Complete chloroplast genomes suggest a single origin of the Indian subcontinent Sonerila (Melastomataceae)

Background Sonerila , the second largest genus within the tribe Sonerileae (Melastomaceae), is primarily distributed across tropical and subtropical Asia, from India and Sri Lanka, where it exhibits a remarkably high degree of endemism, to Papua New Guinea. In this study, we assembled and annotated the chloroplast genomes of 15 Sonerila species from India (14 from the subcontinent and one from Sikkim in the Eastern Himalaya) and compared them to 12 previously published genomes representing species from other regions. We performed comparative analyses of gene structure, sequence alignment, nucleotide diversity and phylogenetic reconstructions to evaluate the utility of plastid regions for resolving phylogenetic relationships and understanding plastome evolution within Sonerila and close relatives. Results Our results demonstrate that the complete chloroplast genome exhibit quadripartite structures, with lengths ranging from 154,014 ( S. nervulosa ) to 155,271 bp ( S. annamica ). The genome structure remains relatively conserved, hosting 129 annotated genes, including 84 protein coding genes, 37 tRNA genes, and 8 rRNA genes. The overall GC contents were almost identical (37.1–37.4%), with an average of 37.2%. 51 to 84 SSRs and long repeat sequences were detected. A comparison of nucleotide diversity among all 27 Sonerila chloroplast genomes revealed seven regions ( ycf1 , rps15 , psbE-petL , trnS-GCU-trnR-UCU, rps16-trnQ-UUG, rbcL-accD, rps18-rpl20 ) displayed relatively high nucleotide diversity (Pi > 0.025). In contrast, the chloroplast genomes from Indian Sonerila species showed lower diversity, with only four regions ( ycf1, rps16, rpl32, rpl22 ) exhibiting notable Pi value (> 0.014). Maximum likelihood phylogenetic analysis strongly confirmed the monophyly of Sonerila within the Sonerileae and showed that the structure of the main clades correlated to species geographic distribution, including a single origin for Sonerila in the Indian subcontinent. Conclusion The chloroplast genomes of Sonerila exhibits conserved structural features and gene content and variations were observed in genome size, sequence divergence, and repeat elements. Overall, long repetitive sequences, simple sequence repeats (SSRs), and regions with high variability are phylogenetically informative. Phylogenetic analyses suggest that Sonerila is a monophyletic entity and the Indian subcontinent species originated from a single ancestor. By providing a comprehensive genomic characterization of Sonerila chloroplast, this study delivers essential genetic insights for advancing future research on the evolutionary history and adaptive diversification of Sonerila species.