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 <i>Anna</i> and <i>Lysionotus</i> 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. <i>psaB-psaA</i>, <i>trnL-UAG</i> and <i>ndhD-psaC</i> were identified as potential molecular markers for <i>Anna</i> species, with <i>clpP</i> and <i>ycf1</i> proposed as effective molecular markers for <i>Lysionotus</i> species; 3. the types of simple sequence repeats (SSRs) and large sequence repeats (LRSs) showed a higher conservation in <i>Lysionotus</i> compared with <i>Anna</i>; 4. the codon usage preferences of the two genera showed convergent evolutionary trends and natural selection played a dominant role, with <i>ycf1</i> and <i>atpH</i> being confirmed as significantly positively selected genes; 6. phylogenetic analyses using multiple approaches (ML, BI and NJ) consistently verified that <i>Anna</i> and <i>Lysionotus</i> 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.