Divergence in Expression between Duplicated Genes in Arabidopsis

Ganko, Eric W.; Meyers, Blake C.; Vision, Todd

doi:10.1093/molbev/msm158

Cited by 226 publications

(215 citation statements)

References 72 publications

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“…First, each of the three paralogous gene sets exhibit evidence of unequal (or asymmetrical) divergence (Wagner, 2002;Ganko et al, 2007) with respect to the root epidermal network because mutants of one member (cpc, gl3, and wer) have a generally greater impact on downstream gene expression than mutants of the other (try, egl3, and myb23), consistent with their morphological effects. Furthermore, we conclude that, among these three paralogous gene sets, the TRY-CPC set appears to have undergone the least diversification and MYB23-WER the most (with respect to the root epidermal network) because (1) TRY-CPC has the smallest frequency (and MYB23-WER the greatest frequency) of target genes exhibiting high sensitivity to the loss of either member (i. e., number of "H" category genes in each set: TRY-CPC …”

Section: Discussion Molecular Dissection Of Duplicate Gene Functionmentioning

confidence: 87%

Tissue-Specific Profiling Reveals Transcriptome Alterations inArabidopsisMutants Lacking Morphological Phenotypes

et al. 2013

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Traditional genetic analysis relies on mutants with observable phenotypes. Mutants lacking visible abnormalities may nevertheless exhibit molecular differences useful for defining gene function. To examine this, we analyzed tissue-specific transcript profiles from Arabidopsis thaliana transcription factor gene mutants with known roles in root epidermis development, but lacking a single-gene mutant phenotype due to genetic redundancy. We discovered substantial transcriptional changes in each mutant, preferentially affecting root epidermal genes in a manner consistent with the known double mutant effects. Furthermore, comparing transcript profiles of single and double mutants, we observed remarkable variation in the sensitivity of target genes to the loss of one or both paralogous genes, including preferential effects on specific branches of the epidermal gene network, likely reflecting the pathways of paralog subfunctionalization during evolution. In addition, we analyzed the root epidermal transcriptome of the transparent testa glabra2 mutant to clarify its role in the network. These findings provide insight into the molecular basis of genetic redundancy and duplicate gene diversification at the level of a specific gene regulatory network, and they demonstrate the usefulness of tissue-specific transcript profiling to define gene function in mutants lacking informative visible changes in phenotype.

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Section: Discussion Molecular Dissection Of Duplicate Gene Functionmentioning

confidence: 87%

Tissue-Specific Profiling Reveals Transcriptome Alterations inArabidopsisMutants Lacking Morphological Phenotypes

et al. 2013

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“…Asymmetric expression pattern was also observed between paralogs in Arabidopsis and rice (Blanc and Wolfe, 2004;Ganko et al, 2007;Throude et al, 2009) and between homoeologs in cotton (Chaudhary et al, 2009). Our expression results showed evidence for transcriptional divergence among different tissue types of some homoeolog pairs, consistent with findings in other plant species.…”

Section: Expression Biases Are Correlated With Sequence Divergencementioning

confidence: 77%

Structural and Functional Divergence of a 1-Mb Duplicated Region in the Soybean (Glycine max) Genome and Comparison to an Orthologous Region fromPhaseolus vulgaris

et al. 2010

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Soybean (Glycine max) has undergone at least two rounds of polyploidization, resulting in a paleopolyploid genome that is a mosaic of homoeologous regions. To determine the structural and functional impact of these duplications, we sequenced two ;1-Mb homoeologous regions of soybean, Gm8 and Gm15, derived from the most recent ;13 million year duplication event and the orthologous region from common bean (Phaseolus vulgaris), Pv5. We observed inversions leading to major structural variation and a bias between the two chromosome segments as Gm15 experienced more gene movement (gene retention rate of 81% in Gm15 versus 91% in Gm8) and a nearly twofold increase in the deletion of long terminal repeat (LTR) retrotransposons via solo LTR formation. Functional analyses of Gm15 and Gm8 revealed decreases in gene expression and synonymous substitution rates for Gm15, for instance, a 38% increase in transcript levels from Gm8 relative to Gm15. Transcriptional divergence of homoeologs was found based on expression patterns among seven tissues and developmental stages. Our results indicate asymmetric evolution between homoeologous regions of soybean as evidenced by structural changes and expression variances of homoeologous genes.

