Evolution of short inverted repeat in cupressophytes, transfer of accD to nucleus in Sciadopitys verticillata and phylogenetic position of Sciadopityaceae.
Evolution of short inverted repeat in cupressophytes, transfer of accD to nucleus in Sciadopitys verticillata and phylogenetic position of Sciadopityaceae.
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铜管植物中短反向重复序列的进化、轮叶石蕨中 accD 向细胞核的转移以及石萼科的系统发育位置
DOI：
10.1038/srep20934
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发表时间：
2016-02-11
影响因子：
4.6
通讯作者：
Wang T
中科院分区：
文献类型：
--
作者：
Li J;Gao L;Chen S;Tao K;Su Y;Wang T
轮叶山核桃是山核桃科唯一的万年青针叶树种，也是一种经济价值较高的建筑用材树种。收购S。轮叶植物叶绿体（cp）基因组的研究将有助于理解针叶树的进化机制和裸子植物的系统发育关系。本研究首次报道了S.轮生植物。基因组全长138，284 bp，由118个独特的基因组成。色葡萄轮叶松CP基因组缺失了一个典型的反向重复序列，与其它柏科植物相比，表现出独特的基因组结构。结果表明，在该群体中共检测到53个简单重复序列位点和18个正向串联重复序列位点。轮枝藻cp基因组。根据柏科植物cp基因组的重排，我们提出了反向重复序列形成的一种机制：首先发生串联重复序列，然后重排将串联重复序列分成位于不同区域的反向重复序列。从59个基因序列和cpDNA组织推断的系统发育估计都表明，S。verticillata与柏科（Cupressaceae）、红豆杉科（Taxaceae）和红豆杉科（Cephaltaxaceae）组成的分支是姐妹分支。此外，还发现accD基因在S.从两个转录组数据中鉴定了轮枝藻cp基因组和核拷贝。
Sciadopitys verticillata is an evergreen conifer and an economically valuable tree used in construction, which is the only member of the family Sciadopityaceae. Acquisition of the S. verticillata chloroplast (cp) genome will be useful for understanding the evolutionary mechanism of conifers and phylogenetic relationships among gymnosperm. In this study, we have first reported the complete chloroplast genome of S. verticillata. The total genome is 138,284 bp in length, consisting of 118 unique genes. The S. verticillata cp genome has lost one copy of the canonical inverted repeats and shown distinctive genomic structure comparing with other cupressophytes. Fifty-three simple sequence repeat loci and 18 forward tandem repeats were identified in the S. verticillata cp genome. According to the rearrangement of cupressophyte cp genome, we proposed one mechanism for the formation of inverted repeat: tandem repeat occured first, then rearrangement divided the tandem repeat into inverted repeats located at different regions. Phylogenetic estimates inferred from 59-gene sequences and cpDNA organizations have both shown that S. verticillata was sister to the clade consisting of Cupressaceae, Taxaceae and Cephalotaxaceae. Moreover, accD gene was found to be lost in the S. verticillata cp genome and a nucleus copy was identified from two transcriptome data.