainly distributed in ccmB and nad4 genes, with leucine showing the highest conversion frequency after editing (43.75%). In addition, the mitogenome contained a 22,495 bp sequence homologous to the chloroplast genome, mainly comprising tRNA genes. Phylogenetic analysis showed that V. philippica belongs to the family Violaceae and has a close relationship with Salicaceae and Passifloraceae. This study presents the first complete V. philippica mitogenome, providing insights into its genetic evolution and a scientific basis for elucidating the species’ phylogenetic relationships and genetic diversity. It expands our understanding of Violaceae genomic evolution and supports the conservation and utilization of this medicinal plant’s germplasm resources.