Species-specific partial gene duplication in Arabidopsis thaliana evolved novel phenotypic effects on morphological traits under strong positive selection.
Species-specific partial gene duplication in Arabidopsis thaliana evolved novel phenotypic effects on morphological traits under strong positive selection.
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DOI：
10.1093/plcell/koab291
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发表时间：
2022-02-03
期刊：
影响因子：
--
通讯作者：
Bergelson J
中科院分区：
文献类型：
--
作者：
Huang Y;Chen J;Dong C;Sosa D;Xia S;Ouyang Y;Fan C;Li D;Mortola E;Long M;Bergelson J
比较基因组学分析表明，基因复制是新基因产生的重要机制。然而，新的重复基因如何促进表型进化在很大程度上仍然未知，特别是在植物中。在这里，我们确定了新的基因EXOV，来自其亲本基因EXOVL在拟南芥的部分基因重复。EXOV是一种物种特异性基因，起源于过去350万年，显示出强烈的正选择信号。出乎意料的是，RNA测序分析显示，尽管EXOV年龄很小，但它已经获得了许多新的直接和间接相互作用，而亲本基因并不参与其中。这一观察结果与其编码蛋白的高选择驱动取代率相一致，与缓慢进化的EXOVL相反，表明EXOV在表型进化中的重要作用。我们观察到在基因组编辑和T-DNA插入单突变体中以及在EXOV和EXOVL中的双T-DNA插入突变体中评估的所有表型的形态变化的显著分化。通过主成分分析，我们发现了表型效应的显著差异，表明新基因的新功能化。这些结果揭示了一个年轻的基因，在生物过程中发挥关键作用，在形态进化的基础在A。thaliana.一个年轻的基因产生的物种特异性的部分基因复制迅速演变的关键发育功能在拟南芥。
Gene duplication is increasingly recognized as an important mechanism for the origination of new genes, as revealed by comparative genomic analysis. However, how new duplicate genes contribute to phenotypic evolution remains largely unknown, especially in plants. Here, we identified the new gene EXOV, derived from a partial gene duplication of its parental gene EXOVL in Arabidopsis thaliana. EXOV is a species-specific gene that originated within the last 3.5 million years and shows strong signals of positive selection. Unexpectedly, RNA-sequencing analyses revealed that, despite its young age, EXOV has acquired many novel direct and indirect interactions in which the parental gene does not engage. This observation is consistent with the high, selection-driven substitution rate of its encoded protein, in contrast to the slowly evolving EXOVL, suggesting an important role for EXOV in phenotypic evolution. We observed significant differentiation of morphological changes for all phenotypes assessed in genome-edited and T-DNA insertional single mutants and in double T-DNA insertion mutants in EXOV and EXOVL. We discovered a substantial divergence of phenotypic effects by principal component analyses, suggesting neofunctionalization of the new gene. These results reveal a young gene that plays critical roles in biological processes that underlie morphological evolution in A. thaliana. A young gene produced by species-specific partial gene duplication quickly evolved critical developmental functions in Arabidopsis.
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DOI：
10.1093/bioinformatics/btu638
发表时间：
2015-01-15
期刊：
Bioinformatics (Oxford, England)
影响因子：
--
作者：
Anders S;Pyl PT;Huber W
通讯作者：
Huber W
影响因子：
4.5
作者：
Ding Y;Zhao L;Yang S;Jiang Y;Chen Y;Zhao R;Zhang Y;Zhang G;Dong Y;Yu H;Zhou Q;Wang W
通讯作者：
Wang W
影响因子：
10.7
作者：
Lee, Yuh Chwen G.;Ventura, Iuri M.;Long, Manyuan
通讯作者：
Long, Manyuan
影响因子：
7.2
作者：
Klepikova, Anna V.;Kasianov, Artem S.;Penin, Aleksey A.
通讯作者：
Penin, Aleksey A.
影响因子：
11.1
作者：
Long M;VanKuren NW;Chen S;Vibranovski MD
通讯作者：
Vibranovski MD