- © 2011 American Society of Plant Biologists
Gene duplications can serve as fodder for evolutionary diversification, with duplicate genes evolving novel functions or subdividing the ancestral gene's functions (reviewed in Van de Peer et al., 2009). Duplications can be small or large scale, with whole-genome duplication (WGD) being the most extreme example of the latter. WGD results in the formation of a polyploid plant either by duplication of the endogenous genome or by merging that genome with an additional compatible genome. WGD events can improve plant vigor by heterotic effects and can increase the plant's range of phenotypes, which may prove advantageous in accessing new ecological niches or surviving ecological crises. Duplicated genes can increase the efficiency of their original pathways or evolve to conduct different functions. Indeed, the history of most flowering plant species includes one or more WGDs. For example, the Arabidopsis genome shows a relatively recent event (WGD-α), a somewhat more ancient event (WGD-β), and a very ancient γ event shared by most eudicots.
After a WGD, the resultant polyploid genome can revert to a functional diploid state by elimination of genes. However, the selective constraints contributing to the retention of genes after WGD are not fully understood: Why do some genes survive genomic housecleaning while others are eliminated? Bekaert et al. (pages 1719–1728) examine this question by mapping the functions of the duplicated genes retained following the Arabidopsis WGDs onto the Arabidopsis metabolic map (see figure). Their examination focuses on two complementary hypotheses: selection on absolute gene dosage and selection on relative gene dosage (dosage balance). The dosage balance hypothesis predicts that central network genes, which have many key interactions with other metabolic components, should be preferentially retained because elimination of such a gene would disturb the stoichiometry of many interactions.
Genes retained after WGD superimposed on the Arabidopsis metabolic network. Reactions are depicted by circles (nodes), which are connected by an edge representing a shared metabolite. Edges are colored to indicate retention following small-scale (single copy) and whole-genome (WGD) duplications. (Reprinted from Bekaert et al. [2011].)
Using a primary metabolic network map developed by de Oliveira Dal'Molin et al. (2010), the authors examined whether 420 duplicated genes retained from the WGD-α and 156 retained from the WGD-β showed nonrandom clustering within the metabolic network. Indeed, they found that genes within the metabolic network were retained more than genes in the rest of the genome and that retained genes tended to form clusters within the metabolic network, indicating selection for relative gene dosage. Genes in specific compartments, such as the chloroplast, were not preferentially retained. Intriguingly, genes retained in WGD-β were associated with reactions of high metabolic flux, indicating selection for absolute gene dosage. Thus, different selective constraints may act at different times after WGD, with relative gene dosage initially acting to retain genes, and absolute gene dosage, possibly along with evolutionary changes in function, being more important for long-term gene retention.
