Divergence between land-snails species
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB41103 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| Other | ||||
| ERR4847991_1.fastq.gz | Fastqsanger.gz | |||
| ERR4847991_2.fastq.gz | Fastqsanger.gz | |||
| ERR4847782_1.fastq.gz | Fastqsanger.gz | |||
| ERR4847782_2.fastq.gz | Fastqsanger.gz |
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Project description:Species and gene divergence in Littorina snails by aCGH
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Project description:Transcriptional profile of snails exposed to irradiated E. paraensei miricidia and four days later challenged with S. mansoni miricidia. Compared to snails exposed to only irradiated E. paraensei miricidia.
2011-07-30 | GSE28293 | GEO
Project description:Transcriptional profile of BS-90 snails injected with a cocktail of four FREP3 specific 27-mer DSiRNA oligos and two hours later exposed to S. mansoni miricidia. Compared to BS-90 snails injected with a cocktail of three GFP specific DSiRNA oligos and two hours later exposed to S. mansoni miricidia. Experiments were done over the course of 49 days. Snails were collected (10each) at 2 and 4 dpe to S. mansoni for comparison.
2012-04-01 | GSE33525 | GEO
Project description:Background: Array comparative genomic hybridization (aCGH) is commonly used to screen different types of genetic variation in humans and model species. Here, we performed aCGH using an oligonucleotide gene-expression array for a non-model species, the intertidal snail Littorina saxatilis. First, we tested what types of genetic variation can be detected by this method using direct re-sequencing and comparison to the Littorina genome draft. Secondly, we performed a genome-wide comparison of four closely related Littorina species: L. fabalis, L. compressa, L. arcana and L. saxatilis and of populations of L. saxatilis found in Spain, Britain and Sweden. Finally, we tested whether we could identify genetic variation underlying “Crab” and “Wave” ecotypes of L. saxatilis. Results: We could reliably detect copy number variations, deletions and high sequence divergence (i.e. above 3%), but not single nucleotide polymorphisms. The overall hybridization pattern and number of significantly diverged genes were in close agreement with earlier phylogenetic reconstructions based on single genes. The trichotomy of L. arcana, L. compressa and L. saxatilis could not be resolved and we argue that these divergence events have occurred recently and very close in time. We found evidence for high levels of segmental duplication in the Littorina genome (10% of the transcripts represented on the array and up to 23% of the analyzed genomic fragments); duplicated genes and regions were mostly the same in all analyzed species. Finally, this method discriminated geographically distant populations of L. saxatilis, but we did not detect any significant genome divergence associated with ecotypes of L. saxatilis. Conclusions: The present study provides new information on the sensitivity and the potential use of oligonucleotide arrays for genotyping of non-model organisms. Applying this method to Littorina species yields insights into genome evolution following the recent species radiation and supports earlier single-gene based phylogenies. Genetic differentiation of L. saxatilis ecotypes was not detected in this study, despite pronounced innate phenotypic differences. The reason may be that these differences are due to single-nucleotide polymorphisms.
