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Abstract <p>As a medicinally significant species within the Cucurbitaceae family, <i>Trichosanthes kirilowii</i> lacks comprehensive chloroplast genomic resources necessary for evolutionary and phylogenetic studies. In this study, we present its complete chloroplast genome: a circular DNA molecule measuring 156 924 bp, featuring a quadripartite structure with an LSC region (85 994 bp), an SSC region (18 334 bp), and two IRs (52 558 bp each). The genome contains 132 functional genes and exhibits a higher GC content in the IRs (43.01%) compared to the LSC (34.89%) and SSC (31.3%). We identified 198 long repeated segments and simple sequence repeat (SSR) motifs, mostly mononucleotide (A/T) variants. Codon usage strongly favors codons ending with A or U, particularly AGA and GAC. Comparative analysis across ten Cucurbitaceae species found conserved IR/SC boundaries, except in <i>Cucumis melo</i> (with divergent <i>rpl2</i> positioning) and <i>Lagenaria siceraria</i> (with the complete loss of <i>ndhF</i>). Hypervariable regions, such as <i>rps16</i> and the <i>psbK</i>-<i>trnS</i> spacer, along with non-coding spacers like <i>trnQ</i>-<i>trnR</i>, showed increased nucleotide diversity (<i>Pi</i>), in contrast with conserved IR regions. Evolutionary rate analysis showed predominant purifying selection (Ka/Ks ≤ 1). Phylogenetic reconstruction placed <i>T. kirilowii</i> in a distinct evolutionary clade, providing genomic foundations for molecular identification and biogeographic studies within Cucurbitaceae. This investigation establishes key chloroplast genomic resources and highlights mutation hotspots for future phylogenetic research.</p>

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Chloroplast Genome Architecture of Trichosanthes kirilowii Maxim.: Structural Evolution, Repetitive Element Dynamics, and Comparative Phylogenetic Insights in Cucurbitaceae

  • 期刊论文

  • 发表日期：

    2026年4月15日

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  • Z. Z. Jiang,
  • X. Y. Ge,
  • Z. H. Yang,
  • R. Y. Yuan

摘要

Abstract

As a medicinally significant species within the Cucurbitaceae family, Trichosanthes kirilowii lacks comprehensive chloroplast genomic resources necessary for evolutionary and phylogenetic studies. In this study, we present its complete chloroplast genome: a circular DNA molecule measuring 156 924 bp, featuring a quadripartite structure with an LSC region (85 994 bp), an SSC region (18 334 bp), and two IRs (52 558 bp each). The genome contains 132 functional genes and exhibits a higher GC content in the IRs (43.01%) compared to the LSC (34.89%) and SSC (31.3%). We identified 198 long repeated segments and simple sequence repeat (SSR) motifs, mostly mononucleotide (A/T) variants. Codon usage strongly favors codons ending with A or U, particularly AGA and GAC. Comparative analysis across ten Cucurbitaceae species found conserved IR/SC boundaries, except in Cucumis melo (with divergent rpl2 positioning) and Lagenaria siceraria (with the complete loss of ndhF). Hypervariable regions, such as rps16 and the psbK-trnS spacer, along with non-coding spacers like trnQ-trnR, showed increased nucleotide diversity (Pi), in contrast with conserved IR regions. Evolutionary rate analysis showed predominant purifying selection (Ka/Ks ≤ 1). Phylogenetic reconstruction placed T. kirilowii in a distinct evolutionary clade, providing genomic foundations for molecular identification and biogeographic studies within Cucurbitaceae. This investigation establishes key chloroplast genomic resources and highlights mutation hotspots for future phylogenetic research.