Comparative Chloroplast Genome and Phylogenetic Analyses of Anna and Lysionotus (Gesneriaceae) Along the Sino-Vietnamese Border

Sympatric species share identical geographical spaces, climatic conditions and survival pressures. Comparative chloroplast genomes among Anna and Lysionotus sympatric species enable exploration of genome-wide evolutionary dynamics of sympatric species. In this study, we assembled and annotated 10 complete chloroplast genomes, representing sympatric species distributed along the Sino-Vietnamese border. We conducted a comparison of chloroplast genomes, characterized their adaptive evolution and used multiple methods to clarify their phylogenetic relationships. Key findings included the following: 1. The number of CDs, rRNA and tRNA varied among different species, whereas they were relatively conserved between the two genera; 2. psaB-psaA, trnL-UAG and ndhD-psaC were identified as potential molecular markers for Anna species, with clpP and ycf1 proposed as effective molecular markers for Lysionotus species; 3. the types of simple sequence repeats (SSRs) and large sequence repeats (LRSs) showed a higher conservation in Lysionotus compared with Anna; 4. the codon usage preferences of the two genera showed convergent evolutionary trends and natural selection played a dominant role, with ycf1 and atpH being confirmed as significantly positively selected genes; 6. phylogenetic analyses using multiple approaches (ML, BI and NJ) consistently verified that Anna and Lysionotus each formed a well-supported monophyletic group. This study offers molecular insights into adaptation and differentiation patterns among distinct plant genera inhabiting the same extreme habitat.