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Keith L Adams - One of the best experts on this subject based on the ideXlab platform.
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differential contributions to the transcriptome of Duplicated Genes in response to abiotic stresses in natural and synthetic polyploids
New Phytologist, 2011Co-Authors: Shaowei Dong, Keith L AdamsAbstract:Summary •Polyploidy has occurred throughout plant evolution and can result in considerable changes to Gene expression when it takes place and over evolutionary time. Little is known about the effects of abiotic stress conditions on Duplicate Gene expression patterns in polyploid plants. •We examined the expression patterns of 60 Duplicated Genes in leaves, roots and cotyledons of allotetraploid Gossypium hirsutum in response to five abiotic stress treatments (heat, cold, drought, high salt and water submersion) using single-strand conformation polymorphism assays, and 20 Genes in a synthetic allotetraploid. •Over 70% of the Genes showed stress-induced changes in the relative expression levels of the Duplicates under one or more stress treatments with frequent variability among treatments. Twelve pairs showed opposite changes in expression levels in response to different abiotic stress treatments. Stress-induced expression changes occurred in the synthetic allopolyploid, but there was little correspondence in patterns between the natural and synthetic polyploids. •Our results indicate that abiotic stress conditions can have considerable effects on Duplicate Gene expression in a polyploid, with the effects varying by Gene, stress and organ type. Differential expression in response to environmental stresses may be a factor in the preservation of some Duplicated Genes in polyploids.
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expression partitioning between Genes Duplicated by polyploidy under abiotic stress and during organ development
Current Biology, 2007Co-Authors: Zhenlan Liu, Keith L AdamsAbstract:Allopolyploidy has been a prominent mode of speciation and a recurrent process during plant evolution and has contributed greatly to the large number of Duplicated Genes in plant genomes [1-4]. Polyploidy often leads to changes in genome organization and Gene expression [5-9]. The expression of Genes that are Duplicated by polyploidy (termed homeologs) can be partitioned between the Duplicates so that one copy is expressed and functions only in some organs and the other copy is expressed only in other organs, indicative of subfunctionalization [10]. To determine how homeologous-Gene expression patterns change during organ development and in response to abiotic stress conditions, we have examined expression of the alcohol dehydrogenase Gene AdhA in allopolyploid cotton (Gossypium hirsutum). Expression ratios of the two homeologs vary considerably during the development of organs from seedlings and fruits. Abiotic stress treatments, including cold, dark, and water submersion, altered homeologous-Gene expression. Most notably, only one copy is expressed in hypocotyls during a water-submersion treatment, and only the other copy is expressed during cold stress. These results imply that subfunctionalization of Genes Duplicated by polyploidy has occurred in response to abiotic stress conditions. Partitioning of Duplicate Gene expression in response to environmental stress may lead to Duplicate Gene retention during subsequent evolution.
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evolution of Duplicate Gene expression in polyploid and hybrid plants
Journal of Heredity, 2007Co-Authors: Keith L AdamsAbstract:Allopolyploidy is a prominent mode of speciation in flowering plants. On allopolyploidy, genomic changes can take place, including chromosomal rearrangement and changes in Gene expression; these processes continue over evolutionary time. Recent studies of Gene expression in polyploid and hybrid plants, reviewed here, have examined expression in natural polyploids and synthetic neopolyploids as well as in diploid and F(1) hybrids. Considerable changes in Gene expression have been observed in allopolyploids, including up- or downregulation of expression in the polyploids compared with their parents, unequal expression of Duplicated Genes, and silencing of one copy. Genes in a variety of functional categories show altered expression, and the patterns vary considerably by Gene. Some changes seem to be stochastic, whereas others are repeatable. Gene expression changes can be organ specific. Reciprocal silencing of Duplicates in different organs has been observed, suggesting subfunctionalization and long-term retention of Duplicates. It has become clear that hybridization has a much greater effect than chromosome doubling on Gene expression in allopolyploids. Diploid and triploid F(1) hybrids can show alterations of expression levels compared with their parents. Parent-of-origin effects on Gene expression have been examined, and loss of Gene imprinting has been shown. Some Gene expression changes in polyploids and hybrids can be correlated with phenotypic effects. Demonstrated mechanisms of Gene expression changes include DNA methylation, histone modifications, and antisense RNA. Several hypotheses have been proposed for why Gene expression is altered in allopolyploids and hybrids.
