Division of Biological Sciences, University of Missouri-Columbia, Columbia, Missouri, United States of America.
Department of Biochemistry, University of Missouri-Columbia, Columbia, Missouri, United States of America.
PLoS Genet. 2018 Mar 28;14(3):e1007267. doi: 10.1371/journal.pgen.1007267. eCollection 2018 Mar.
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.
多倍体现象越来越被认为是进化创新和生态成功的驱动因素。多倍体生物成功的一个原因可能是它们起源于两个不同物种的基因组融合和混合（例如异源多倍体）。使用 POInT（多倍体同源推断工具），我们模拟了三个异源多倍体事件的解决方案，其中一个来自面包酵母（酿酒酵母），一个来自拟南芥，一个来自包括高粱在内的禾本科植物。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本亚基因组的概率（即来自二倍体祖先生物），从而在所有基因组中产生了同源片段。我们的模型在所有三个谱系中都检测到了存在偏分离的统计学上可靠的证据，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，这种偏分离丢失模式的驱动因素是来自同一亲本基因组的基因的共同保留，这些基因具有功能相互作用。拟南芥和禾本科植物异源多倍体事件后偏分离的模式在时间上非常稳定，同一亲本基因组在整个谱系历史中都受到青睐。相比之下，酵母异源多倍体事件仅在事件后立即显示出偏分离的证据，最近基因丢失更加平衡。从单个亚基因组中快速丢失具有功能关联的基因与遗传漂变的作用难以调和，并表明选择可能有利于去除特定的重复基因。结合拟南芥 At-α事件后持续存在的、具有功能关联的偏分离证据，我们认为，异源多倍体形成后，不同亚基因组中编码的相互作用基因之间存在功能冲突，最终通过优先丢失重复基因来解决。
