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Duplicate genes increase expression diversity in closely related species and allopolyploids

ABSTRACT: Duplicate genes increase expression diversity in closely related species and allopolyploids

OTHER RELATED OMICS DATASETS IN: GSE9513GSE13468

PROVIDER: PRJNA103311 | ENA |

REPOSITORIES: ENA

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Duplicate genes increase expression diversity in closely related species and allopolyploids

Project description:Polyploidy or whole genome duplication (WGD) provides raw genetic materials for sequence and expression evolution of duplicate genes. However, the mode and tempo of expression divergence between WGD duplicate genes in closely relates species and recurrent allopolyploids are poorly understood. Arabidopsis is a suitable system for testing the hypothesis that duplicate genes increase expression diversity and regulatory networks. In Arabidopsis, WGD occurred more than once prior to the split between Arabidopsis thaliana and Arabidopsis arenosa, and both natural and human-made allotetraploids are available. Comparative genomic hybridization analysis indicated that single-copy and duplicate genes after WGD were well preserved in A. thaliana and A. arenosa. Analysis of gene expression microarrays showed that duplicate genes generally had higher levels of expression divergence between two closely related species than single-copy genes. The proportion of the progenitors' duplicate genes that were nonadditively expressed in the resynthesized and natural allotetraploids was significantly higher than that of single-copy genes. Duplicate genes related to environmental stresses tended to be differentially expressed, and multi-copy duplicate genes were likely to diverge expression between progenitors and in the allotetraploids. Compared to single-copy genes, duplicate genes tend to contain TATA boxes and less DNA methylation in the promoter regions, facilitating transcriptional regulation by binding transcription factors and/or cis-and trans- acting proteins. The data suggest an important role of WGD duplicate genes in modulating diverse and novel gene expression changes in response to external environmental cues as well as internal genetic turmoil such as recurrent polyploidy events.

2008-11-20 | GSE9513 | GEO

Thermal adaptation in closely related virbios

Project description:Thermal adaptation in closely related virbios

| PRJNA325804 | ENA

Using high-density exon arrays to profile gene expression in closely related species

Project description:This SuperSeries is composed of the following subset Series: GSE15626: Using high-density exon arrays to profile gene expression in closely related species (Exon 1.0 ST) GSE15665: Using high-density exon arrays to profile gene expression in closely related species (HJAY) Refer to individual Series

2009-05-04 | E-GEOD-15666 | biostudies-arrayexpress

Duplicate genes increase expression diversity in closely related species and allopolyploids.

Project description: Not available

| S-EPMC2650150 | biostudies-literature

Binding site turnover produces pervasive quantitative changes in TF binding between closely related Drosophila species

Project description:[original title] Binding site turnover produces pervasive quantitative changes in transcription factor binding between closely related Drosophila species. We demonstrate extensive quantitative changes in binding of six factors that control early embryonic patterning between two closely related Drosophila species

2010-02-18 | GSE20369 | GEO

Binding site turnover produces pervasive quantitative changes in TF binding between closely related Drosophila species

2010-02-18 | E-GEOD-20369 | biostudies-arrayexpress

Using high-density exon arrays to profile gene expression in closely related species

Project description:Using high-density exon arrays to profile gene expression in closely related species

| PRJNA115613 | ENA

Using high-density exon arrays to profile gene expression in closely related species (HJAY)

Project description:Global comparisons of gene expression profiles between species provide significant insight into gene regulation, evolutionary processes, and disease mechanisms. In this work, we describe a flexible and intuitive approach for global expression profiling of closely related species, using high-density exon arrays designed for a single reference genome. The high-density probe coverage of exon arrays allows us to select the identical set of perfect-match probes for measuring expression levels of orthologous genes. This eliminates a serious confounding factor in probe affinity effects of species-specific microarray probes, and enables direct comparisons of estimated expression indexes across species. Keywords: analysis of gene expression in tissues We conducted Affymetrix Human Exon Junction array (HJAY array) profiling of RNAs from human, chimpanzee and rhesus macaque cerebellums, with three replicates per species.

2010-05-19 | E-GEOD-15665 | biostudies-arrayexpress

Using high-density exon arrays to profile gene expression in closely related species (HJAY)

2009-05-05 | GSE15665 | GEO

Thermal adaptation in closely related virbios

Project description:Here, we investigate the genetic mechanisms that underlie thermal specialization of closely-related vibrios isolated from coastal water at the Beaufort Inlet (Beaufort, NC, USA). This location experiences large seasonal temperature fluctuations (annual range of ~20°C), and a clear seasonal shift in vibrio diversity has been observed (Yung et al. 2015). This previous study suggested that the mechanisms of thermal adaptation apparently differ based on evolutionary timescale: shifts in the temperature of maximal growth occur between deeply branching clades but the shape of the thermal performance curve changes on shorter time scales (Yung et al. 2015). The observed thermal specialization in vibrio populations over relatively short evolutionary time scales indicates that few genes or cellular processes may contribute to the differences in thermal performance between populations. In order to understand the molecular mechanisms that underlie adaptation to local thermal regimes in environmental vibrio populations, we employ genomic and transcriptomic approaches to examine transcriptomic changes that occur within strains grown at their thermal optima and under heat and cold stress. Moreover, we compare two closely-related strains with different laboratory thermal preferences to identify in situ evolutionary responses to different thermal environments in genome content and alleles as well as gene expression.

2018-07-31 | GSE83396 | GEO

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