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novel patterns of Gene expression in polyploid plants
Trends in Genetics, 2005Co-Authors: Keith L Adams, Jonathan F WendelAbstract:Genome doubling, or polyploidy, is a major factor accounting for Duplicate Genes found in most eukaryotic genomes. Polyploidy has considerable effects on Duplicate Gene expression, including silencing and up- or downregulation of one of the Duplicated Genes. These changes can arise with the onset of polyploidization or within several Generations after polyploid formation and they can have epiGenetic causal factors. Many expression alterations are organ-specific. Specific Genes can be independently and repeatedly silenced during polyploidization, whereas patterns for other Genes appear to be more stochastic. Three recent reports have provided intriguing new insights into the patterns, timing and mechanisms of Gene expression changes that accompany polyploidy in plants.
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Genes Duplicated by polyploidy show unequal contributions to the transcriptome and organ specific reciprocal silencing
Proceedings of the National Academy of Sciences of the United States of America, 2003Co-Authors: Keith L Adams, Richard Cronn, Ryan Percifield, Jonathan F WendelAbstract:Most eukaryotes have genomes that exhibit high levels of Gene redundancy, much of which seems to have arisen from one or more cycles of genome doubling. Polyploidy has been particularly prominent during flowering plant evolution, yielding Duplicated Genes (homoeologs) whose expression may be retained or lost either as an immediate consequence of polyploidization or on an evolutionary timescale. Expression of 40 homoeologous Gene pairs was assayed by cDNA-single-stranded conformation polymorphism in natural (1- to 2-million-yr-old) and synthetic tetraploid cotton (Gossypium) to determine whether homoeologous Gene pairs are expressed at equal levels after polyploid formation. Silencing or unequal expression of one homoeolog was documented for 10 of 40 Genes examined in ovules of Gossypium hirsutum. Assays of homoeolog expression in 10 organs revealed variable expression levels and silencing, depending on the Gene and organ examined. Remarkably, silencing and biased expression of some Gene pairs are reciprocal and developmentally regulated, with one homoeolog showing silencing in some organs and the other being silenced in other organs, suggesting rapid subfunctionalization. Duplicate Gene expression was examined in additional natural polyploids to characterize the pace at which expression alteration evolves. Analysis of a synthetic tetraploid revealed homoeolog expression and silencing patterns that sometimes mirrored those of the natural tetraploid. Both long-term and immediate responses to polyploidization were implicated. Data suggest that some silencing events are epiGenetically induced during the allopolyploidization process.
Jonathan F Wendel - One of the best experts on this subject based on the ideXlab platform.
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Gene body cg methylation and divergent expression of Duplicate Genes in rice
Scientific Reports, 2017Co-Authors: Jonathan F Wendel, Xutong Wang, Zhibin Zhang, Lei Gong, Bao LiuAbstract:Gene and genome duplication fosters Genetic novelty, but redundant Gene copies would undergo mutational decay unless preserved via selective or neutral forces. Molecular mechanisms mediating Duplicate preservation remain incompletely understood. Several recent studies showed an association between DNA methylation and expression divergence of Duplicated Genes and suggested a role of epiGenetic mechanism in Duplicate retention. Here, we compare genome-wide Gene-body CG methylation (BCGM) and Duplicate Gene expression between a rice mutant null for OsMet1-2(a major CG methytransferase in rice) and its isogenic wild-type. We demonstrate a causal link between BCGM divergence and expression difference of Duplicate copies. Interestingly, the higher- and lower-expressing copies of Duplicates as separate groups show broadly different responses with respect to direction of expression alteration upon loss of BCGM. A role for BCGM in conditioning expression divergence between copies of Duplicates Generally holds for Duplicates Generated by whole genome duplication (WGD) or by small-scale duplication processes. However, differences are evident among these categories, including a higher proportion of WGD Duplicates manifesting expression alteration, and differential propensities to lose BCGM by the higher- and lower-expression copies in the mutant. Together, our results support the notion that differential epiGenetic marking may facilitate long-term retention of Duplicate Genes.
