Browsing by Subject "Whole genome duplication"
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Item Mechanisms of gene expression evolution in polyploids(2008-12) Ha, Misook; Chen, Z. JeffreyPolyploidy, or whole genome duplication (WGD), is a fundamental evolutionary mechanism for diverse organisms including many plants and some animals. Duplicate genes from WGD are a major source of expression and functional diversity. However, the biological and evolutionary mechanisms for gene expression changes within and between species following WGD are poorly understood. Using genome-wide gene expression microarrays and high-throughput sequencing technology, I studied the genetic and evolutionary mechanisms for gene expression changes in synthetic and natural allopolyploids that are derived from hybridization between closely related species. To investigate evolutionary fate of duplicate genes, I tested how duplicate genes respond to developmental and environmental changes within species and how ancient duplicate genes contribute to gene expression diversity in resynthesized allopolyploids. We found that expression divergence between gene duplicates was significantly higher in response to environmental stress than to developmental process. Furthermore, duplicate genes related to external stresses showed higher expression divergence between two closely related species and in resynthesized and natural allotetraploids than single-copy genes. A slow rate of expression divergence of duplicate genes during development may offer dosage-dependent selective advantage, whereas a high rate of expression divergence between gene duplicates in response to external changes may enhance adaptation. To investigate molecular mechanisms of expression diversity among allopolyploids, I analyzed high-throughput sequencing data of small RNAs in allopolyploids and their progenitors. Small interfering RNAs (siRNAs) induce epigenetic modification and gene silencing of repeats, while microRNAs (miRNAs) and trans-acting siRNAs (ta-siRNAs) induce expression modulation of protein coding genes. Our data showed that siRNA populations in progenitors were highly maintained in allopolyploids, and alteration of miRNA abundance in allopolyploids was significantly correlated with expression changes of miRNA target genes. These results suggest that stable inheritance of parental siRNAs in allopolyploids helps maintain genome stability in response to genome duplication, whereas expression diversity of miRNAs leads to interspecies variation in gene expression, growth, and development. Results from these research objectives show that genome-wide analysis of high throughput gene expression and small RNAs provides new insights into molecular and evolutionary mechanisms for gene expression diversity and phenotypic variation between closely related species and in the new allopolyploids.Item Search for selection pressures associated with aggregation propensity following whole genome duplication in S.cerevisiae.(2011-12) Wittig, Michael David; Press, William H.; Marcotte, Edward M.It has been theorized that most proteins are under selection pressure to be soluble in crowded cellular spaces. To maintain solubility a proteins’ aggregation propensity should be inversely proportional to their maximum likely concentration. This theory was examined by comparing the proteome of the model organism S. cerevisiae, which has previously undergone a Whole Genome Duplication (WGD) event to the proteome of the closely related yeast K. waltii, which has not undergone WGD. This comparison revealed the following: 1) Predicted aggregation propensities are higher in S. cerevisiae than K. waltii. 2) Aggregation propensity does not predict which genes reverted to a single copy after WGD. 3) In genes which were retained as duplicates in S. cerevisiae after WGD, aggregation propensities rose from the inferred common ancestral protein. 4) Genes retained as duplicates showed less of an increase relative to their homologues in K. waltii than genes which were not retained as duplicates. 5) The relationship between the log predicted aggregation propensity and log mRNA expression level or log protein abundance was not linear as previously predicted. These results suggest that while there is broad selection pressure for reduced aggregation pressure for genes which have been duplicated, the precise relationship between aggregation propensity and gene expression is more complicated than previously predicted. These results also allow speculation that the whole genome duplication in S.cerevisiae may have been made possible by a general relaxation of aggregation-related selection pressure.