Complete chloroplast genome sequences from Korean ginseng (Panax schinseng Nees) and comparative analysis of sequence evolution among 17 vascular plants
Complete chloroplast genome sequences from Korean ginseng (Panax schinseng Nees) and comparative analysis of sequence evolution among 17 vascular plants
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DOI：
10.1093/dnares/11.4.247
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发表时间：
2004-08-31
期刊：
影响因子：
4.1
通讯作者：
Lee, HL
中科院分区：
文献类型：
--
作者：
Kim, KJ;Lee, HL
朝鲜人参（Panax schinseng Nees）叶绿体基因组的核苷酸序列已测定完成（AY582139）。这种环状双链DNA由156,318个碱基对组成，包含一对反向重复区域（IRa和IRb），每个区域有26,071个碱基对，它们分别被86,106个碱基对的小单拷贝区和18,070个碱基对的大单拷贝区隔开。反向重复区域进一步延伸到大单拷贝区，其中包括rps19基因的5'部分。与烟草相比，在朝鲜人参的叶绿体基因组中还观察到4个与形成茎环结构的短回文序列相关的短倒位。然而，114个基因（75个编码肽的基因、30个tRNA基因、4个rRNA基因和5个保守的开放阅读框[ycfs]）的基因组含量和相对位置与烟草的叶绿体DNA相同。16个基因含有1个内含子，2个基因有2个内含子。在这些内含子中，只有1个（trnL - UAA）属于自我剪接的I类；其余所有内含子都具有属于II类的6个结构域的特征。从朝鲜人参的叶绿体基因组中已鉴定出18个简单序列重复。其中几个SSR位点显示出种内变异。对维管植物中17个已知的已完成测序的叶绿体基因组进行详细比较，可以确定编码区段和内含子序列的进化模式，以及评估叶绿体基因的系统发育效用。此外，通过对几个叶绿体基因组的详细比较，确定了以倒位端点、插入缺失突变事件和高频率碱基替换为主的进化热点。大尺寸的插入缺失通常与序列末端的直接重复相关，这有利于分子内重组。
The nucleotide sequence of Korean ginseng (Panax schinseng Nees) chloroplast genome has been completed (AY582139). The circular double-stranded DNA, which consists of 156,318 bp, contains a pair of inverted repeat regions (IRa and IRb) with 26,071 bp each, which are separated by small and large single copy regions of 86,106 bp and 18,070 bp, respectively. The inverted repeat region is further extended into a large single copy region which includes the 5' parts of the rps19 gene. Four short inversions associated with short palindromic sequences that form stem-loop structures were also observed in the chloroplast genome of P. schinseng compared to that of Nicotiana tabacum. The genome content and the relative positions of 114 genes (75 peptide-encoding genes, 30 tRNA genes, 4 rRNA genes, and 5 conserved open reading frames [ycfs]), however, are identical with the chloroplast DNA of N. tabacum. Sixteen genes contain one intron while two genes have two introns. Of these introns, only one (trnL-UAA) belongs to the self-splicing group I; all remaining introns have the characteristics of six domains belonging to group II. Eighteen simple sequence repeats have been identified from the chloroplast genome of Korean ginseng. Several of these SSR loci show infra-specific variations. A detailed comparison of 17 known completed chloroplast genomes from the vascular plants allowed the identification of evolutionary modes of coding segments and intron sequences, as well as the evaluation of the phylogenetic utilities of chloroplast genes. Furthermore, through the detailed comparisons of several chloroplast genomes, evolutionary hotspots predominated by the inversion end points, indel mutation events, and high frequencies of base substitutions were identified. Large-sized indels were often associated with direct repeats at the end of the sequences facilitating intra-molecular recombination.