Evolution of plastid genomes of Holcoglossum (Orchidaceae) with recent radiation
Evolution of plastid genomes of Holcoglossum (Orchidaceae) with recent radiation
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最近辐射下 Holcoglossum（兰科）质体基因组的进化
DOI：
10.1186/s12862-019-1384-5
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发表时间：
2019-02-26
影响因子：
3.4
通讯作者：
Jin, Xiao-Hua
中科院分区：
文献类型：
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作者：
Li, Zhang-Hai;Ma, Xiao;Jin, Xiao-Hua
研究背景质体是一种具有自身基因组的半自主细胞器。质体基因组已被广泛用作研究植物发生、物种形成和适应性进化的模型。然而，目前的研究主要集中在高分类水平上的质体基因组进化比较，而在属内或种内水平上的质体基因组进化比较研究还很薄弱。本文报道了12种沟舌兰属植物和1种万代兰属植物的15个完整的质体基因组，它们的质体基因组总长度在145 ~ 148 kb之间，编码102个基因。全唇兰属的ndh基因家族都被截短或假基因化。在质体基因cf2的编码区发现发夹倒位。结论通过比较质体组分析，我们发现同一物种不同个体间的indel都是由短重复序列拷贝数的变异引起的，这种变异可能是由复制滑移引起的。对串联重复序列的注释表明，由串联重复序列引入的变异在质体基因组中广泛存在。叶绿体基因cf2中的发夹倒位在兰科植物中随机发生。
BackgroundThe plastid is a semiautonomous organelle with its own genome. Plastid genomes have been widely used as models for studying phylogeny, speciation and adaptive evolution. However, most studies focus on comparisons of plastid genome evolution at high taxonomic levels, and comparative studies of the process of plastome evolution at the infrageneric or intraspecific level remain elusive.Holcoglossumis a small genus of Orchidaceae, consisting of approximately 20 species of recent radiation.This made it an ideal group to explore the plastome mutation mode at the infrageneric or intraspecific level.ResultsIn this paper, we reported 15 complete plastid genomes from 12 species ofHolcoglossumand 1 species ofVanda.The plastid genomes ofHolcoglossumhave a total length range between 145 kb and 148 kb, encoding a set of 102 genes. The whole set ofndh-gene families inHolcoglossumhave been truncated or pseudogenized. Hairpin inversion in the coding region of the plastid geneycf2has been found.ConclusionsUsing a comprehensive comparative plastome analysis, we found that all the indels between different individuals of the same species resulted from the copy number variation of the short repeat sequence, which may be caused by replication slippage. Annotation of tandem repeats shows that the variation introduced by tandem repeats is widespread in plastid genomes. The hairpin inversion found in the plastid geneycf2occurred randomly in the Orchidaceae.