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evolutionary rate variation genomic dominance and Duplicate Gene expression evolution during allotetraploid cotton speciation
New Phytologist, 2010Co-Authors: Lex E Flagel, Jonathan F WendelAbstract:Here, we describe the evolution of Gene expression among a diversified cohort of five allopolyploid species in the cotton genus (Gossypium). Using this phyloGenetic framework and comparisons with expression changes accompanying F(1) hybridization, we provide a temporal perspective on expression diversification following a shared genome duplication. Global patterns of Gene expression were studied by the hybridization of petal RNAs to a custom microarray. This platform measures total expression for c. 42 000 Duplicated Genes, and genome-specific expression for c. 1400 homoeologs (Genes Duplicated by polyploidy). We report homoeolog expression bias favoring the allopolyploid D genome over the A genome in all species (among five polyploid species, D biases ranging from c. 54 to 60%), in addition to conservation of biases among Genes. Furthermore, we find surprising levels of transgressive up- and down-regulation in the allopolyploids, a diminution of the level of bias in genomic expression dominance but not in its magnitude, and high levels of rate variation among allotetraploid species. We illustrate how phyloGenetic and temporal components of expression evolution may be partitioned and revealed following allopolyploidy. Overall patterns of expression evolution are similar among the Gossypium allotetraploids, notwithstanding a high level of interspecific rate variation, but differ strikingly from the direction of genomic expression dominance patterns in the synthetic F(1) hybrid.
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Duplicate Gene expression in allopolyploid gossypium reveals two temporally distinct phases of expression evolution
BMC Biology, 2008Co-Authors: Lex E Flagel, Joshua A Udall, Dan Nettleton, Jonathan F WendelAbstract:Polyploidy has played a prominent role in shaping the genomic architecture of the angiosperms. Through allopolyploidization, several modern Gossypium (cotton) species contain two divergent, although largely redundant genomes. Owing to this redundancy, these genomes can play host to an array of evolutionary processes that act on Duplicate Genes. We compared homoeolog (Genes Duplicated by polyploidy) contributions to the transcriptome of a natural allopolyploid and a synthetic interspecific F1 hybrid, both derived from a merger between diploid species from the Gossypium A-genome and D-genome groups. Relative levels of A- and D-genome contributions to the petal transcriptome were determined for 1,383 Gene pairs. This comparison permitted partitioning of homoeolog expression biases into those arising from genomic merger and those resulting from polyploidy. Within allopolyploid Gossypium, approximately 24% of the Genes with biased (unequal contributions from the two homoeologous copies) expression patterns are inferred to have arisen as a consequence of genomic merger, indicating that a substantial fraction of homoeolog expression biases occur instantaneously with hybridization. The remaining 76% of biased homoeologs reflect long-term evolutionary forces, such as Duplicate Gene neofunctionalization and subfunctionalization. Finally, we observed a greater number of Genes biased toward the paternal D-genome and that expression biases have tended to increases during allopolyploid evolution. Our results indicate that allopolyploidization entails significant homoeolog expression modulation, both immediately as a consequence of genomic merger, and secondarily as a result of long-term evolutionary transformations in Duplicate Gene expression.
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novel patterns of Gene expression in polyploid plants
Trends in Genetics, 2005Co-Authors: Keith L Adams, Jonathan F WendelAbstract:Genome doubling, or polyploidy, is a major factor accounting for Duplicate Genes found in most eukaryotic genomes. Polyploidy has considerable effects on Duplicate Gene expression, including silencing and up- or downregulation of one of the Duplicated Genes. These changes can arise with the onset of polyploidization or within several Generations after polyploid formation and they can have epiGenetic causal factors. Many expression alterations are organ-specific. Specific Genes can be independently and repeatedly silenced during polyploidization, whereas patterns for other Genes appear to be more stochastic. Three recent reports have provided intriguing new insights into the patterns, timing and mechanisms of Gene expression changes that accompany polyploidy in plants.
