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<p><i>Coccinia</i> species are endemic to Africa, except for <i>Coccinia grandis,</i> which is also native to southern Asia and exhibits an intricate taxonomic history. However, limited information is available regarding its molecular biology and chloroplast diversity. This study analyzed eight plastomes of four <i>Coccinia</i> species to assess their structural variations, phylogenetic relationships, and evolutionary patterns. The findings revealed that the sizes of the complete chloroplast genomes ranged from 157,035 to 157,558&#xa0;bp. The complete plastomes depicted a quadripartite structure comprising large single copy, small single copy, and two inverted repeats regions and 129 genes; 84 protein-coding genes, eight rRNAs, and 37 tRNAs. Comparative analysis indicated that the gene content and order among <i>Coccinia</i> species were highly identical. RNA editing displayed that <i>Coccinia</i> plastomes exhibited 192 editing events, activating corresponding codon changes across 78 protein-coding genes. Eight non-coding and five coding regions were revealed to exhibit high nucleotide variability. The phylogenetic analysis depicted <i>Coccinia</i> as a monophyletic genus with <i>C. grandis</i> populations from Asia and Africa forming a single clade. This suggests that the morphological difference in corolla color among populations of <i>C</i>. <i>grandis</i> results from intraspecific variation and thus supports their synonymization. The divergence times analysis indicated that <i>Coccinia</i> diverged around 4.4 million years ago. These findings advance molecular taxonomy in clarifying phylogenetic relationships within Cucurbitaceae and establish DNA barcodes that could contribute to further studies in phylogeny and population genetics in <i>Coccinia</i>.</p>

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Comparative chloroplast genome analysis of Coccinia species: Insights into delimitation, phylogeny, and divergence time estimation

  • 期刊论文

  • 发表日期：

    2025年9月30日

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  • Jacinta Katunge Kawenze,
  • Elijah Mbandi Mkala,
  • Clintone Onyango Ochieng,
  • Emmanuel Nyongesa Waswa,
  • Elizabeth Syowai Mutinda,
  • Victoire Izabayo,
  • Harriet Melany Nyamvula,
  • Paul Musili,
  • Guang-Wan Hu

摘要

Coccinia species are endemic to Africa, except for Coccinia grandis, which is also native to southern Asia and exhibits an intricate taxonomic history. However, limited information is available regarding its molecular biology and chloroplast diversity. This study analyzed eight plastomes of four Coccinia species to assess their structural variations, phylogenetic relationships, and evolutionary patterns. The findings revealed that the sizes of the complete chloroplast genomes ranged from 157,035 to 157,558 bp. The complete plastomes depicted a quadripartite structure comprising large single copy, small single copy, and two inverted repeats regions and 129 genes; 84 protein-coding genes, eight rRNAs, and 37 tRNAs. Comparative analysis indicated that the gene content and order among Coccinia species were highly identical. RNA editing displayed that Coccinia plastomes exhibited 192 editing events, activating corresponding codon changes across 78 protein-coding genes. Eight non-coding and five coding regions were revealed to exhibit high nucleotide variability. The phylogenetic analysis depicted Coccinia as a monophyletic genus with C. grandis populations from Asia and Africa forming a single clade. This suggests that the morphological difference in corolla color among populations of C. grandis results from intraspecific variation and thus supports their synonymization. The divergence times analysis indicated that Coccinia diverged around 4.4 million years ago. These findings advance molecular taxonomy in clarifying phylogenetic relationships within Cucurbitaceae and establish DNA barcodes that could contribute to further studies in phylogeny and population genetics in Coccinia.