Evolutionary relationship of Panax ginseng and P. quinquefolius inferred from sequencing and comparative analysis of expressed sequence tags
Evolutionary relationship of Panax ginseng and P. quinquefolius inferred from sequencing and comparative analysis of expressed sequence tags
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DOI：
10.1007/s10722-012-9926-3
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发表时间：
2013-04-01
影响因子：
2
通讯作者：
Yang, Tae-Jin
中科院分区：
文献类型：
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作者：
Choi, Hong-Il;Kim, Nam-Hoon;Yang, Tae-Jin
长期以来，基因和基因组复制事件一直被认为是被子植物进化的驱动力。人参和西洋参分别产于东亚和北美东部，是著名的药用植物，在生长条件、形态特征和遗传特征上具有相似之处。然而，目前还没有关于它们进化的分子数据。本研究从人参和西洋参的表达序列标签(EST)文库中提取EST序列，通过比较分析，揭示人参和西洋参在基因组水平上的复制和物种形成。对文库中的5,760个克隆进行测序和组装，得到了4,552个人参的unEST，并对这些克隆进行了初始注释步骤。与公共数据库中检索到的西洋参ESTs和转录组数据进行比较分析。平行配对和对每个同义位点(Ks)的同义替换分布的分析表明，两种人参都有两个重合的峰，这意味着它们的共同祖先经历了两轮基因组复制。直系同源基因的比较显示，一个Ks峰比从平行对数分析中鉴定出的两个峰年轻。然而，需要对基因组复制和物种形成事件进行绝对年代测定，以解决与它们较长的世代时间有关的警告，据推测，它们在野外的世代时间可能超过8-10年。这是首次在全基因组水平上研究人参属植物的进化关系，为解开神秘的人参属和五加科植物的基因组结构奠定了基础。
Gene and genome duplication events have long been accepted as driving forces in the evolution of angiosperms. Panax ginseng C. A. Meyer and Panax quinquefolius L., which inhabit eastern Asia and eastern North America, respectively, are famous medicinal herbs and are similar in growth condition, morphological and genetic characteristics. However, no molecular data regarding their evolution has been available. In this study, expressed sequence tags (ESTs) were generated from a cDNA library of P. ginseng and comparative analyses were conducted to reveal genome-level duplication and speciation of P. ginseng and P. quinquefolius by in-depth comparison of paralog and orthlog ESTs. Sequencing and assembly of 5,760 clones from the cDNA library resulted in 4,552 uniESTs of P. ginseng and these were subjected to initial annotation steps. Comparative analysis was conducted with the uniESTs and transcriptome data of P. quinquefolius retrieved from the public database. Paralog pairing and analysis of the distribution of synonymous substitutions per synonymous site (Ks) showed two coincident peaks in both Panax species, implying two rounds of genome duplication in their common ancestor. Comparison of orthologs revealed one Ks peak that is younger than the two peaks identified from the analysis of paralogs. However, absolute dating of genome duplication and speciation events is needed to address caveats related to their long generation times, speculated to be more than 8-10 years in the wild. This is the first report regarding the evolutionary relationship of Panax species at the genome-wide level, and will provide a foundation to unravel the genome structure of the enigmatic genus Panax and the family Araliaceae.