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Genes Duplicated by polyploidy show unequal contributions to the transcriptome and organ specific reciprocal silencing
Proceedings of the National Academy of Sciences of the United States of America, 2003Co-Authors: Keith L Adams, Richard Cronn, Ryan Percifield, Jonathan F WendelAbstract:Most eukaryotes have genomes that exhibit high levels of Gene redundancy, much of which seems to have arisen from one or more cycles of genome doubling. Polyploidy has been particularly prominent during flowering plant evolution, yielding Duplicated Genes (homoeologs) whose expression may be retained or lost either as an immediate consequence of polyploidization or on an evolutionary timescale. Expression of 40 homoeologous Gene pairs was assayed by cDNA-single-stranded conformation polymorphism in natural (1- to 2-million-yr-old) and synthetic tetraploid cotton (Gossypium) to determine whether homoeologous Gene pairs are expressed at equal levels after polyploid formation. Silencing or unequal expression of one homoeolog was documented for 10 of 40 Genes examined in ovules of Gossypium hirsutum. Assays of homoeolog expression in 10 organs revealed variable expression levels and silencing, depending on the Gene and organ examined. Remarkably, silencing and biased expression of some Gene pairs are reciprocal and developmentally regulated, with one homoeolog showing silencing in some organs and the other being silenced in other organs, suggesting rapid subfunctionalization. Duplicate Gene expression was examined in additional natural polyploids to characterize the pace at which expression alteration evolves. Analysis of a synthetic tetraploid revealed homoeolog expression and silencing patterns that sometimes mirrored those of the natural tetraploid. Both long-term and immediate responses to polyploidization were implicated. Data suggest that some silencing events are epiGenetically induced during the allopolyploidization process.
Edward S Buckler - One of the best experts on this subject based on the ideXlab platform.
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tripsacum de novo transcriptome assemblies reveal parallel Gene evolution with maize after ancient polyploidy
The Plant Genome, 2018Co-Authors: Christine M Gault, Karl A Kremling, Edward S BucklerAbstract:Plant genomes reduce in size following a whole-genome duplication event, and one Gene in a Duplicate Gene pair can lose function in absence of selective pressure to maintain Duplicate Gene copies. Maize ( L.) and its sister genus, , share a genome duplication event that occurred 5 to 26 million years ago. Because few genomic resources for exist, it is unknown whether grasses and maize have maintained a similar set of Genes that have resisted decay into pseudoGenes. Here we present high-quality de novo transcriptome assemblies for two species: (L.) L. and Porter ex Vasey. Genes with experimental protein evidence in maize were good candidates for Genes resistant to pseudogenization in both Genera because pseudoGenes by definition do not produce protein. We tested whether 15,160 maize Genes with protein evidence are resisting Gene loss and whether their homologs are also resisting Gene loss. Protein-encoding maize transcripts and their homologs have higher guanine-cytosine (GC) content, higher Gene expression levels, and more conserved expression levels than putatively untranslated maize transcripts and their homologs. These results suggest that similar Genes may be decaying into pseudoGenes in both Genera after a shared ancient polyploidy event. The transcriptome assemblies provide a high-quality genomic resource that can provide insight into the evolution of maize, a highly valuable crop worldwide.
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tripsacum de novo transcriptome assemblies reveal parallel Gene evolution with maize after ancient polyploidy
bioRxiv, 2018Co-Authors: Christine M Gault, Karl A Kremling, Edward S BucklerAbstract:Plant genomes reduce in size following a whole genome duplication event, and one Gene in a Duplicate Gene pair can lose function in absence of selective pressure to maintain Duplicate Gene copies. Maize and its sister genus, Tripsacum , share a genome duplication event that occurred 5 to 26 million years ago. Because few genomic resources for Tripsacum exist, it is unknown whether Tripsacum grasses and maize have maintained a similar set of Genes under purifying selection. Here we present high quality de novo transcriptome assemblies for two species: Tripsacum dactyloides and Tripsacum floridanum . Genes with experimental protein evidence in maize were good candidates for Genes under purifying selection in both Genera because pseudoGenes by definition do not produce protein. We tested whether Genes with protein evidence are resisting Gene loss in maize and whether their homologs are also resisting Gene loss in Tripsacum . Protein-encoding maize transcripts and their Tripsacum homologs have higher GC content, higher Gene expression levels, and more conserved expression levels than putatively untranslated maize transcripts and their Tripsacum homologs. These results indicate that Gene loss is occurring in a similar fashion in both Genera after a shared ancient polyploidy event. The Tripsacum transcriptome assemblies provide a high quality genomic resource that can provide insight into the evolution of maize, an highly valuable crop worldwide.
Andreas Wagner - One of the best experts on this subject based on the ideXlab platform.
