芸香科植物叶绿体基因组结构和系统发育分析

Chloroplast Genome Structural and Phylogenetic Analysis of Rutaceae

本研究对已公布的芸香科12属43个物种叶绿体全基因组序列的结构特征进行了比较分析。芸香科叶绿体基因组大小为157~161 kb,基因数目为119~138,蛋白质编码基因数目为83~92。蛋白质编码基因中,11个为重复基因,共有基因为79个,13个基因存在不同程度的丢失。长度≥200 bp的蛋白质编码共有基因中,变异率最高的5个基因依次为ndhA、clpP、matK、rps16和rpl16。重复序列分析结果表明,最主要的重复序列类型为串联重复和回文重复,山小橘属2个物种的重复序列显著多于其他物种。大部分SSR (Simple sequence repeats)位点都偏向于A或者T组成,柑橘属中以三核苷酸重复最多,花椒属中主要为二核苷酸重复(单核苷酸重复除外)。基于基因组序列和蛋白质编码基因,均得到支持率高,拓扑结构基本一致的系统发育树结果。芸香科为单系类群,科下形成两个大分支,其中柑橘亚科为单系和芸香属形成一支;另一大支中,香肉果属是最早分化出来的类群,黄檗属+吴茱萸属为花椒属的姐妹群。本研究结果有助于更好的了解芸香科物种的系统进化。

In this study, we compared structural characteristics of chloroplast genome of 43 species representing12 genera of Rutaceae. The genome size of Rutaceae ranged from 157 kilo base pairs(kb) to 161 kb. The total number of genes varied from 119 to 138, including 83 to 92 protein-coding genes. Among the protein-coding gene,11 genes were duplicated, and 79 genes conserved in Rutaceae, while gene loss did occur in 13 genes. For protein-coding genes with length ≥200 bp, the 5 genes with highest percentage of variable sites were: ndhA, clpP,matK, rps16 and rpl16. Results of repeat sequences detection showed that tandem repeats and palindromic repeats were the most frequent type of repeats. In two species of Glycosmis, the number of repeats sequences was found to be significantly higher than in other species. Most of the SSRs were composed of A or T. The most frequent type of SSRs in Citrus and Zanthoxylum were three-and double-nucleotide SSRs, respectively(single-nucleotide SSRs was excluded). The phylogenetic tree based on genome and protein-coding genes provided consistent topology with strong support. The monophyly of Rutaceae was supported, and two major clades were formed. The first clade comprised an Aurantioideae lineage sister to Ruta. Within the second clade, Casimiroa was the early-diverging clade, and Tetradium + Phellodendron formed a clade sister to Zanthoxylum. Our research will contribute to a better understanding of the phylogenetic relationships of Rutaceae.