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Project description:Background: Array comparative genomic hybridization (aCGH) is commonly used to screen different types of genetic variation in humans and model species. Here, we performed aCGH using an oligonucleotide gene-expression array for a non-model species, the intertidal snail Littorina saxatilis. First, we tested what types of genetic variation can be detected by this method using direct re-sequencing and comparison to the Littorina genome draft. Secondly, we performed a genome-wide comparison of four closely related Littorina species: L. fabalis, L. compressa, L. arcana and L. saxatilis and of populations of L. saxatilis found in Spain, Britain and Sweden. Finally, we tested whether we could identify genetic variation underlying M-bM-^@M-^\CrabM-bM-^@M-^] and M-bM-^@M-^\WaveM-bM-^@M-^] ecotypes of L. saxatilis. Results: We could reliably detect copy number variations, deletions and high sequence divergence (i.e. above 3%), but not single nucleotide polymorphisms. The overall hybridization pattern and number of significantly diverged genes were in close agreement with earlier phylogenetic reconstructions based on single genes. The trichotomy of L. arcana, L. compressa and L. saxatilis could not be resolved and we argue that these divergence events have occurred recently and very close in time. We found evidence for high levels of segmental duplication in the Littorina genome (10% of the transcripts represented on the array and up to 23% of the analyzed genomic fragments); duplicated genes and regions were mostly the same in all analyzed species. Finally, this method discriminated geographically distant populations of L. saxatilis, but we did not detect any significant genome divergence associated with ecotypes of L. saxatilis. Conclusions: The present study provides new information on the sensitivity and the potential use of oligonucleotide arrays for genotyping of non-model organisms. Applying this method to Littorina species yields insights into genome evolution following the recent species radiation and supports earlier single-gene based phylogenies. Genetic differentiation of L. saxatilis ecotypes was not detected in this study, despite pronounced innate phenotypic differences. The reason may be that these differences are due to single-nucleotide polymorphisms. Genomic DNA samples of L. fabalis, L. compressa, L. arcana and 3 geographic populations x 2 ecotypes of L. saxatilis (n=4 per group) have been hybridized to a transcriptomic oligoarray.
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Project description:Transcriptional profile of snails exposed to irradiated E. paraensei miricidia and four days later challenged with S. mansoni miricidia. Compared to snails exposed to only irradiated E. paraensei miricidia. Each replicate is comprised of 1 individual snail from the specified treatment group. Six replicates of each treatment were analyzed on the Snail oligo array.
2011-07-29 | E-GEOD-28293 | biostudies-arrayexpress
Project description:Transcriptional profile of BS-90 snails injected with a cocktail of four FREP3 specific 27-mer DSiRNA oligos and two hours later exposed to S. mansoni miricidia. Compared to BS-90 snails injected with a cocktail of three GFP specific DSiRNA oligos and two hours later exposed to S. mansoni miricidia. Experiments were done over the course of 49 days. Snails were collected (10each) at 2 and 4 dpe to S. mansoni for comparison. Each replicate is comprised of 1 individual snail from the specified treatment group. Ten replicates of each treatment were analyzed on the Snail oligo array.
2012-03-31 | E-GEOD-33525 | biostudies-arrayexpress
Project description:The differential production of pheromones is a major barrier to mating between species in Drosophila. Individuals from morphologically similar sister species can produce different sets of cuticular hydrocarbons that allow potential mates to identify them as a suitable partner. In order to elucidate cis-regulatory mechanisms behind speciation, we looked for allele-specific expression in hydrocarbon-producing oenocytes from F1 hybrids of the sister species D. simulans and D. sechellia. By focusing on cis-regulatory changes specific to female oenocytes, we rapidly identified a small number of candidate genes. Oour RNA-seq approach proved to be far more efficient than QTL mapping in identifying candidate genes, and it can be used to pinpoint the genetic basis for a wide range of traits differing due to cis-regulatory divergence between any interfertile species.
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Project description:1. Radioactively labelled cholecalciferol was injected into the land snails Levantina hiersolyma and Theba pisana. Three metabolites (C, D and E), more polar than cholecalciferol, were found. 2. Metabolite C was found to be identical with 25-hydroxycholecalciferol. On injection of 25-hydroxy[26,27-3H]cholecalciferol, metabolite E was predominantly formed. Metabolite D was predominantly formed from cholecalciferol. Metabolites D and E differ from any known cholecalciferol metabolites. 3. The intestine was found to be the tissue capable of carrying out the transformation of 25-hydroxycholecalciferol into metabolite E. 4. 25-Hydroxycholecalciferol and metabolite E were localized in the digestive gland of the snail, the tissue responsible for the absorption of Ca2+ and its storage. Metabolite D was not localized in any specific tissue.
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