Center for Applied Genetic Technologies, University of Georgia, Athens, 30602, GA, USA.
Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China.
Plant Cell Environ. 2018 Sep;41(9):2033-2044. doi: 10.1111/pce.13127. Epub 2018 Mar 4.
Soybean (Glycine max) and common bean (Phaseolus vulgaris) share a polyploidy event ~59 MYA, followed by a Glycine-specific whole genome duplication (WGD) ~8-13 MYA. Duplicated genes were classified into five categories: singletons, dispersed, proximal, tandem, or WGD/segmental and found strong correlations between gene category and functional annotation. Photosynthesis and transcriptional regulation-related Gene Ontology terms were significantly over-represented in singletons and WGD genes, respectively, aligning with the gene balance hypothesis. We found that the divergence of gene expression and DNA methylation between WGD-derived paralogs increased with age and that WGD genes, initially retained via dosage constraints, subsequently underwent expression divergence, associated with other factors such as DNA methylation. Genes derived from different modes of duplication differed in breadth, level, and specificity of expression in both species. Orthologous genes and ungrouped genes (genes not in an ortholog group) differed in expression patterns. The protein divergence rates of WGD paralog pairs containing an ungrouped gene were higher than those for which both copies had orthologs. We propose that many ungrouped genes are derived from divergent and redundant gene copies, concordant with the neofunctionalization hypothesis. Tandemly duplicated genes were distinct from WGD-derived genes, indicating that mode of duplication contributes to the evolutionary fate of duplicated genes.
大豆（Glycine max）和普通菜豆（Phaseolus vulgaris）共享一个约 5900 万年前的多倍体事件，随后发生了约 8-1300 万年前的 Glycine 特异性全基因组复制（WGD）。复制基因被分为五类：单拷贝基因、分散基因、近端基因、串联基因或 WGD/片段基因，并发现基因类别与功能注释之间存在很强的相关性。单拷贝基因和 WGD 基因分别与光合作用和转录调控相关的基因本体论术语显著富集，这与基因平衡假说一致。我们发现，WGD 衍生的同源基因之间的基因表达和 DNA 甲基化差异随着年龄的增长而增加，并且最初通过剂量限制保留的 WGD 基因随后经历了表达差异，这与 DNA 甲基化等其他因素有关。来自不同复制模式的基因在两种物种中的表达广度、水平和特异性上存在差异。直系同源基因和未分组基因（不在直系同源基因组中的基因）的表达模式不同。含有未分组基因的 WGD 同源基因对的蛋白质分歧率高于两个拷贝都有直系同源基因的同源基因对。我们提出，许多未分组基因是从不同和冗余的基因拷贝中衍生出来的，这与新功能化假说一致。串联重复基因与 WGD 衍生基因不同，表明复制模式有助于重复基因的进化命运。
