Abstract
BackgroundGene duplication has played an important role in the evolution and domestication of flowering plants. Yet little is known about how plant duplicate genes evolve and are retained over long timescales, particularly those arising from small-scale duplication (SSD) rather than whole-genome duplication (WGD) events.ResultsWe address this question in the Poaceae (grass) family by analyzing gene expression data from nine tissues of Brachypodium distachyon, Oryza sativa japonica (rice), and Sorghum bicolor (sorghum). Consistent with theoretical predictions, expression profiles of most grass genes are conserved after SSD, suggesting that functional conservation is the primary outcome of SSD in grasses. However, we also uncover support for widespread functional divergence, much of which occurs asymmetrically via the process of neofunctionalization. Moreover, neofunctionalization preferentially targets younger (child) duplicate gene copies, is associated with RNA-mediated duplication, and occurs quickly after duplication. Further analysis reveals that functional divergence of SSD-derived genes is positively correlated with both sequence divergence and tissue specificity in all three grass species, and particularly with anther expression in B. distachyon.ConclusionsOur results suggest that SSD-derived grass genes often undergo rapid functional divergence that may be driven by natural selection on male-specific phenotypes. These observations are consistent with those in several animal species, suggesting that duplicate genes take similar evolutionary trajectories in plants and animals.
Highlights
Gene duplication has played an important role in the evolution and domestication of flowering plants
Findings stemming from comparative genomic and experimental studies have led researchers to hypothesize that this extraordinary diversity is primarily a product of gene duplication events [1,2,3]
It is important to note that the most recent whole-genome duplication (WGD) event in monocots occurred approximately 65 million years ago (MYA) [14], which is before the divergence of B. distachyon, O. sativa japonica, and Sorghum bicolor
Summary
Gene duplication has played an important role in the evolution and domestication of flowering plants. A number of studies have shown that gene duplication can promote the origin of novel plant phenotypes [1, 3], and that it was likely a key driving factor in the domestication of flowering plants [6,7,8,9] Many of these findings are associated with studies of duplicates derived from whole-genome duplication (WGD) events, which occurred several times during the past 200 million years of angiosperm evolution [1, 10,11,12,13,14,15]. An open question is how SSD-derived genes in angiosperms evolve and are retained over long evolutionary timescales
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