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

As a medicinally significant species within the Cucurbitaceae family, Trichosanthes kirilowii is currently lacking comprehensive chloroplast genomic resources that are essential for conducting evolutionary and phylogenetic studies. In this study, we present a characterization of its complete chloroplast genome, which consists of a circular DNA molecule measuring 156,924 bp with a quadripartite structure: LSC (85,994 bp), SSC (18,334 bp), and two IRs (52,558 bp each). This genome encompasses 132 functional genes and exhibits elevated GC content in the IRs (43.01%) compared to the LSC (34.89%) and SSC (31.3%). Analysis of repetitive sequences identified 198 long repeats as well as SSR motifs predominantly consisting of mononucleotide (A/T) variants. Codon usage displayed a strong preference for A/U-ending codons, revealing an extreme bias towards AGA and GAC. Comparative analysis across ten Cucurbitaceae species uncovered conserved IR/SC boundaries except in Cucumis melo —which exhibited divergent positioning of rpl2 —and Lagenaria siceraria —which showed a complete loss of ndhF . Hypervariable regions such as rps16 and psbK - trnS along with non-coding spacers like trnQ - trnR exhibited increased nucleotide diversity (Pi), contrasting sharply with the conservation observed in the IR regions. Evolutionary rate analysis indicated predominant purifying selection with Ka/Ks ratios ≤ 1. Phylogenetic reconstruction successfully positioned T. kirilowii within a distinct evolutionary clade, thus providing valuable genomic foundations for molecular identification and biogeographic studies within the Cucurbitaceae family. This investigation establishes critical chloroplast genomic resources while also identifying mutation hotspots which can be explored further in future phylogenetic research endeavors.