Plastid phylogenomics resolving phylogeny and evolution of Semiliquidambar cathayensis

Abstract

Semiliquidambar cathayensis is treated as a grade-two protected plant in China. However, its phylogenetic relationships with species from Hamamelidaceae and Altingiaceae remain unclear. In order to analyze the phylogenetic relationships and adaptive evolution of chloroplast genomes between S. cathayensis and its closely related taxa including species from Hamamelidaceae and Altingiaceae, we reconstructed the maximum likelihood tree and the Bayesian tree to discover the phylogenetic relationships between S. cathayensis and its closely related taxa from 24 sequences that representing 22 species, and further detected the correlation between adaptive sites and selective pressure of protein coding genes under varying models including site model, clade model and branch model. Altingiaceae clade was chosen as the foreground clade. The results were as follows: (1) A total of 133 genes were annotated, including 88 protein-coding genes (11 genes with intron), 37 tRNA genes and eight rRNA genes. (2) Eight chloroplast genomes representing eight species from S. cathayensis and Altingia, Liquidambar were relatively conservative in sequence length, gene number and composition, GC content, and there was not obvious diversity in the four boundaries. Relatively high variation interspecific were also detected in LSC and SSC regions among these eight chloroplast genomes, while the IR regions were high conservatism. (3) Phylogenetic trees showed that S. cathayensis and sampled species of Altingiaceae clustered a group, which further divided into three clades, namely Clade I, Clade Ⅱ and Clade Ⅲ. The phylogenetic relationships among these clades remain unclear due to hybridization or incomplete lineage sorting (ILS) according to the results of test of ILS. (4) The chloroplast genes such as ndhA, ndhG and rps12 were subjected to selection pressure under the clade model and branch model. Furthermore, 28 sites of ten genes were detected under positive selection with P-value greater than 0.99 based on the site model, which may be related to the adaptive evolution of Altingiaceae. In this study, the results of plastid phylogenomics supports that S. cathayensis belongs to Altingiaceae. Several coding genes among these species of Altingiaceae may have adaptive evolution. These results will provide data for the further resource protection of homonym drugs and pharmacognostic researches of ethnodrug.

Keywords

• semiliquidambar cathayensis
• altingiaceae
• chloroplast genome
• phylogeny
• adaptive evolution