Population Level Purifying Selection and Gene Expression Shape Subgenome Evolution in Maize.
Population Level Purifying Selection and Gene Expression Shape Subgenome Evolution in Maize.
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DOI：
10.1093/molbev/msv191
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发表时间：
2015-12
影响因子：
10.7
通讯作者：
S. Pophaly;A. Tellier
中科院分区：
文献类型：
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作者：
S. Pophaly;A. Tellier
玉米的祖先经历了最近的全基因组重复（WGD），随后发生了基因侵蚀，产生了两个亚基因组，显性亚基因组（玉米1）经历了比玉米2少的缺失。我们利用玉米中广泛的多态性和基因表达数据来研究WGD保留的亲本对之间的纯化选择和基因表达差异。我们首先报告了一个强相关性的核苷酸多样性之间的重复对，除了上游区域。然后，我们表明，玉米1基因下更强的净化选择比玉米2。WGD保留的基因具有较高的基因剂量和偏向的基因本体与以前的研究一致。跨组织的旁系同源物的相对基因表达表明，98%的重复对要么以组织方式亚功能化，要么在其表达中一致地发散，从而防止功能互补。组织亚功能化似乎是转录因子的一个标志，而大分子复合物发生一致的抑制。我们表明，显性基因的表达是一个强大的决定因素的净化选择的强度，解释推断较强的负选择玉米1基因。我们提出了一种新的表达为基础的分类的重复，这是更强大的解释观察到的多态性模式比亚基因组位置。最后，阻遏基因的上游区域表现出丰富的转座因子，这表明表达分歧的可能机制。
The maize ancestor experienced a recent whole-genome duplication (WGD) followed by gene erosion which generated two subgenomes, the dominant subgenome (maize1) experiencing fewer deletions than maize2. We take advantage of available extensive polymorphism and gene expression data in maize to study purifying selection and gene expression divergence between WGD retained paralog pairs. We first report a strong correlation in nucleotide diversity between duplicate pairs, except for upstream regions. We then show that maize1 genes are under stronger purifying selection than maize2. WGD retained genes have higher gene dosage and biased Gene Ontologies consistent with previous studies. The relative gene expression of paralogs across tissues demonstrates that 98% of duplicate pairs have either subfunctionalized in a tissuewise manner or have diverged consistently in their expression thereby preventing functional complementation. Tissuewise subfunctionalization seems to be a hallmark of transcription factors, whereas consistent repression occurs for macromolecular complexes. We show that dominant gene expression is a strong determinant of the strength of purifying selection, explaining the inferred stronger negative selection on maize1 genes. We propose a novel expression-based classification of duplicates which is more robust to explain observed polymorphism patterns than the subgenome location. Finally, upstream regions of repressed genes exhibit an enrichment in transposable elements which indicates a possible mechanism for expression divergence.