Maintenance of duplicate genes and their functional redundancy by reduced expression

Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA.
Trends in Genetics (Impact Factor: 9.92). 10/2010; 26(10):425-30. DOI: 10.1016/j.tig.2010.07.002
Source: PubMed


Although evolutionary theories predict functional divergence between duplicate genes, many old duplicates still maintain a high degree of functional similarity and are synthetically lethal or sick, an observation that has puzzled many geneticists. We propose that expression reduction, a special type of subfunctionalization, facilitates the retention of duplicates and the conservation of their ancestral functions. Consistent with this hypothesis, gene expression data from both yeasts and mammals show a substantial decrease in the level of gene expression after duplication. Whereas the majority of the expression reductions are likely to be neutral, some are apparently beneficial to rebalancing gene dosage after duplication.

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Available from: Ben-Yang Liao, Oct 09, 2015
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    • "The malic acid database of apple germplasm also provides an opportunity to investigate the genetic basis of fruit acidity using the association mapping method. Since duplicated genes often share redundant functions (Qian et al., 2010), we investigated the effect of homologs of the Ma1 gene on fruit acidity using candidate gene-based association mapping. The subcellular localization and functionality of the Ma1 gene were also investigated. "
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    ABSTRACT: A gene encoding aluminum-activated malate transporter (ALMT)
    The Plant Genome 11/2015; 8(3). DOI:10.3835/plantgenome2015.03.0016 · 3.93 Impact Factor
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    • "Conceivably, the observed trend for paralogs to become more specialized in their expression patterns than expected from the strict DDC model (Table 1) as well as a significant positive correlation between gene expression and sequence divergence for within-species paralog measurements (Figures 1(c) and 1(d)) and the nonmonotonic dependency of the Z-scores and ranking scores on sequence divergence (Figures 1(a) and 1(b)) can be explained by selection for rebalancing of expression in different tissues and environmental conditions (Figure 2) [34]. This scenario, the “protein dosage rebalancing” [34], is consistent with several previous studies which suggest that rebalancing of expression after duplications, at least for some genes, could be beneficial [37–39, 41–44]. For example, Qian and colleagues have shown that yeast and mammalian genes often experienced a significant decrease in the level of expression after duplication. "
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    ABSTRACT: Ongoing debates about functional importance of gene duplications have been recently intensified by a heated discussion of the "ortholog conjecture" (OC). Under the OC, which is central to functional annotation of genomes, orthologous genes are functionally more similar than paralogous genes at the same level of sequence divergence. However, a recent study challenged the OC by reporting a greater functional similarity, in terms of gene ontology (GO) annotations and expression profiles, among within-species paralogs compared to orthologs. These findings were taken to indicate that functional similarity of homologous genes is primarily determined by the cellular context of the genes, rather than evolutionary history. Subsequent studies suggested that the OC appears to be generally valid when applied to mammalian evolution but the complete picture of evolution of gene expression also has to incorporate lineage-specific aspects of paralogy. The observed complexity of gene expression evolution after duplication can be explained through selection for gene dosage effect combined with the duplication-degeneration-complementation model. This paper discusses expression divergence of recent duplications occurring before functional divergence of proteins encoded by duplicate genes.
    08/2014; 2014:516508. DOI:10.1155/2014/516508
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    • "Gene duplication plays an important role in the development of expression patterns of members of a gene family. For example, gene duplication promotes expression divergence of gene copies [31] that affects the retention and functionalization of redundant gene duplicates [32,33]. Divergence in expression of paralogous genes is positively correlated with ages of genes [34], and is likely affected by changes of cis- and trans-regulatory elements [35-37]. "
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    ABSTRACT: Background Predatory marine gastropods of the genus Conus exhibit substantial variation in venom composition both within and among species. Apart from mechanisms associated with extensive turnover of gene families and rapid evolution of genes that encode venom components (‘conotoxins’), the evolution of distinct conotoxin expression patterns is an additional source of variation that may drive interspecific differences in the utilization of species’ ‘venom gene space’. To determine the evolution of expression patterns of venom genes of Conus species, we evaluated the expression of A-superfamily conotoxin genes of a set of closely related Conus species by comparing recovered transcripts of A-superfamily genes that were previously identified from the genomes of these species. We modified community phylogenetics approaches to incorporate phylogenetic history and disparity of genes and their expression profiles to determine patterns of venom gene space utilization. Results Less than half of the A-superfamily gene repertoire of these species is expressed, and only a few orthologous genes are coexpressed among species. Species exhibit substantially distinct expression strategies, with some expressing sets of closely related loci (‘under-dispersed’ expression of available genes) while others express sets of more disparate genes (‘over-dispersed’ expression). In addition, expressed genes show higher dN/dS values than either unexpressed or ancestral genes; this implies that expression exposes genes to selection and facilitates rapid evolution of these genes. Few recent lineage-specific gene duplicates are expressed simultaneously, suggesting that expression divergence among redundant gene copies may be established shortly after gene duplication. Conclusions Our study demonstrates that venom gene space is explored differentially by Conus species, a process that effectively permits the independent and rapid evolution of venoms in these species.
    BMC Evolutionary Biology 06/2014; 14(1):123. DOI:10.1186/1471-2148-14-123 · 3.37 Impact Factor
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