Ontology highlight
ABSTRACT:
PROVIDER: PRJNA659559 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR12526226_1.fastq.gz | Fastqsanger.gz | |||
| SRR12526226_2.fastq.gz | Fastqsanger.gz | |||
| SRR12526227_1.fastq.gz | Fastqsanger.gz | |||
| SRR12526227_2.fastq.gz | Fastqsanger.gz | |||
| SRR12526228_1.fastq.gz | Fastqsanger.gz |
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Project description:We used microarrays and a previously established linkage map to localize the genetic determinants of brain gene expression for a backcross family of lake whitefish species pairs (Coregonus sp.). Our goals were to elucidate the genomic distribution and sex-specificity of brain expression QTL (eQTL) and to determine the extent to which genes controlling transcriptional variation may underlie adaptive divergence in the recently evolved dwarf (limnetic) and normal (benthic) whitefish. We observed a sex-bias in transcriptional genetic architecture, with more eQTL observed in males, as well as divergence in genome location of eQTL between sexes. Hotspots of nonrandom aggregations of up to 32 eQTL in one location were observed. We identified candidate genes for species pair divergence involved with energetic metabolism, protein synthesis, and neural development based on co-localization of eQTL for these genes with eight previously identified adaptive phenotypic QTL and four previously identified outlier loci from a genome scan in natural populations. 88% of eQTL-phenotypic QTL co-localization involved growth rate and condition factor QTL, two traits central to adaptive divergence between whitefish species pairs. Hotspots co-localized with phenotypic QTL in several cases, revealing possible locations where master regulatory genes, such as a zinc finger protein in one case, control gene expression directly related to adaptive phenotypic divergence. We observed little evidence of co-localization of brain eQTL with behavioral QTL, which provides insight on the genes identified by behavioral QTL studies. These results extend to the transcriptome level previous work illustrating that selection has shaped recent parallel divergence between dwarf and normal lake whitefish species pairs and that metabolic, more than morphological differences appear to play a key role in this divergence. Keywords: eQTL mapping, gene expression, linkage mapping, adaptive radiation, Coregonus, microarrays
2008-09-01 | GSE12068 | GEO
Project description:Whole-genome methylomes and total transcriptomes for muscle and liver tissues of Lake Malawi cichlid species characterised in the context of phenotypic diversification.
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Project description:We used microarrays and a previously established linkage map to localize the genetic determinants of brain gene expression for a backcross family of lake whitefish species pairs (Coregonus sp.). Our goals were to elucidate the genomic distribution and sex-specificity of brain expression QTL (eQTL) and to determine the extent to which genes controlling transcriptional variation may underlie adaptive divergence in the recently evolved dwarf (limnetic) and normal (benthic) whitefish. We observed a sex-bias in transcriptional genetic architecture, with more eQTL observed in males, as well as divergence in genome location of eQTL between sexes. Hotspots of nonrandom aggregations of up to 32 eQTL in one location were observed. We identified candidate genes for species pair divergence involved with energetic metabolism, protein synthesis, and neural development based on co-localization of eQTL for these genes with eight previously identified adaptive phenotypic QTL and four previously identified outlier loci from a genome scan in natural populations. 88% of eQTL-phenotypic QTL co-localization involved growth rate and condition factor QTL, two traits central to adaptive divergence between whitefish species pairs. Hotspots co-localized with phenotypic QTL in several cases, revealing possible locations where master regulatory genes, such as a zinc finger protein in one case, control gene expression directly related to adaptive phenotypic divergence. We observed little evidence of co-localization of brain eQTL with behavioral QTL, which provides insight on the genes identified by behavioral QTL studies. These results extend to the transcriptome level previous work illustrating that selection has shaped recent parallel divergence between dwarf and normal lake whitefish species pairs and that metabolic, more than morphological differences appear to play a key role in this divergence. Keywords: eQTL mapping, gene expression, linkage mapping, adaptive radiation, Coregonus, microarrays The objective of this study was to elucidate the genomic distribution and sex-specificity of brain eQTL in dwarf and normal lake whitefish. Dissected brain tissue (250-350 mg) was sampled for 55 individuals from a hybrid x dwarf backcross mapping family. We used a loop design (YANG and SPEED 2002; CHURCHILL 2002) to maximize the number of sampled meioses. Each of 55 samples was technically replicated on two distinct slides, while performing dye swapping (Cy3 and Alexa) to estimate the dye intensity variation bias. After correcting for local background, raw intensity values were both log2 transformed and normalized using the regional LOWESS method implemented in the R/MANOVA software (KERR et al. 2000). We used a previously generated linkage map based on the same backcross individuals for which gene expression was measured. eQTL mapping was performed with QTL Cartographer.
2008-09-01 | E-GEOD-12068 | biostudies-arrayexpress
Project description:This dataset was gene expression from natural sockeye salmon populations used to test the preservation of coexpression networks that were found in lake whitefish. Here is the abstract of the manuscript:BackgroundM-BM- : A functional understanding of processes involved in adaptive divergence is one of the awaiting opportunities afforded by high throughput transcriptomic technologies. Functional analysis of co-expressed genes has succeeded in the biomedical field in identifying key drivers of disease pathways. However, in ecology and evolutionary biology, functional interpretation of transcriptomic data is still limited. ResultsM-BM- : Here we used Weighted Gene Co-Expression Network Analysis (WGCNA) to identify modules of co-expressed genes in muscle and brain tissue of a lake whitefish backcross progeny. Modules were connected to gradients of known adaptive traits involved in the ecological speciation process between benthic and limnetic ecotypes. Key drivers, i.e. hub genes of functional modules related to reproduction, growth, and behavior were identified, and module preservation was assessed in natural populations. Using this approach, we identified modules of co-expressed genes involved in phenotypic divergence and their key drivers, and further characterized the underlying regulatory structure governing these complex traits. ConclusionsM-BM- : Functional analysis of transcriptomic data can significantly contribute to the understanding of the mechanisms underlying ecological speciation. Our findings point to BMP and Calcium signaling as common pathways involved in coordinated evolution of trophic behavior, trophic morphology (gill rakers), and reproduction. Results also point to housekeeping pathways implicating hemoglobins and constitutive stress response (HSP70) governing growth in lake whitefish. Here are 49 female sockeye salmon transcriptomes as measured by the 16k cGRASP microarray.
2013-02-01 | E-GEOD-42985 | biostudies-arrayexpress
Project description:Epigenetic variation has the potential to control environmentally dependent development and contribute to phenotypic responses to local environments. Environmental epigenetic studies of sexual organisms confirm the responsiveness of epigenetic variation, which should be even more important when genetic variation is lacking. A previous study of an asexual snail, Potamopyrgus antipodarum, demonstrated that different populations derived from a single clonal lineage differed in both shell phenotype and methylation signature when comparing lake versus river populations. Here, we examine methylation variation among lakes that differ in environmental disturbance and pollution histories. The differential DNA methylation regions (DMRs) identified among the different lake comparisons suggested a higher number of DMRs and variation between rural Lake 1 and one urban Lake 2 and between the two urban Lakes 2 and 3, but limited variation between the rural Lake 1 and urban Lake 3. DMR genomic characteristics and gene associations were investigated. Observations suggest there is no effect of geographic distance or any consistent pattern of DMRs between urban and rural lakes. Environmental factors may influence epigenetic response.
2019-09-27 | GSE133502 | GEO