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increased Gene dosage plays a predominant role in the initial stages of evolution of Duplicate tem 1 beta lactamase Genes
Evolution, 2014Co-Authors: Andreas Wagner, Riddhiman Dhar, Tobias BergmillerAbstract:Gene duplication is important in evolution, because it provides new raw material for evolutionary adaptations. Several existing hypotheses about the causes of Duplicate retention and diversification differ in their emphasis on Gene dosage, subfunctionalization, and neofunctionalization. Little experimental data exist on the relative importance of Gene expression changes and changes in coding regions for the evolution of Duplicate Genes. Furthermore, we do not know how strongly the environment could affect this importance. To address these questions, we performed evolution experiments with the TEM-1 beta lactamase Gene in Escherichia coli to study the initial stages of Duplicate Gene evolution in the laboratory. We mimicked tandem duplication by inserting two copies of the TEM-1 Gene on the same plasmid. We then subjected these copies to repeated cycles of mutaGenesis and selection in various environments that contained antibiotics in different combinations and concentrations. Our experiments showed that Gene dosage is the most important factor in the initial stages of Duplicate Gene evolution, and overshadows the importance of point mutations in the coding region.
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Pervasive Indels and Their Evolutionary Dynamics after the Fish-Specific Genome Duplication
Molecular biology and evolution, 2012Co-Authors: Baocheng Guo, Ming Zou, Andreas WagnerAbstract:Insertions and deletions (indels) in protein-coding Genes are important sources of Genetic variation. Their role in creating new proteins may be especially important after Gene duplication. However, little is known about how indels affect the divergence of Duplicate Genes. We here study thousands of Duplicate Genes in five fish (teleost) species with completely sequenced genomes. The ancestor of these species has been subject to a fish-specific genome duplication (FSGD) event that occurred approximately 350 Ma. We find that Duplicate Genes contain at least 25% more indels than single-copy Genes. These indels accumulated preferentially in the first 40 my after the FSGD. A lack of widespread asymmetric indel accumulation indicates that both members of a Duplicate Gene pair typically experience relaxed selection. Strikingly, we observe a 30-80% excess of deletions over insertions that is consistent for indels of various lengths and across the five genomes. We also find that indels preferentially accumulate inside loop regions of protein secondary structure and in regions where amino acids are exposed to solvent. We show that Duplicate Genes with high indel density also show high DNA sequence divergence. Indel density, but not amino acid divergence, can explain a large proportion of the tertiary structure divergence between proteins encoded by Duplicate Genes. Our observations are consistent across all five fish species. Taken together, they suggest a General pattern of Duplicate Gene evolution in which indels are important driving forces of evolutionary change.
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asymmetric sequence divergence of Duplicate Genes
Genome Research, 2003Co-Authors: Gavin C Conant, Andreas WagnerAbstract:Much like humans, Gene Duplicates may be created equal, but they do not stay that way for long. For four completely sequenced genomes we show that 20%-30% of Duplicate Gene pairs show asymmetric evolution in the amino acid sequence of their protein products. That is, one of the Duplicates evolves much faster than the other. The greater this asymmetry, the greater the ratio Ka/Ks of amino acid substitutions (Ka) to silent substitutions (Ks) in a Gene pair. This indicates that most asymmetric divergence may be caused by relaxed selective constraints on one of the Duplicates. However, we also find some candidate Duplicates where positive (directional) selection of beneficial mutations (Ka/Ks > 1) may play a role in asymmetric divergence. Our analysis rests on a codon-based model of molecular evolution that allows a test for asymmetric divergence in Ka. The method is also more sensitive in detecting positive selection (Ka/Ks > 1) than models relying only on pairwise Gene comparisons.
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asymmetric functional divergence of Duplicate Genes in yeast
Molecular Biology and Evolution, 2002Co-Authors: Andreas WagnerAbstract:Most Duplicate Genes are eliminated from a genome shortly after duplication, but those that remain are an important source of biochemical diversity. Here, I present evidence from genome-scale protein-protein interaction data, microarray expression data, and large-scale Gene knockout data that this diversification is often asymmetrical: one Duplicate usually shows significantly more molecular or Genetic interactions than the other. I propose a model that can explain this divergence pattern if asymmetrically diverging Duplicate Gene pairs show increased robustness to deleterious mutations.
Jeremy E Coate - One of the best experts on this subject based on the ideXlab platform.
