Beringian birds
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA393740 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Gene-expression divergence between species shapes morphological evolution, but the molecular basis is largely unknown. Here we show cis- and trans-regulatory elements and chromatin modifications on gene-expression diversity in genetically tractable Arabidopsis allotetraploids. In Arabidopsis thaliana and Arabidopsis arenosa, both cis and trans with predominant cis-regulatory effects mediate gene-expression divergence. The majority of genes with both cis- and trans-effects are subjected to compensating interactions and stabilizing selection. Interestingly, chromatin modifications correlate with cis - and trans -regulation. In F1 allotetraploids, Arabidopsis arenosa trans factors predominately affect allelic expression divergence. Arabidopsis arenosa trans factors tend to upregulate Arabidopsis thaliana alleles, whereas Arabidopsis thaliana trans factors up- or down-regulate Arabidopsis arenosa alleles. In resynthesized and natural allotetraploids, trans effects drive expression of both homoeologous loci into the same direction. We provide evidence for natural selection and chromatin regulation in shaping gene-expression diversity during plant evolution and speciation. Examination of gene expression in 5 tetraploid Arabidopsis using mRNA-seq
2012-05-31 | E-GEOD-29687 | biostudies-arrayexpress
Project description:Gene-expression divergence between species shapes morphological evolution, but the molecular basis is largely unknown. Here we show cis- and trans-regulatory elements and chromatin modifications on gene-expression diversity in genetically tractable Arabidopsis allotetraploids. In Arabidopsis thaliana and Arabidopsis arenosa, both cis and trans with predominant cis-regulatory effects mediate gene-expression divergence. The majority of genes with both cis- and trans-effects are subjected to compensating interactions and stabilizing selection. Interestingly, chromatin modifications correlate with cis - and trans -regulation. In F1 allotetraploids, Arabidopsis arenosa trans factors predominately affect allelic expression divergence. Arabidopsis arenosa trans factors tend to upregulate Arabidopsis thaliana alleles, whereas Arabidopsis thaliana trans factors up- or down-regulate Arabidopsis arenosa alleles. In resynthesized and natural allotetraploids, trans effects drive expression of both homoeologous loci into the same direction. We provide evidence for natural selection and chromatin regulation in shaping gene-expression diversity during plant evolution and speciation.
2012-05-31 | GSE29687 | GEO
Project description:Genomes of closely-related species or populations often display localized regions of enhanced relative sequence divergence, termed genomic islands. It has been proposed that these islands arise through selective sweeps and/or barriers to gene flow. Here, we genetically dissect a genomic island that controls flower color pattern differences between two subspecies of Antirrhinum, A.m.striatum and A.m.pseudomajus, and relate it to clinal variation across a natural hybrid zone. We show that selective sweeps likely raised relative divergence at two tightly-linked MYB-like transcription factors, leading to distinct flower patterns in the two subspecies. The two patterns provide alternate floral guides and create a strong barrier to gene flow where populations come into contact. This barrier affects the selected flower color genes and tightly linked loci, but does not extend outside of this domain, allowing gene flow to lower relative divergence for the rest of the chromosome. Thus, both selective sweeps and barriers to gene flow play a role in shaping genomic islands: sweeps cause elevation in relative divergence while heterogeneous gene flow flattens the surrounding “sea”, making the island of divergence stand out. By showing how selective sweeps establish alternative adaptive phenotypes that lead to barriers to gene flow, our study sheds light on possible mechanisms leading to reproductive isolation and speciation.
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Project description:Using comparative genomics, we discovered that a previously uncharacterized gene (1700011H14RIK/C14ORF105/CCDC198) hereby named FAME (Factor Associated with Metabolism and Energy) shows an unusually high rate of evolutionary divergence in birds and mammals. By comparing SNVs, we identified gene-flow of FAME from Neandertals into modern humans. FAME knockout animals demonstrated increased body weight and decreased energy expenditure, corresponding to GWAS linking FAME with higher BMI, diabetes-related pathologies, and macular degeneration in humans. The analysis of gene expression and subcellular localization revealed that FAME is a membrane-bound protein enriched in kidneys. Although a gene knockout resulted in structurally normal kidneys, we detected higher Albumin in urine and lowered ferritin in the blood. The experiment confirmed interactions between FAME and ferritin and showed co-localization in vesicular and plasma membranes. Overall, our results show that FAME plays a role in tuning metabolite excretion and energy expenditure, partly explaining why it evolves at a high rate in birds and mammals. Here, we provide data related to identification of FAME interactome using the co-immunoprecipitation method.
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