The footprint of polygenic adaptation on stress-responsive cis-regulatory divergence in the Arabidopsis genus
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA318999 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR3405430_1.fastq.gz | Fastqsanger.gz | |||
| SRR3405430_2.fastq.gz | Fastqsanger.gz | |||
| SRR3405440_1.fastq.gz | Fastqsanger.gz | |||
| SRR3405440_2.fastq.gz | Fastqsanger.gz | |||
| SRR3405431_1.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 36 |
Similar Datasets
Project description:We generated F1 hybrids of each of the sister species A. halleri and A. lyrata with their outgroup relative of A. thaliana and monitored allele-specific levels of expression in standard growth conditions, in response to dehydration or cold exposure. This data allowed us to map the genome-wide distribution of cis-regulatory mutations active in three distinct environments reflecting divergent adaptations of the two species. Because the sister species were both crossed to an outgroup species, it was possible to assign a phylogenetic origin to cis-acting mutations. Cis-acting mutations observed in only one of the two hybrids were likely to be derived, whereas those observed in both hybrids either predate predated the split between the two species or arose along the A. thaliana lineage. By contrasting the distribution of cis-regulatory mutations derived in the A. halleri to those derived on the A. lyrata lineage, we could establish relative rates of cis-acting evolution across polygenic molecular functions and detect lineage-specific polygenic adaptation to environmental challenges. A.thalianaxA.lyrata under cold, dehydration and standard conditions, 3 biological replicates; A.thalianaxA.halleri under cold, dehydration and standard conditions, 3 biological replicates; toal 18 RNA-seq samples
2016-06-01 | E-GEOD-80462 | biostudies-arrayexpress
Project description:We generated F1 hybrids of each of the sister species A. halleri and A. lyrata with their outgroup relative of A. thaliana and monitored allele-specific levels of expression in standard growth conditions, in response to dehydration or cold exposure. This data allowed us to map the genome-wide distribution of cis-regulatory mutations active in three distinct environments reflecting divergent adaptations of the two species. Because the sister species were both crossed to an outgroup species, it was possible to assign a phylogenetic origin to cis-acting mutations. Cis-acting mutations observed in only one of the two hybrids were likely to be derived, whereas those observed in both hybrids either predate predated the split between the two species or arose along the A. thaliana lineage. By contrasting the distribution of cis-regulatory mutations derived in the A. halleri to those derived on the A. lyrata lineage, we could establish relative rates of cis-acting evolution across polygenic molecular functions and detect lineage-specific polygenic adaptation to environmental challenges.
2016-06-01 | GSE80462 | GEO
Project description:Abstract Efforts to unravel the genomic basis of incipient speciation are hampered by a mismatch between our toolkit and our understanding of the ecology and genetics of adaptation. While the former is focused on detecting selective sweeps involving few independently acting or linked speciation genes, the latter states that divergence typically occurs in polygenic traits under stabilizing selection. Here, we ask whether a role of stabilizing selection on polygenic traits in population divergence may be unveiled by using a phenotypically informed integrative approach, based on genome‐wide variation segregating in divergent populations. We compare three divergent populations of seed beetles (Callosobruchus maculatus) where previous work has demonstrated a prominent role for stabilizing selection on, and population divergence in, key life history traits that reflect rate‐dependent metabolic processes. We derive and assess predictions regarding the expected pattern of covariation between genetic variation segregating within populations and genetic differentiation between populations. Population differentiation was considerable (mean FST = 0.23–0.26) and was primarily built by genes showing high selective constraints and an imbalance in inferred selection in different populations (positive Tajima's DNS in one and negative in one), and this set of genes was enriched with genes with a metabolic function. Repeatability of relative population differentiation was low at the level of individual genes but higher at the level of broad functional classes, again spotlighting metabolic genes. Absolute differentiation (dXY) showed a very different general pattern at this scale of divergence, more consistent with an important role for genetic drift. Although our exploration is consistent with stabilizing selection on polygenic metabolic phenotypes as an important engine of genome‐wide relative population divergence and incipient speciation in our study system, we note that it is exceedingly difficult to firmly exclude other scenarios. We ask whether a role of stabilizing selection on polygenic traits in population divergence can be unveiled by using a phenotypically informed integrative approach, testing predictions regarding the expected pattern of covariation between genetic variation segregating within populations and genetic differentiation between populations. Differentiation was primarily built by genes showing high selective constraints and an imbalance in inferred selection in different populations and this set of genes was enriched with genes with a metabolic function. Overall, our results are consistent with stabilizing selection on polygenic metabolic phenotypes being an engine of genome‐wide relative population divergence and incipient speciation.
| S-EPMC9608792 | biostudies-literature
Project description:Detecting Cd adaptation footprint in C. riparius with a multi-genomic approach
| PRJEB48137 | ENA
Project description:Gene expression in adipose and other tissues of polygenic Fat and Lean mice.<br>
2011-11-04 | E-MEXP-3091 | biostudies-arrayexpress
Project description:Both cis- and trans-acting changes could accumulate and participate in complex interactions, so to isolate the cis-regulatory component of patterning evolution, we measured allele-specific spatial gene expression patterns in Drosophila melanogaster × D. simulans hybrid embryos. RNA-seq of cryosectioned slices revealed 55 genes with strong spatially-varying allele-specific expression, and several hundred more with weaker but significant spatial divergence. Combined with mathematical modeling and regulatory locus editing, we determine the SNP responsible for the allele-specific expression observed in the gene hunchback.
2017-08-04 | GSE102233 | GEO
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:The footprint of polygenic adaptation on stress-responsive cis-regulatory divergence in the Arabidopsis genus
| PRJNA472444 | ENA
Project description:The trans-10, cis-12-isomer of conjugated linoleic acid (CLA) causes a rapid reduction of body and adipose mass in mice by decreasing adipocyte size and number. In addition to changes in adipose tissue, numerous studies have reported alterations in hepatic lipid metabolism. Livers of CLA fed mice gain mass due to lipid accumulation; however, the precise molecular mechanisms are unknown. To elucidate these mechanisms, we examined fatty acid composition and gene expression profiles of livers from a polygenic obese line of mice fed 1% trans-10, cis-12 CLA. Following examination of the fatty acid profile it was concluded that stearoyl CoA desaturase (SCD) activity was unaffected by CLA. Analysis of gene expression data led to the identification of 1393 genes differentially expressed in the liver of CLA fed mice at a nominal P-value of 0.01 and 775 were considered significant using a false discovery rate threshold of 0.05. Following Bonferroni correction and excluding lowly expressed transcripts, 198 genes were identified as being differentially expressed with 17 genes having ⥠2-fold change. Pathway analysis of the 775 genes considered significant using FDR found that 38 of these genes are controlled by Hepatocyte Nuclear Factor 4α, a transcription factor thought to be important in controlling liver metabolic status. The list of significant differentially expressed genes found in the liver of mice fed CLA vs. LA is linked below as a supplementary file. Experiment Overall Design: Functional genomic analysis of liver tissue extracted from polygenic obese male mice fed either a control (1% linoleic acid) or treatment (1% trans 10, cis 12 conjugated linoleic acid) diet after fourteen days. Four or five mice were pooled for each labeling. There is 1 replicate for each experiment, for a total of 4 microarrays.
2009-03-07 | E-GEOD-10865 | biostudies-arrayexpress
Project description:Here we derive human and chimpanzee cranial neural crest cells (CNCCs) and profile histone modifications, transcription factors, chromatin accessibility and gene expression to systematically and quantitatively annotate evolutionary divergence of craniofacial cis-regulatory landscapes.
2015-09-11 | GSE70751 | GEO