Coate Jeremy E, Song Michael J, Bombarely Aureliano, Doyle Jeff J
Department of Biology, Reed College, Portland, OR, 97202, USA.
Department of Horticulture, Virginia Tech, Blacksburg, VA, 24061, USA.
New Phytol. 2016 Dec;212(4):1083-1093. doi: 10.1111/nph.14090. Epub 2016 Jul 15.
Retention or loss of paralogs following duplication correlates strongly with the function of the gene and whether the gene was duplicated by whole-genome duplication (WGD) or by small-scale duplication. Selection on relative gene dosage (to maintain proper stoichiometry among interacting proteins) has been invoked to explain these patterns of duplicate gene retention and loss. In order for gene dosage to be visible to natural selection, there must necessarily be a correlation between gene copy number and gene expression level (transcript abundance), but this has rarely been examined. We used RNA-Seq data from seven Glycine subgenus Glycine species (three recently formed allotetraploids and their four diploid progenitors) to determine if expression patterns and gene dosage responses at the level of transcription are consistent with selection on relative gene dosage. As predicted, metabolic pathways and gene ontologies that are putatively dosage-sensitive based on duplication history exhibited reduced expression variance across species, and more coordinated expression responses to recent WGD, relative to putatively dosage-insensitive networks. We conclude that selection on relative dosage has played an important role in shaping gene networks in Glycine.
基因复制后旁系同源基因的保留或丢失与基因功能以及该基因是通过全基因组复制（WGD）还是小规模复制密切相关。有人提出对相对基因剂量的选择（以维持相互作用蛋白之间的适当化学计量）来解释这些重复基因保留和丢失的模式。为了使基因剂量能够被自然选择所察觉，基因拷贝数与基因表达水平（转录本丰度）之间必然存在相关性，但这一点很少被研究。我们使用了来自七个大豆属大豆亚属物种（三个最近形成的异源四倍体及其四个二倍体祖先）的RNA测序数据，以确定转录水平上的表达模式和基因剂量反应是否与对相对基因剂量的选择一致。正如预测的那样，基于复制历史推测对剂量敏感的代谢途径和基因本体在物种间表现出较低的表达方差，并且相对于推测对剂量不敏感的网络，对近期全基因组复制有更协调的表达反应。我们得出结论，对相对剂量的选择在塑造大豆基因网络中发挥了重要作用。
