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Background <p><i>Prinsepia uniflora</i> is a shrub of considerable medicinal and ecological importance. Although a chromosome-scale nuclear genome assembly is available for this species, the mitochondrial (mt) genome remains uncharacterized, which has significantly restricted more comprehensive genomic and evolutionary studies of this species.</p> Results <p>Using PacBio HiFi sequencing, we assembled the circular mt genome of <i>P. uniflora</i>, which spanned 328,095&#xa0;bp and contained 35 protein-coding genes (PCGs), 18 tRNA genes, and 3 rRNA genes. Further analyses were conducted to characterize the mt genome, including assessments of codon usage, repeat sequences, and selective pressure. The results revealed an abundance of short repetitive sequences and preferential use of A/T-ending codons. The codon usage bias observed in PCGs appeared to be influenced by natural and artificial selection. In addition, 20 large fragments were identified as having been transferred from chloroplast genome to the mt genome. Collinearity analysis of the mt genome across Rosaceae species revealed a close relationship among <i>P. uniflora</i>, <i>Prunus padus</i>, and <i>Prunus cerasus</i>. Phylogenetic analyses using both maximum likelihood (ML) and Bayesian inference methods further clarified the evolutionary position of <i>P. uniflora</i>.</p> Conclusion <p>This study presents the first mt genome assembly for the genus <i>Prinsepia</i> and provides a valuable genomic resource for future molecular research on this genus. Our study provides key insights into evolutionary relationships with the Rosaceae family.</p>

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The complete mitochondrial genome of Prinsepia uniflora (Rosaceae): De novo assembly, characterization, and phylogenetic analysis

  • 期刊论文

  • 出版模式：

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  • 发表日期：

    2026年2月11日

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  • Dandan Ma,
  • Lu Ma,
  • Jiawen Cui,
  • Erdong Zhang,
  • Ting Guo,
  • Lei Zhang

摘要

Background

Prinsepia uniflora is a shrub of considerable medicinal and ecological importance. Although a chromosome-scale nuclear genome assembly is available for this species, the mitochondrial (mt) genome remains uncharacterized, which has significantly restricted more comprehensive genomic and evolutionary studies of this species.

Results

Using PacBio HiFi sequencing, we assembled the circular mt genome of P. uniflora, which spanned 328,095 bp and contained 35 protein-coding genes (PCGs), 18 tRNA genes, and 3 rRNA genes. Further analyses were conducted to characterize the mt genome, including assessments of codon usage, repeat sequences, and selective pressure. The results revealed an abundance of short repetitive sequences and preferential use of A/T-ending codons. The codon usage bias observed in PCGs appeared to be influenced by natural and artificial selection. In addition, 20 large fragments were identified as having been transferred from chloroplast genome to the mt genome. Collinearity analysis of the mt genome across Rosaceae species revealed a close relationship among P. uniflora, Prunus padus, and Prunus cerasus. Phylogenetic analyses using both maximum likelihood (ML) and Bayesian inference methods further clarified the evolutionary position of P. uniflora.

Conclusion

This study presents the first mt genome assembly for the genus Prinsepia and provides a valuable genomic resource for future molecular research on this genus. Our study provides key insights into evolutionary relationships with the Rosaceae family.