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

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.