Comparative and phylogenetic analysis of chloroplast genomes in the subtribe Leptoboeinae (Gesneriaceae)

The subtribe Leptoboeinae (Gesneriaceae: Trichosporeae) comprises seven genera-<i>Rhynchotechum</i> Blume, <i>Boeica</i> C.B.Clarke, <i>Beccarinda</i> Kuntze, <i>Leptoboea</i> Benth., <i>Platystemma</i> Wall., <i>Crassicaulis</i> Lei Cai & Mich.Moller, and <i>Championia</i> Gardner. It is highly valuable in horticulture and medicine. However, long-standing taxonomic issues, including the polyphyly of <i>Boeica</i> and the uncertain placement of <i>Championia</i>, remain unresolved. To address these problems, we sequenced and assembled complete chloroplast genomes for 17 species representing all seven genera, and conducted comparative genomic and phylogenomic analyses. The genomes ranged from 153,114 to 154,647 bp and exhibited a typical quadripartite structure consistent with other Gesneriaceae. A total of 1,861 SSRs, 1,179 dispersed repeats, and 29 high-frequency codons with similar usage patterns were identified. We also detected 10 highly variable regions that may serve as potential molecular markers. the plastid tree and coalescent tree constructed based on CDS sequences in this study showed highly congruent topologies at the generic level, supporting the division of <i>Boeica</i> into five clades, two of which can be distinguished morphologically. <i>Championia</i> formed a sister relationship with all sampled genera of Trichosporeae and Epithemateae, confirming that it does not belong to Leptoboeinae. Moreover, structural variation in the plastome helped clarify the polyphyly of <i>Boeica</i>: the five clades exhibited significant differences in total GC content, LSC GC content, and SSC GC content. Given the overlapping geographic distributions of these clades, we infer that plastome divergence may reflect independent lineage evolution. Overall, this study offers new insights into the phylogenetic relationships within Leptoboeinae and provides a foundation for future taxonomic revision and evolutionary research.