Comparative analysis the chloroplast genomes of Begonia species Provide insights into molecular evolution, species identification and phylogenetic relationship

The chloroplast genome (plastome) plays a pivotal in plant evolution, phylogenetics, and adaptive studies. Begonia, a hyperdiverse angiosperm genus widely distributed across tropical and subtropical regions, holds significant scientific value for investigating plastome evolution and variation. In this study, we sequenced and assembled the plastome of 25 Chinese Begonia species, and combined these with 51 publicly available Begonia plastomes from the NCBI database to systematically analyze plastome structural characteristics, diversity mechanisms, adaptive evolution in low-light environments, and hypervariable regions. The 25 newly sequenced Begonia plastomes exhibited a typical quadripartite structure, with lengths ranging from 167,365 bp to 169,901 bp, and relatively conserved gene content, including 92-93 protein-coding genes, 42 tRNA genes, and 8 rRNA genes. Simple sequence repeat (SSR) analysis revealed that mononucleotide repeats were the most abundant, with A/T-rich motifs predominating, while complex repeats were primarily palindromic and forward repeats. Relative synonymous codon usage (RSCU) showed consistent bias across species, suggesting shared environmental pressures. Inverted Repeat (IR)/Single-Copy (SC) boundaries were highly conserved, with no significant expansion or contraction. Comparative screening identified 11 hypervariable regions with high nucleotide diversity (Pi) and parsimony-informative sites, which hold potential as DNA barcodes. Phylogenetic analysis corresponded with geographic distribution, clarifying the taxonomic position of Begonia mashanica and demonstrating that plastomes can effectively resolve evolutionary relationships within the genus. Additionally, positive selection analysis detected 5 genes with signatures of adaptive evolution. Overall, this study systematically characterizes the plastome structures of 25 Chinese Begonia species, explores their diversity mechanisms and adaptation to low-light conditions, provides valuable insights for evolutionary studies across multiple taxonomic levels (from populations to the genus), enriches the Begonia plastome database, and lays a foundation for future research on population-level adaptation and the genetic basis of functional traits.