The Complete Chloroplast Genome Sequences of Salvia reflexa and Genome Comparison: Implications for Phylogeny and...

Salvia reflexa is an invasive plant of global concern due to its strong invasiveness and toxicity. However, limited chloroplast genomic information has hindered a comprehensive understanding of its phylogenetic relationships and evolutionary history. To investigate the genomic features associated with invasiveness, the complete chloroplast genome of S. reflexa was sequenced and characterized, and a comparative analysis was conducted with other invasive and non-invasive species of the Salvia. The chloroplast genome of S. reflexa spanned 150,629 bp and possessed a typical quadripartite structure, including 82,054 bp large single-copy region, 17,569 bp small single-copy region, and two inverted repeats of 25,503 bp each. A total of 133 genes were identified, consisting of 88 protein-coding genes, 37 transfer RNA genes, and 8 ribosomal RNA genes. A total of 710 long repeats and 542 SSRs were identified across the analyzed Salvia chloroplast genomes. Comparative genomic analysis revealed that chloroplast genomes within Salvia are highly conserved, although several hypervariable regions, including ndhC-trnV, ndhF, rpl32-trnL, rps15-ycf1, and ycf1, were identified as potential molecular markers. Selective pressure analysis indicated that most genes are under purifying selection, whereas ycf2 shows evidence of positive selection. Furthermore, phylogenetic analysis supported that S. reflexa is most closely related to S. japonica, while clustering into different clades with the invasive plant S. tiliifolia, suggesting distinct evolutionary trajectories. These findings provide valuable genomic resources for species identification, phylogenetic analysis, and population genetic research in Salvia, contributing to a deeper understanding of its evolutionary dynamics.