Comparative genomics of Begonia chloroplasts: insights into molecular evolution, species identification, and phylogeny

Background Begonia , a hyperdiverse genus with ecological and medicinal values, confronts challenges in species identification and phylogenetic resolution due to remarkable morphological plasticity and ambiguous taxonomic boundaries. Chloroplast genomes (plastomes) serve as powerful molecular tools for addressing these issues, yet comprehensive plastomic data for Chinese Begonia species remain insufficient. This study presents the largest plastome dataset for Chinese Begonia (76 plastomes total), identifies hypervariable markers, and resolves a specific taxonomic issue, clarifying the phylogenetic position. Methods We sequenced and assembled plastomes of 25 Chinese Begonia species, integrating 51 public plastomes for comparative analyses, including plastome structure, repeat dynamics, codon usage, nucleotide polymorphism, phylogenetics (ML/BI), and positive selection ( Ka/Ks , BEB tests). Results All 25 assembled plastomes exhibited a conserved quadripartite structures (167,365 − 169,901 bp) with 142–143 genes. Eleven hypervariable regions (e.g., ycf1 , petB , ndhF-rpl32 ) were identified as potential DNA barcodes. Phylogenetic tree aligned with geographic distributions, clarifying taxonomic positions (e.g., B. mashanica ). Five genes ( matK , ndhB , ndhD , rps8 , and rps15 ) showed candidate signals of positive selection, suggesting candidate loci for shade adaptation that require functional validation. Conclusion This study enriches Begonia plastome resources, provides reliable molecular markers for species authentication, and sheds light on adaptive evolution. The findings support sustainable utilization of medicinal Begonia and advancing genus-level evolutionary and taxonomic research.