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Gene balance predicts transcriptional responses immediately following ploidy change in arabidopsis thaliana
The Plant Cell, 2020Co-Authors: Michael J Song, Jeff J Doyle, Barney Potter, Jeremy E CoateAbstract:The Gene balance hypothesis postulates that there is selection on Gene copy number (Gene dosage) to preserve the stoichiometric balance among interacting proteins. This presupposes that Gene product abundance is governed by Gene dosage and that Gene dosage responses are consistent for interacting Genes in a dosage-balance-sensitive network or complex. Gene dosage responses, however, have rarely been quantified, and the available data suggest that they are highly variable. We sequenced the transcriptomes of two synthetic autopolyploid accessions of Arabidopsis (Arabidopsis thaliana) and their diploid progenitors, as well as one natural tetraploid and its synthetic diploid produced via haploid induction, to estimate transcriptome size and dosage responses immediately following ploidy change. Similar to what has been observed in previous studies, overall transcriptome size does not exhibit a simple doubling in response to genome doubling, and individual Gene dosage responses are highly variable in all three accessions, indicating that expression is not strictly coupled with Gene dosage. Nonetheless, putatively dosage balance-sensitive Gene groups (Gene Ontology terms, metabolic networks, Gene families, and predicted interacting proteins) exhibit smaller and more coordinated dosage responses than do putatively dosage-insensitive Gene groups, suggesting that constraints on dosage balance operate immediately following whole-genome duplication and that Duplicate Gene retention patterns are shaped by selection to preserve dosage balance.
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Gene balance predicts transcriptional responses immediately following ploidy change in arabidopsis thaliana
bioRxiv, 2019Co-Authors: Barney Potter, Jeff J Doyle, Michael J Song, Jeremy E CoateAbstract:The Gene Balance Hypothesis postulates that there is selection on Gene copy number (Gene dosage) to preserve stoichiometric balance among interacting proteins. This presupposes that Gene product abundance is governed by Gene dosage, and that the way in which Gene product abundance is governed by Gene dosage is consistent for all Genes in a dosage-sensitive network or complex. Gene dosage responses, however, have rarely been quantified and the available data suggest that they are highly variable. We sequenced the transcriptomes of two synthetic autopolyploid accessions of Arabidopsis thaliana and their diploid progenitors, as well as one natural tetraploid and its synthetic diploid produced via haploid induction, to estimate transcriptome size and Gene dosage responses immediately following ploidy change. We demonstrate that overall transcriptome size does not exhibit a simple doubling in response to genome doubling, and that individual Gene dosage responses are highly variable in all three accessions, indicating that expression is not strictly coupled with Gene dosage. Nonetheless, putatively dosage-sensitive Gene groups (GO terms, metabolic networks, Gene families, and predicted interacting protein pairs) exhibit both smaller and more coordinated dosage responses than do putatively dosage-insensitive Gene groups, suggesting that constraints on dosage balance operate immediately following whole genome duplication. This supports the hypothesis that Duplicate Gene retention patterns are shaped by selection to preserve dosage balance.
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expression level support for Gene dosage sensitivity in three glycine subgenus glycine polyploids and their diploid progenitors
New Phytologist, 2016Co-Authors: Jeremy E Coate, Michael J Song, Aureliano Bombarely, Jeff J DoyleAbstract:Summary Retention or loss of paralogs following duplication correlates strongly with the function of the Gene and whether the Gene was Duplicated by whole-genome duplication (WGD) or by small-scale duplication. Selection on relative Gene dosage (to maintain proper stoichiometry among interacting proteins) has been invoked to explain these patterns of Duplicate Gene retention and loss. In order for Gene dosage to be visible to natural selection, there must necessarily be a correlation between Gene copy number and Gene expression level (transcript abundance), but this has rarely been examined. We used RNA-Seq data from seven Glycine subgenus Glycine species (three recently formed allotetraploids and their four diploid progenitors) to determine if expression patterns and Gene dosage responses at the level of transcription are consistent with selection on relative Gene dosage. As predicted, metabolic pathways and Gene ontologies that are putatively dosage-sensitive based on duplication history exhibited reduced expression variance across species, and more coordinated expression responses to recent WGD, relative to putatively dosage-insensitive networks. We conclude that selection on relative dosage has played an important role in shaping Gene networks in Glycine.
