Department of Ecology, Evolution and Organismal Biology, Iowa State University, Ames, IA 50011, USA.
Heredity (Edinb). 2013 Feb;110(2):171-80. doi: 10.1038/hdy.2012.94. Epub 2012 Nov 21.
Allopolyploidy is an evolutionary and mechanistically intriguing process, in that it entails the reconciliation of two or more sets of diverged genomes and regulatory interactions. In this study, we explored gene expression patterns in interspecific hybrid F(1), and synthetic and natural allopolyploid cotton using RNA-Seq reads from leaf transcriptomes. We determined how the extent and direction of expression level dominance (total level of expression for both homoeologs) and homoeolog expression bias (relative contribution of homoeologs to the transcriptome) changed from hybridization through evolution at the polyploid level and following cotton domestication. Genome-wide expression level dominance was biased toward the A-genome in the diploid hybrid and natural allopolyploids, whereas the direction was reversed in the synthetic allopolyploid. This biased expression level dominance was mainly caused by up- or downregulation of the homoeolog from the 'non-dominant' parent. Extensive alterations in homoeolog expression bias and expression level dominance accompany the initial merger of two diverged diploid genomes, suggesting a combination of regulatory (cis or trans) and epigenetic interactions that may arise and propagate through the transcriptome network. The extent of homoeolog expression bias and expression level dominance increases over time, from genome merger through evolution at the polyploid level. Higher rates of transgressive and novel gene expression patterns as well as homoeolog silencing were observed in natural allopolyploids than in F(1) hybrid and synthetic allopolyploid cottons. These observations suggest that natural selection reconciles the regulatory mismatches caused by initial genomic merger, while new gene expression conditions are generated for evaluation by selection.
异源多倍体是一个进化和机制上引人入胜的过程，因为它需要调和两个或更多套分化的基因组和调控相互作用。在这项研究中，我们使用叶转录组的 RNA-Seq 读数探索了种间杂种 F1 和合成及天然异源多倍体棉花中的基因表达模式。我们确定了表达水平优势（两个同源等位基因的总表达水平）和同源等位基因表达偏向（同源等位基因对转录组的相对贡献）从杂交到多倍体水平进化以及棉花驯化的程度和方向如何变化。在二倍体杂种和天然异源多倍体中，基因组-wide 表达水平优势偏向 A 基因组，而在合成异源多倍体中方向相反。这种偏向的表达水平优势主要是由“非优势”亲本同源等位基因的上调或下调引起的。同源等位基因表达偏向和表达水平优势的广泛改变伴随着两个分化的二倍体基因组的初始合并，这表明可能出现了调控（顺式或反式）和表观遗传相互作用，并通过转录组网络传播。从基因组合并到多倍体水平进化，同源等位基因表达偏向和表达水平优势的程度增加。在天然异源多倍体中观察到的同源等位基因沉默和新基因表达模式的超越和新颖性高于 F1 杂种和合成异源多倍体棉花。这些观察结果表明，自然选择调和了由初始基因组合并引起的调控不匹配，同时为选择提供了新的基因表达条件进行评估。
