Rapid functional divergence after small-scale gene duplication in grasses
Rapid functional divergence after small-scale gene duplication in grasses
复制标题
DOI：
10.1186/s12862-019-1415-2
复制
发表时间：
2019-05-02
影响因子：
3.4
通讯作者：
Assis, Raquel
中科院分区：
文献类型：
--
作者：
Jiang, Xueyuan;Assis, Raquel
研究背景基因复制在有花植物的进化和驯化过程中起着重要作用。然而，很少有人知道植物重复基因的演变和保留在很长的时间尺度，特别是那些产生的小规模重复（SSD），而不是全基因组重复（WGD）events.ResultsWe解决这个问题在禾本科（草）家庭通过分析基因表达数据从九个组织的短柄草二穗草，水稻（水稻），高粱（高粱）。与理论预测一致，大多数草基因的表达谱是保守的SSD后，这表明功能的保护是SSD在禾本科植物中的主要结果。然而，我们也发现支持广泛的功能分歧，其中大部分是通过neofunctionalization过程不对称地发生。此外，新功能化优先靶向年轻（儿童）重复基因拷贝，与RNA介导的复制相关，并在复制后迅速发生。进一步的分析表明，SSD衍生基因的功能差异与所有三种禾本科植物的序列差异和组织特异性均呈正相关，尤其是与B的花粉囊表达正相关。结论我们的研究结果表明，SSD衍生的草基因往往经历快速的功能分歧，可能是由自然选择男性特异性表型。这些观察结果与几种动物物种的观察结果一致，表明重复基因在植物和动物中具有相似的进化轨迹。
BackgroundGene duplication has played an important role in the evolution and domestication of flowering plants. Yet little is known about how plant duplicate genes evolve and are retained over long timescales, particularly those arising from small-scale duplication (SSD) rather than whole-genome duplication (WGD) events.ResultsWe address this question in the Poaceae (grass) family by analyzing gene expression data from nine tissues of Brachypodium distachyon, Oryza sativa japonica (rice), and Sorghum bicolor (sorghum). Consistent with theoretical predictions, expression profiles of most grass genes are conserved after SSD, suggesting that functional conservation is the primary outcome of SSD in grasses. However, we also uncover support for widespread functional divergence, much of which occurs asymmetrically via the process of neofunctionalization. Moreover, neofunctionalization preferentially targets younger (child) duplicate gene copies, is associated with RNA-mediated duplication, and occurs quickly after duplication. Further analysis reveals that functional divergence of SSD-derived genes is positively correlated with both sequence divergence and tissue specificity in all three grass species, and particularly with anther expression in B. distachyon.ConclusionsOur results suggest that SSD-derived grass genes often undergo rapid functional divergence that may be driven by natural selection on male-specific phenotypes. These observations are consistent with those in several animal species, suggesting that duplicate genes take similar evolutionary trajectories in plants and animals.