Analysis of six chloroplast genomes provides insight into the evolution ofChrysosplenium(Saxifragaceae)

Background ChrysospleniumL. (Saxifragaceae) is a genus of plants widely distributed in Northern Hemisphere and usually found in moist, shaded valleys and mountain slopes. This genus is ideal for studying plant adaptation to low light conditions. Although some progress has been made in the systematics and biogeography ofChrysosplenium, its chloroplast genome evolution remains to be investigated. Results To fill this gap, we sequenced the chloroplast genomes of sixChrysospleniumspecies and analyzed their genome structure, GC content, and nucleotide diversity. Moreover, we performed a phylogenetic analysis and calculated non-synonymous (Ka) /synonymous (Ks) substitution ratios using the combined protein-coding genes of 29 species within Saxifragales and two additional species as outgroups, as well as a pair-wise estimation for each gene withinChrysosplenium. Compared with the outgroups in Saxifragaceae, the sixChrysospleniumchloroplast genomes had lower GC contents; they also had conserved boundary regions and gene contents, as only therpl32gene was lost in four of theChrysospleniumchloroplast genomes. Phylogenetic analyses suggested that theChrysospleniumseparated to two major clades (the opposite group and the alternate group). The selection pressure estimation (Ka/Ks ratios) of genes in theChrysospleniumspecies showed thatmatKandycf2were subjected to positive selection. Conclusion This study provides genetic resources for exploring the phylogeny ofChrysospleniumand sheds light on plant adaptation to low light conditions. The lower average GC content and the lacking gene ofrpl32indicated selective pressure in their unique habitats. Different from results previously reported, our selective pressure estimation suggested that the genes related to photosynthesis (such asycf2) were under positive selection at sites in the coding region.