Preferential retention of genes from one parental genome after polyploidy illustrates the nature and scope of the genomic conflicts induced by hybridization.
Preferential retention of genes from one parental genome after polyploidy illustrates the nature and scope of the genomic conflicts induced by hybridization.
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DOI：
10.1371/journal.pgen.1007267
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发表时间：
2018-03
期刊：
影响因子：
4.5
通讯作者：
Conant GC
中科院分区：
文献类型：
--
作者：
Emery M;Willis MMS;Hao Y;Barry K;Oakgrove K;Peng Y;Schmutz J;Lyons E;Pires JC;Edger PP;Conant GC
多倍体越来越被视为进化创新和生态成功的驱动力。多倍体生物成功的一个来源可能是它们起源于两个不同物种的基因组的合并和混合(例如，异源多倍体)。使用POINT(多倍体正交推理工具)，我们模拟了三个异源多倍体事件的分辨率，一个来自面包师酵母(Saccharmyces Cerevisiae)，一个来自水芹(Arabiopsis Thaliana)，以及一个来自包括高粱在内的牧草。分析了总共21个基因组，我们为每个基因分配了来自每个亲代亚基因组(即来自二倍体祖先物种)的概率，产生了所有基因组的同源片段。我们的模型检测到了统计上强有力的证据，证明在所有三个谱系中都存在有偏见的分裂，即来自两个亚基因组之一的基因比来自另一个亚基因组的基因更有可能丢失。我们进一步发现，这种偏向丢失模式的一个驱动因素是来自共享功能相互作用的同一亲本基因组的基因的共同保留。在拟南芥和草类异源多倍体事件之后，偏向分裂的模式在时间上令人惊讶地保持不变，在整个谱系的历史上，相同的亲本基因组受到青睐。与之形成强烈对比的是，酵母异源多倍体事件仅在事件发生后立即显示出偏向分离的证据，最近出现了平衡的基因丢失。单个亚基因组中功能相关基因的迅速丢失很难与遗传漂移的作用相一致，这表明选择可能有利于特定重复序列的移除。再加上A.thaliana at-α事件后持续的、功能相关的偏向分离的证据，我们认为，在异源多倍体之后，不同亚基因组中编码的相互作用的基因之间存在功能冲突，这些冲突最终通过优先重复丢失来解决。基因组复制/多倍体可以瞬间使生物体的基因含量加倍。然而，这种加倍的状态是不稳定的，多倍体创始人的后代很快就会失去许多重复的基因。在这里，我们描述了一个系统基因组管道，它允许我们在一组现代基因组中追踪基因丢失的历史，这些基因组都来自相同的三个多倍体事件(两个在开花植物中，一个在酵母中)。多倍体通常由相关但不相同的谱系杂交而发生，先前对单个多倍体基因组的研究发现，一个谱系在多倍体后丢失的基因比另一个少(称为有偏分离)。然而，单基因组研究可能会被误导，因为错误地假设共享基因序列的短区域来自相同的亲本基因组，从而推断出有偏见的分离。通过对21个基因组(10个植物和11个酵母)这三个多倍体事件的系统发育建模，我们证实了植物中存在有偏见的分离，并在酵母中提供了新的证据(在酵母中，这种分离只发生在多倍体后的很短时间内)。我们还表明，来自替代亲本基因组的基因倾向于编码物理上不相互作用的产物，这表明在共同适应复合体中维持功能的选择有助于推动这种丢失模式的偏见。
Polyploidy is increasingly seen as a driver of both evolutionary innovation and ecological success. One source of polyploid organisms’ successes may be their origins in the merging and mixing of genomes from two different species (e.g., allopolyploidy). Using POInT (the Polyploid Orthology Inference Tool), we model the resolution of three allopolyploidy events, one from the bakers’ yeast (Saccharomyces cerevisiae), one from the thale cress (Arabidopsis thaliana) and one from grasses including Sorghum bicolor. Analyzing a total of 21 genomes, we assign to every gene a probability for having come from each parental subgenome (i.e., derived from the diploid progenitor species), yielding orthologous segments across all genomes. Our model detects statistically robust evidence for the existence of biased fractionation in all three lineages, whereby genes from one of the two subgenomes were more likely to be lost than those from the other subgenome. We further find that a driver of this pattern of biased losses is the co-retention of genes from the same parental genome that share functional interactions. The pattern of biased fractionation after the Arabidopsis and grass allopolyploid events was surprisingly constant in time, with the same parental genome favored throughout the lineages’ history. In strong contrast, the yeast allopolyploid event shows evidence of biased fractionation only immediately after the event, with balanced gene losses more recently. The rapid loss of functionally associated genes from a single subgenome is difficult to reconcile with the action of genetic drift and suggests that selection may favor the removal of specific duplicates. Coupled to the evidence for continuing, functionally-associated biased fractionation after the A. thaliana At-α event, we suggest that, after allopolyploidy, there are functional conflicts between interacting genes encoded in different subgenomes that are ultimately resolved through preferential duplicate loss. Genome duplications/polyploidies can transiently double an organism’s gene content. However, this doubled condition is unstable and descendants of polyploid founders rapidly lose many of their duplicate genes. Here, we describe a phylogenomic pipeline that allows us to trace this history of gene loss across a set of modern genomes that all descend from the same three polyploidy events (two in flowering plants and one in yeasts). Polyploidy often occurs by the hybridization of related but not identical lineages, and previous studies in single polyploid genomes have identified a tendency for one lineage to lose fewer genes after polyploidy than the other (known as biased fractionation). However, single genome studies can be misled into inferring biased fractionation by incorrectly assuming that short regions of shared gene order are derived from the same parental genome. By phylogenetically modeling the resolution of these three polyploidy events across 21 genomes (10 plants and 11 yeasts), we confirm the existence of biased fractionation in plants and provide new evidence for it in yeasts (where it occurred only for a short interval post-polyploidy). We also show that genes from alternative parental genomes tend to encode products that do not physically interact, suggesting that selection to maintain function in co-adapted complexes helped to drive this bias in loss patterns.
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影响因子：
9.8
作者：
Conant GC;Wolfe KH
通讯作者：
Wolfe KH
影响因子：
64.8
作者：
Aury, Jean-Marc;Jaillon, Olivier;Wincker, Patrick
通讯作者：
Wincker, Patrick
DOI：
10.1073/pnas.1300127110
发表时间：
2013-02-19
影响因子：
11.1
作者：
De Smet, Riet;Adams, Keith L.;Van de Peer, Yves
通讯作者：
Van de Peer, Yves
影响因子：
10.7
作者：
Conant, Gavin C.
通讯作者：
Conant, Gavin C.
影响因子：
4.9
作者：
Buggs, Richard J. A.;Chamala, Srikar;Barbazuk, W. Brad
通讯作者：
Barbazuk, W. Brad