Comparative analysis of chloroplast genomes within Saxifraga sect. Ciliatae: insights into their adaptation to the alpine environment

Saxifraga sect. Ciliatae, comprising about 200 species, primarily concentrated in the Qinghai-Tibet Plateau (QTP), exhibits high species richness in alpine regions, showing variations in habitat, morphology, physiology, and life cycles. Its adaptation to alpine environments renders it ideal for understanding the genetic basis of how species cope with cold climates. In this study, we sequenced, assembled and analyzed the chloroplast genomes of 20 Saxifraga sect. Ciliatae species and found that chloroplast genomes are generally conserved, with three highly variable regions: psbI-trnS, petG-trnW, and gene ycf1. Phylogenetic analyses (ML and BI) supported the monophyly of Saxifraga sect. Ciliatae, identifying three main clades. Genes cemA, infA and psbB were found to be associated with high-altitude adaptation. Furthermore, psbB may have undergone intracellular gene transfer and exhibited different selective pressures between the transcriptome and chloroplast genome.