Phylotranscriptomics Illuminates the Placement of Whole Genome Duplications and Gene Retention in Ferns.
Phylotranscriptomics Illuminates the Placement of Whole Genome Duplications and Gene Retention in Ferns.
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DOI：
10.3389/fpls.2022.882441
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发表时间：
2022
影响因子：
5.6
通讯作者：
Sessa, Emily B.
中科院分区：
文献类型：
--
作者：
Pelosi, Jessie A.;Kim, Emily H.;Barbazuk, W. Brad;Sessa, Emily B.
蕨类植物是维管植物的第二大分支，拥有 10,000 多种物种，但该类群基因组资源的产生却落后于其他主要植物分支。转录组数据已被证明是评估系统发育关系的强大工具，它使用在整个基因组中很大程度上保守的数千个标记，并且无需对整个基因组进行测序。我们收集了迄今为止最大的蕨类植物核系统发育数据集，包括来自 247 个转录组（242 个蕨类植物，五个外类群）的 2884 个单拷贝核基因座，并研究了整个蕨类植物树的系统发育关系、全基因组重复 (WGD) 的位置以及 WGD 后的基因保留模式。我们生成了一个得到充分支持的蕨类植物系统发育图，并确定了蕨类植物系统发育图中的几个区域，这些区域表现出高水平的基因树-物种树冲突，这些区域很大程度上对应于难以解决的系统发育区域。通过综合使用多种方法，我们确定了整个系统发育中的 27 个 WGD，其中包括 18 个大型事件（涉及多个采样分类单元）和 9 个小规模事件（仅涉及一个采样分类单元）。大多数推断的 WGD 发生在单一谱系（例如，目、科）内，而不是在系统发育的主干上，尽管两个推断事件是由薄囊蕨类（不包括紫萁目）和水龙骨目（不包括 Lindsaeineae 和 Saccolomatineae）所共有的，这两个分支对应于大多数蕨类植物的多样性。我们进一步检查了WGD后保留的重复基因如何在独立事件中进行比较，发现保留基因的功能在很大程度上趋同，涉及结合、对刺激的反应和某些细胞器的过程在旁系同源物中过多，而涉及运输、源自内共生事件的细胞器和信号传导的过程代表性不足。迄今为止，我们的研究是对核蕨类植物系统发育最全面的研究，尽管未来研究的几个途径仍未探索。
Ferns are the second largest clade of vascular plants with over 10,000 species, yet the generation of genomic resources for the group has lagged behind other major clades of plants. Transcriptomic data have proven to be a powerful tool to assess phylogenetic relationships, using thousands of markers that are largely conserved across the genome, and without the need to sequence entire genomes. We assembled the largest nuclear phylogenetic dataset for ferns to date, including 2884 single-copy nuclear loci from 247 transcriptomes (242 ferns, five outgroups), and investigated phylogenetic relationships across the fern tree, the placement of whole genome duplications (WGDs), and gene retention patterns following WGDs. We generated a well-supported phylogeny of ferns and identified several regions of the fern phylogeny that demonstrate high levels of gene tree–species tree conflict, which largely correspond to areas of the phylogeny that have been difficult to resolve. Using a combination of approaches, we identified 27 WGDs across the phylogeny, including 18 large-scale events (involving more than one sampled taxon) and nine small-scale events (involving only one sampled taxon). Most inferred WGDs occur within single lineages (e.g., orders, families) rather than on the backbone of the phylogeny, although two inferred events are shared by leptosporangiate ferns (excluding Osmundales) and Polypodiales (excluding Lindsaeineae and Saccolomatineae), clades which correspond to the majority of fern diversity. We further examined how retained duplicates following WGDs compared across independent events and found that functions of retained genes were largely convergent, with processes involved in binding, responses to stimuli, and certain organelles over-represented in paralogs while processes involved in transport, organelles derived from endosymbiotic events, and signaling were under-represented. To date, our study is the most comprehensive investigation of the nuclear fern phylogeny, though several avenues for future research remain unexplored.
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影响因子：
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作者：
Cheng S;Melkonian M;Smith SA;Brockington S;Archibald JM;Delaux PM;Li FW;Melkonian B;Mavrodiev EV;Sun W;Fu Y;Yang H;Soltis DE;Graham SW;Soltis PS;Liu X;Xu X;Wong GK
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