The complete chloroplast DNA sequence of Eleutherococcus senticosus (Araliaceae); Comparative evolutionary analyses with other three asterids
The complete chloroplast DNA sequence of Eleutherococcus senticosus (Araliaceae); Comparative evolutionary analyses with other three asterids
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DOI：
10.1007/s10059-012-2281-6
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发表时间：
2012-05
影响因子：
3.8
通讯作者：
Dong-Keun Yi;Hae-Lim Lee;Byung-Yun Sun;M. Chung;Ki-Joong Kim
中科院分区：
文献类型：
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作者：
Dong-Keun Yi;Hae-Lim Lee;Byung-Yun Sun;M. Chung;Ki-Joong Kim
报道了濒危植物刺五加（Eleutherococcus senticosus）（GenBank：JN 637765）的叶绿体DNA全序列。基因组长度为156，768 bp，包含一对各为25，930 bp的反向重复（IR）区域、一个86，755 bp的大单拷贝（LSC）区域和一个18，153 bp的小单拷贝（SSC）区域。对E.刺五加叶绿体基因组与典型陆地植物cpDNA相似。本研究对参属、胡萝卜属和烟草属三个不同分类层次的86个编码基因、19个内含子和113个基因间间隔区（IGS）进行了序列比对和分析。插入缺失的分布、多态位点的数目和核苷酸多样性表明，位置约束对菊类cp基因组序列的进化比功能约束更重要。例如，LSC区域中的内含子序列表现出比IR区域高5-11倍的碱基替换率，而SSC区域中的内含子序列比IR区域中的内含子序列进化快7-14倍。此外，基因编码序列的Ka/Ks比支持IR区域中比LSC或SSC区域中更强的进化约束。因此，我们的数据表明，通过碱基收集机制的选择性扫描更频繁地消除IR区域中的多态性。具有高水平碱基替换的叶绿体基因组区域也显示出较高的插入缺失发生率。在刺五加叶绿体基因组中共检测到35个SSR位点。其中，27种是均聚物，6种是二聚物，2种是三聚物。除了SSR位点，我们还确定了18个中等大小的重复单位，范围从22至79 bp，其中11个分布在IGS或内含子区域。这些中等大小的重复序列可能有助于开发cp基因组特异性基因导入载体，因为该区域可能用于特异性重组位点。
This study reports the complete chloroplast (cp) DNA sequence ofEleutherococcus senticosus(GenBank: JN 637765), an endangered endemic species. The genome is 156,768 bp in length, and contains a pair of inverted repeat (IR) regions of 25,930 bp each, a large single copy (LSC) region of 86,755 bp and a small single copy (SSC) region of 18,153 bp. The structural organization, gene and intron contents, gene order, AT content, codon usage, and transcription units of theE. senticosuschloroplast genome are similar to that of typical land plant cp DNA. We aligned and analyzed the sequences of 86 coding genes, 19 introns and 113 intergenic spacers (IGS) in three different taxonomic hierarchies;Eleutherococcusvs.Panax, Eleutherococcusvs.Daucus, andEleutherococcusvs.Nicotiana. The distribution of indels, the number of polymorphic sites and nucleotide diversity indicate that positional constraint is more important than functional constraint for the evolution of cp genome sequences in Asterids. For example, the intron sequences in the LSC region exhibited base substitution rates 5–11-times higher than that of the IR regions, while the intron sequences in the SSC region evolved 7–14-times faster than those in the IR region. Furthermore, the Ka/Ks ratio of the gene coding sequences supports a stronger evolutionary constraint in the IR region than in the LSC or SSC regions. Therefore, our data suggest that selective sweeps by base collection mechanisms more frequently eliminate polymorphisms in the IR region than in other regions. Chloroplast genome regions that have high levels of base substitutions also show higher incidences of indels. Thirty-five simple sequence repeat (SSR) loci were identified in theEleutherococcuschloroplast genome. Of these, 27 are homopolymers, while six are di-polymers and two are tri-polymers. In addition to the SSR loci, we also identified 18 medium size repeat units ranging from 22 to 79 bp, 11 of which are distributed in the IGS or intron regions. These medium size repeats may contribute to developing a cp genome-specific gene introduction vector because the region may use for specific recombination sites.