Department of Bioscience and Bioinformatics, Kyushu Institute of Technology, Iizuka, Fukuoka, Japan.
Mol Biol Evol. 2021 Apr 13;38(4):1447-1459. doi: 10.1093/molbev/msaa302.
Gene duplication is a major mechanism to create new genes. After gene duplication, some duplicated genes undergo functionalization, whereas others largely maintain redundant functions. Duplicated genes comprise various degrees of functional diversification in plants. However, the evolutionary fate of high and low diversified duplicates is unclear at genomic scale. To infer high and low diversified duplicates in Arabidopsis thaliana genome, we generated a prediction method for predicting whether a pair of duplicate genes was subjected to high or low diversification based on the phenotypes of knock-out mutants. Among 4,017 pairs of recently duplicated A. thaliana genes, 1,052 and 600 are high and low diversified duplicate pairs, respectively. The predictions were validated based on the phenotypes of generated knock-down transgenic plants. We determined that the high diversified duplicates resulting from tandem duplications tend to have lineage-specific functions, whereas the low diversified duplicates produced by whole-genome duplications are related to essential signaling pathways. To assess the evolutionary impact of high and low diversified duplicates in closely related species, we compared the retention rates and selection pressures on the orthologs of A. thaliana duplicates in two closely related species. Interestingly, high diversified duplicates resulting from tandem duplications tend to be retained in multiple lineages under positive selection. Low diversified duplicates by whole-genome duplications tend to be retained in multiple lineages under purifying selection. Taken together, the functional diversities determined by different duplication mechanisms had distinct effects on plant evolution.
基因复制是创造新基因的主要机制。基因复制后，一些复制基因经历了功能化，而另一些则在很大程度上保持了冗余功能。复制基因在植物中具有不同程度的功能多样化。然而，在基因组规模上，高分化和低分化复制基因的进化命运尚不清楚。为了推断拟南芥基因组中高分化和低分化的复制基因，我们基于敲除突变体的表型生成了一种预测方法，用于预测一对重复基因是否经历了高分化或低分化。在 4017 对最近复制的拟南芥基因中，分别有 1052 对和 600 对是高分化和低分化的重复基因对。通过生成的敲低转基因植物的表型对预测进行了验证。我们确定，串联复制产生的高分化重复基因往往具有谱系特异性功能，而全基因组复制产生的低分化重复基因与必需的信号通路有关。为了评估高分化和低分化重复基因在近缘物种中的进化影响，我们比较了两个近缘物种中拟南芥重复基因的直系同源物的保留率和选择压力。有趣的是，串联复制产生的高分化重复基因倾向于在多个谱系中受到正选择而保留。全基因组复制产生的低分化重复基因倾向于在多个谱系中受到纯化选择而保留。总之，不同复制机制决定的功能多样性对植物进化有不同的影响。