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“…Previous studies comparing gene expression levels of duplicate genes revealed that expression divergence between copies occurs rapidly (31)(32)(33)(34)(35)(36)(37)(38) and can be asymmetric (32,35,38). However, our analysis is unique in that it uses expression data and phylogenetic relationships among genes to explicitly classify the evolutionary processes underlying the retention of duplicates on a genome-wide scale.…”

Section: Discussionmentioning

confidence: 99%

Neofunctionalization of young duplicate genes in Drosophila

Assis

Bachtrog

2013

Proc. Natl. Acad. Sci. U.S.A.

191

332

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Gene duplication is a key source of genetic innovation that plays a role in the evolution of phenotypic complexity. Although several evolutionary processes can result in the long-term retention of duplicate genes, their relative contributions in nature are unknown. Here we develop a phylogenetic approach for comparing genome-wide expression profiles of closely related species to quantify the roles of conservation, neofunctionalization, subfunctionalization, and specialization in the preservation of duplicate genes. Application of our method to pairs of young duplicates in Drosophila shows that neofunctionalization, the gain of a novel function in one copy, accounts for the retention of almost twothirds of duplicate genes. Surprisingly, novel functions nearly always originate in younger (child) copies, whereas older (parent) copies possess functions similar to those of ancestral genes. Further examination of such pairs reveals a strong bias toward RNAmediated duplication events, implicating asymmetric duplication and positive selection in the evolution of new functions. Moreover, we show that young duplicate genes are expressed primarily in testes and that their expression breadth increases over evolutionary time. This finding supports the "out-of-testes" hypothesis, which posits that testes are a catalyst for the emergence of new genes that ultimately evolve functions in other tissues. Thus, our study highlights the importance of neofunctionalization and positive selection in the retention of young duplicates in Drosophila and illustrates how duplicates become incorporated into novel functional networks over evolutionary time.G ene duplication produces two copies of an existing gene.Evolutionary theory predicts that functional redundancy of duplicate genes causes one copy to undergo a brief period of relaxed selection after duplication (1). In nearly all cases, this should result in an accumulation of deleterious mutations and pseudogenization of the copy within a few million years (2). However, most sequenced eukaryotic genomes contain many functional duplicates, some of which are hundreds of millions of years old (3-8), suggesting that duplicate genes play important roles in evolution.Four processes can result in the evolutionary preservation of duplicate genes: conservation, neofunctionalization, subfunctionalization, and specialization. Under conservation, ancestral functions are maintained in both copies, likely because increased gene dosage is beneficial (1). Under neofunctionalization, one copy retains its ancestral functions, and the other acquires a novel function (1). Under subfunctionalization, mutations damage different functions of each copy, such that both copies are required to preserve all ancestral gene functions (9, 10). Finally, under specialization, subfunctionalization and neofunctionalization act in concert, producing two copies that are functionally distinct from each other and from the ancestral gene (11). Theoretical work has shown that different conditions can result in the retention of...

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Divergence in Expression between Duplicated Genes in Arabidopsis

Cited by 226 publications

References 72 publications

Tissue-Specific Profiling Reveals Transcriptome Alterations inArabidopsisMutants Lacking Morphological Phenotypes

Tissue-Specific Profiling Reveals Transcriptome Alterations inArabidopsisMutants Lacking Morphological Phenotypes

Structural and Functional Divergence of a 1-Mb Duplicated Region in the Soybean (Glycine max) Genome and Comparison to an Orthologous Region fromPhaseolus vulgaris

Neofunctionalization of young duplicate genes in Drosophila

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