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<p>In recent years, the study of chloroplast genomes has gained increasing attention due to its significance in understanding plant evolution, phylogenetics, and genetic engineering. <i>Canavalia ensiformis</i> is an underutilized legume of agricultural and ecological relevance, and characterization of its chloroplast genome provides insights into species divergence, and potential biotechnological applications. Here, we assembled and comprehensively annotated the complete chloroplast genome of <i>C. ensiformis</i> and performed comparative analyses with other members of the tribe Phaseoleae (Fabaceae). The <i>C. ensiformis</i> chloroplast genome was assembled as a single circular molecule of 157,809&#xa0;bp and comprises four regions: a large single-copy (77,529&#xa0;bp), a small single-copy (18,934&#xa0;bp), and a pair of inverted repeats (30,673&#xa0;bp). The genome contains 89 protein-coding genes, 8 rRNA genes, and 39 tRNA genes. Relative synonymous codon usage analysis revealed a pronounced bias toward A/U-ending codons, reflecting plastid mutational pressure and translational selection. Repeat sequence analyses identified abundant A/T-rich simple sequence repeats and long repeats predominantly concentrated in the LSC region, thus&#xa0;indicating potential hotspots for structural variation. Nucleotide diversity analysis further detected elevated polymorphism in genes such as <i>ycf1</i> and <i>accD</i>, supporting their suitability as informative plastid markers for phylogenetic and population-level research. Phylogenomic analyses based on complete plastome sequences clarified the evolutionary placement of <i>C. ensiformis</i> within Phaseoleae, clustering it with other <i>Canavalia</i> species. These results contribute to a broader understanding of plastid genome evolution in legumes, one of the most species-rich plant families, and provide valuable genomic resources for future research in molecular phylogenetics and crop improvement.</p>

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Complete chloroplast genome of the underutilized legume jack bean (Canavalia ensiformis, Fabaceae) reveals genetic makeup, mutational hotspots, and phylogenetic relationships

  • 期刊论文

  • 发表日期：

    2026年2月11日

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  • Isna Arofatun Nikmah,
  • Wendy A. Mustaqim,
  • Wisnu H. Ardi,
  • Rugayah Rugayah,
  • Miftahur Rizqi Akbar,
  • Rizky Dwi Satrio

摘要

In recent years, the study of chloroplast genomes has gained increasing attention due to its significance in understanding plant evolution, phylogenetics, and genetic engineering. Canavalia ensiformis is an underutilized legume of agricultural and ecological relevance, and characterization of its chloroplast genome provides insights into species divergence, and potential biotechnological applications. Here, we assembled and comprehensively annotated the complete chloroplast genome of C. ensiformis and performed comparative analyses with other members of the tribe Phaseoleae (Fabaceae). The C. ensiformis chloroplast genome was assembled as a single circular molecule of 157,809 bp and comprises four regions: a large single-copy (77,529 bp), a small single-copy (18,934 bp), and a pair of inverted repeats (30,673 bp). The genome contains 89 protein-coding genes, 8 rRNA genes, and 39 tRNA genes. Relative synonymous codon usage analysis revealed a pronounced bias toward A/U-ending codons, reflecting plastid mutational pressure and translational selection. Repeat sequence analyses identified abundant A/T-rich simple sequence repeats and long repeats predominantly concentrated in the LSC region, thus indicating potential hotspots for structural variation. Nucleotide diversity analysis further detected elevated polymorphism in genes such as ycf1 and accD, supporting their suitability as informative plastid markers for phylogenetic and population-level research. Phylogenomic analyses based on complete plastome sequences clarified the evolutionary placement of C. ensiformis within Phaseoleae, clustering it with other Canavalia species. These results contribute to a broader understanding of plastid genome evolution in legumes, one of the most species-rich plant families, and provide valuable genomic resources for future research in molecular phylogenetics and crop improvement.