Analysis of Six Chloroplast Genomes Provides Insight into the Evolution of Chrysosplenium (Saxifragaceae)

Abstract

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 Chrysosplenium and sheds light on plant adaptation to low light conditions. The lower average GC content and the lacking gene of rpl32 indicated selective pressure in their unique habitats. Different from results previously reported, our selective pressure estimation suggested that the genes related to photosynthesis (such as ycf2) were under positive selection at sites in the coding region.

Complete chloroplast genomes provide insights into evolution and phylogeny of Zingiber (Zingiberaceae)

“…The lhbA gene were lost in both Hedychium coccineum and Hedychium neocarneum [25]. However, the chloroplast genomes of Zingiber species were highly conserved in current study, which is in agreement with previous studies at genus level Camellia [39], Sinosenecio [40], and Chrysosplenium [41]. Plastomes are very conservative which was maintained by multiple molecular mechanisms including uniparental inheritance, rarity of plastid fusion, and the presence of an active repair mechanism [21,35].…”

Comparative chloroplast genome analyses of Amomum: insights into evolutionary history and species identification

“…1) [44] and this might be one of the causes for the IR region to be more conserved than LSC and SSC regions [45]. This phenomenon is also evident in many other angiosperms [46,47]. There are 79 protein-coding genes in the three Amomum plastomes, meanwhile, 70 up to 88 such genes are reported present in angiosperm plastomes [48].…”

Chloroplast phylogenomics and the dynamic evolution of Santalum (Santalaceae)

“…2). The number of SSR in the Santalum chloroplast genome was low compared to photoautotrophic plant lineages [31][32][33][34].…”

“…These different mechanisms might be responsible for the observed differences in indel length. Mutation hotspot regions in the chloroplast genome have been identi ed in most plant lineages, and studies have identi ed those markers were more variable than universal chloroplast markers [22,33,37,38]. We identi ed three variable regions (ccsA-trnL, ΨndhE-ΨndhG-rps15, and ycf1) compared with the Santalum chloroplast genome.…”