Complete sequencing of five araliaceae chloroplast genomes and the phylogenetic implications.
Complete sequencing of five araliaceae chloroplast genomes and the phylogenetic implications.
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DOI：
10.1371/journal.pone.0078568
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发表时间：
2013
期刊：
影响因子：
3.7
通讯作者：
Yi TS
中科院分区：
文献类型：
--
作者：
Li R;Ma PF;Wen J;Yi TS
人参科包括许多经济上重要的植物物种。以前的系统发育研究限定了核心人参植物家族中的三个主要分支，但由于这些谱系的快速辐射，每个主要群体的内部关系都没有得到很好的解决。最近的研究表明，基于叶绿体基因组的生理基因组学为解决复杂关系提供了一种可行的方法。利用新一代测序技术，报道了五种五加科叶绿体基因组的完整核苷酸序列。5个叶绿体基因组的长度为156,333-156,459 bp，包括一对倒置重复序列（25,551-26,108 bp），由大单拷贝区（86,028-86,566 bp）和小单拷贝区（18,021-19,117 bp）分开。每个叶绿体基因组包含114个相同的独特基因，其中包括30个转移RNA基因、4个核糖体RNA基因和80个蛋白质编码基因。所有五缘科叶绿体基因组的基因大小、含量和顺序、AT含量和IR/SC边界结构相似。在5个叶绿体基因组中共鉴定出140个重复序列，其中以回文重复最为常见。基于全叶绿体基因组的简约性、似然性和贝叶斯推断的系统基因组分析有力地支持了亚洲棕榈类群和木本植物类群的单系性。在此基础上，分析了亚洲棕榈属群内各类群间的关系。鉴定出26个变异位点百分比大于5%的DNA标记，为五加科植物的系统发育研究提供了参考。五加科植物叶绿体基因组在基因组特征的各个方面都高度保守。基于叶绿体DNA全序列的大规模系统发育数据对五加科植物的系统发育重建是有效的。
The ginseng family (Araliaceae) includes a number of economically important plant species. Previously phylogenetic studies circumscribed three major clades within the core ginseng plant family, yet the internal relationships of each major group have been poorly resolved perhaps due to rapid radiation of these lineages. Recent studies have shown that phyogenomics based on chloroplast genomes provides a viable way to resolve complex relationships. We report the complete nucleotide sequences of five Araliaceae chloroplast genomes using next-generation sequencing technology. The five chloroplast genomes are 156,333–156,459 bp in length including a pair of inverted repeats (25,551–26,108 bp) separated by the large single-copy (86,028–86,566 bp) and small single-copy (18,021–19,117 bp) regions. Each chloroplast genome contains the same 114 unique genes consisting of 30 transfer RNA genes, four ribosomal RNA genes, and 80 protein coding genes. Gene size, content, and order, AT content, and IR/SC boundary structure are similar among all Araliaceae chloroplast genomes. A total of 140 repeats were identified in the five chloroplast genomes with palindromic repeat as the most common type. Phylogenomic analyses using parsimony, likelihood, and Bayesian inference based on the complete chloroplast genomes strongly supported the monophyly of the Asian Palmate group and the Aralia-Panax group. Furthermore, the relationships among the sampled taxa within the Asian Palmate group were well resolved. Twenty-six DNA markers with the percentage of variable sites higher than 5% were identified, which may be useful for phylogenetic studies of Araliaceae. The chloroplast genomes of Araliaceae are highly conserved in all aspects of genome features. The large-scale phylogenomic data based on the complete chloroplast DNA sequences is shown to be effective for the phylogenetic reconstruction of Araliaceae.
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