Analyses of transcriptome sequences reveal multiple ancient large-scale duplication events in the ancestor of Sphagnopsida (Bryophyta)
Analyses of transcriptome sequences reveal multiple ancient large-scale duplication events in the ancestor of Sphagnopsida (Bryophyta)
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DOI：
10.1111/nph.13887
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发表时间：
2016-07-01
期刊：
影响因子：
9.4
通讯作者：
Shaw, A. Jonathan
中科院分区：
文献类型：
--
作者：
Devos, Nicolas;Szovenyi, Peter;Shaw, A. Jonathan
本研究的目的是调查泥鳅（pehagnum）或泥鳅纲（Sphagnopsida）的祖先中是否存在全基因组重复（WGD），并确定任何这种重复的时间和平行保留模式是否有助于解释泥鳅的快速辐射和当前的生态优势。对苔藓植物Sphagnopsida（苔藓植物门）9个分类群进行了RNA测序（RNA-seq）。对同源基因对的同义替换频率图（K-s）和578个基因树的和解进行了分析，以评估每个转录组中大规模或全基因组重复事件的证据。Ks频率图和基于基因树的分析表明，Sphagnopsida在历史上有多次重复事件。最近的WGD事件早于Sphagnum从其他两个属Sphagnopsida分化出来。重复保留在不同物种之间是高度可变的，这可能最好的解释是局部适应。我们的分析表明，最后的WGD可能是泥炭地多样化的一个重要因素，并促进了泥炭地的生态优势地位。讨论了复制事件发生的时间及其在泥炭藓类进化史上的意义。
The goal of this research was to investigate whether there has been a whole-genome duplication (WGD) in the ancestry of Sphagnum (peatmoss) or the class Sphagnopsida, and to determine if the timing of any such duplication(s) and patterns of paralog retention could help explain the rapid radiation and current ecological dominance of peatmosses.RNA sequencing (RNA-seq) data were generated for nine taxa in Sphagnopsida (Bryophyta). Analyses of frequency plots for synonymous substitutions per synonymous site (K-s) between paralogous gene pairs and reconciliation of 578 gene trees were conducted to assess evidence of large-scale or genome-wide duplication events in each transcriptome.Both Ks frequency plots and gene tree-based analyses indicate multiple duplication events in the history of the Sphagnopsida. The most recent WGD event predates divergence of Sphagnum from the two other genera of Sphagnopsida. Duplicate retention is highly variable across species, which might be best explained by local adaptation.Our analyses indicate that the last WGD could have been an important factor underlying the diversification of peatmosses and facilitated their rise to ecological dominance in peatlands. The timing of the duplication events and their significance in the evolutionary history of peat mosses are discussed.