Preferential subfunctionalization of slow-evolving genes after allopolyploidization in Xenopus laevis
Preferential subfunctionalization of slow-evolving genes after allopolyploidization in Xenopus laevis
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DOI：
10.1073/pnas.0708705105
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发表时间：
2008-06-17
影响因子：
11.1
通讯作者：
Wolfe, Kenneth H.
中科院分区：
文献类型：
--
作者：
Semon, Marie;Wolfe, Kenneth H.
随着古多倍体基因组的进化，保留基因对的表达谱预计会出现分歧。为了研究这种分歧的过程中大规模的脊椎动物系统中，我们比较非洲爪蟾，它保留了近40%的基因座在最近的全基因组复制（WGD）后，重复，其未重复的相对志留纪（非洲爪蟾）热带。这种内组对与外组的比较允许针对一组1，300 X来推断表达谱的变化方向。laevis对，相对于它们在S. tropicalis，在11个组织中。我们确定了68对，其中X。推断自WGD以来，在至少两种组织中，Iaevis经历了表达的显著降低。在这些对中，三分之一显示出亚功能化的证据，在两种不同组织中不同基因拷贝的表达水平降低。令人惊讶的是，我们发现进化速度慢的基因特别容易发生亚功能化，即使是在高度表达的基因进化缓慢的趋势得到控制的情况下。我们解释这一结果是异源多倍化的影响。然后，我们比较的结果，这个WGD与一个独立的发生在硬骨鱼谱系。我们发现，如果一个基因对被保留在X laevis的一式两份，orthopathy对更有可能已被保留在斑马鱼的一式两份，这表明类似的因素，其中subfunctionalization，确定哪些基因对存活后的两个WGD的一式两份。
As paleopolyploid genomes evolve, the expression profiles of retained gene pairs are expected to diverge. To examine this divergence process on a large scale in a vertebrate system, we compare Xenopus laevis, which has retained approximate to 40% of loci in duplicate after a recent whole-genome duplication (WGD), with its unduplicated relative Silurana (Xenopus) tropicalis. This comparison of ingroup pairs to an outgroup allows the direction of change in expression profiles to be inferred for a set of 1,300X. laevis pairs, relative to their single orthologs in S. tropicalis, across 11 tissues. We identify 68 pairs in which X. laevis is inferred to have undergone a significant reduction of expression in at least two tissues since WGD. Of these pairs, one-third show evidence of subfunctionalization, with decreases in the expression levels of different gene copies in two different tissues. Surprisingly, we find that genes with slow rates of evolution are particularly prone to subfunctionalization, even when the tendency for highly expressed genes to evolve slowly is controlled for. We interpret this result to be an effect of allopolyploidization. We then compare the outcomes of this WGD with an independent one that happened in the teleost fish lineage. We find that if a gene pair was retained in duplicate in X laevis, the orthologous pair is more likely to have been retained in duplicate in zebrafish, suggesting that similar factors, among them subfunctionalization, determined which gene pairs survived in duplicate after the two WGDs.