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

作者：Zhihua Wu, Rui Jin Liao, Tiange Yang, Xiang Dong, Deqing Lan, Rui Qin, Hong Liu · 发表于：BMC Genomics · 年份：2020 · DOI：10.1186/s12864-020-07045-4 · 被引用次数：137 · 研究领域：Genomics and Phylogenetic Studies、Photosynthetic Processes and Mechanisms、Plant Diversity and Evolution

BACKGROUND: Chrysosplenium L. (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 of Chrysosplenium, its chloroplast genome evolution remains to be investigated. RESULTS: To fill this gap, we sequenced the chloroplast genomes of six Chrysosplenium species 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 within Chrysosplenium. Compared with the outgroups in Saxifragaceae, the six Chrysosplenium chloroplast genomes had lower GC contents; they also had conserved boundary regions and gene contents, as only the rpl32 gene was lost in four of the Chrysosplenium chloroplast genomes. Phylogenetic analyses suggested that the Chrysosplenium separated to two major clades (the opposite group and the alternate group). The selection pressure estimation (Ka/Ks ratios) of genes in the Chrysosplenium species showed that matK and ycf2 were subjected to positive selection. CONCLUSION: This study provides genetic resources for exploring the phylogeny of Chrys...