Complete chloroplast DNA sequence from a Korean endemic genus, Megaleranthis saniculifolia, and its evolutionary implications
Complete chloroplast DNA sequence from a Korean endemic genus, Megaleranthis saniculifolia, and its evolutionary implications
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DOI：
10.1007/s10059-009-0047-6
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发表时间：
2009-03-01
影响因子：
3.8
通讯作者：
Kim, Ki-Joong
中科院分区：
文献类型：
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作者：
Kim, Young-Kyu;Park, Chong-wook;Kim, Ki-Joong
本研究完成了特有单型濒危植物 Megaleranthis saniculifolia 的叶绿体 DNA 序列（GenBank FJ597983）。基因组长度为 159,924 bp。它包含一对 IR 区域，每个区域包含 26,608 bp。 LSC 和 SSC 区域的长度分别为 88,326 bp 和 18,382 bp。大花叶绿体基因组的结构组织、基因和内含子内容、基因顺序、AT 内容、密码子使用和转录单位与典型陆地植物 cp DNA 相似。然而，大花草叶绿体基因组的详细特征与同属于毛茛科的毛茛属植物有很大不同。首先，由于IR区域扩展到SSC区域以及在巨花cp基因组的几个间隔区域中重复的序列元件，巨花cp DNA比毛茛属长4,797 bp。其次，大花和毛茛属的叶绿体基因组分别证明编码区有 5.6% 的序列差异，内含子区域有 8.9% 的序列差异，基因间间隔区有 18.7% 的序列差异。在编码区和非编码区，平均核苷酸取代率显着不同，具体取决于基因组位置。我们的数据强烈暗示了叶绿体基因进化模式的位置效应。表现出较高水平碱基取代的基因也具有较高的 indel 突变发生率和较低的 Ka/Ks 比率。从 Megaleranthis cp 基因组中鉴定出总共 54 个简单序列重复基因座。巨斑藻 cp 基因组中丰富的 cp SSR 位点的存在为研究该濒危物种的种群遗传结构提供了难得的机会。我们的系统发育树基于两个独立的标记，即核 ITS 和叶绿体 matK 序列，强烈支持将 Megaleranthis 纳入金莲花属。因此，我们的分子树支持 Ohwi 最初的治疗方法。
The chloroplast DNA sequences of Megaleranthis saniculifolia, an endemic and monotypic endangered plant species, were completed in this study (GenBank FJ597983). The genome is 159,924 bp in length. It harbors a pair of IR regions consisting of 26,608 bp each. The lengths of the LSC and SSC regions are 88,326 bp and 18,382 bp, respectively. The structural organizations, gene and intron contents, gene orders, AT contents, codon usages, and transcription units of the Megaleranthis chloroplast genome are similar to those of typical land plant cp DNAs. However, the detailed features of Megaleranthis chloroplast genomes are substantially different from that of Ranunculus, which belongs to the same family, the Ranunculaceae. First, the Megaleranthis cp DNA was 4,797 bp longer than that of Ranunculus due to an expanded IR region into the SSC region and duplicated sequence elements in several spacer regions of the Megaleranthis cp genome. Second, the chloroplast genomes of Megaleranthis and Ranunculus evidence 5.6% sequence divergence in the coding regions, 8.9% sequence divergence in the intron regions, and 18.7% sequence divergence in the intergenic spacer regions, respectively. In both the coding and noncoding regions, average nucleotide substitution rates differed markedly, depending on the genome position. Our data strongly implicate the positional effects of the evolutionary modes of chloroplast genes. The genes evidencing higher levels of base substitutions also have higher incidences of indel mutations and low Ka/Ks ratios. A total of 54 simple sequence repeat loci were identified from the Megaleranthis cp genome. The existence of rich cp SSR loci in the Megaleranthis cp genome provides a rare opportunity to study the population genetic structures of this endangered species. Our phylogenetic trees based on the two independent markers, the nuclear ITS and chloroplast matK sequences, strongly support the inclusion of the Megaleranthis to the Trollius. Therefore, our molecular trees support Ohwi's original treatment of Megaleranthis saniculiforia to Trollius chosenensis Ohwi.