Pink sea fan genome
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB61094 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| Other | ||||
| ERR11243031.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 2 of 2 |
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Project description:Rare, long-distance dispersal underpins genetic connectivity in the pink sea fan, Eunicella verrucosa.
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Project description:Lack of resistance to pink snow mould (Microdochium nivale) is seen as a major constraint for adaptation of perennial ryegrass (Lolium perenne L.) at higher latitudes. Plants generally become more resistant to snow moulds after cold acclimation, and almost all investigations of genetic variation in resistance have been performed using cold acclimated plants. However, there may be variation in resistance mechanisms that are functioning independently of cold acclimation. In this study our aim was to identify candidate genes involved in such resistance mechanisms. We first characterized variation in resistance to M. nivale among non-acclimated plants of eight genotypes from the Norwegian cultivar Fagerlin and selected one resistant and one susceptible genotype for transcriptome analysis. Total RNA was extracted from leaf blade tissue of plants exposed to three different treatments: non-inoculated and non-incubated plants, non-inoculated plants after four days of incubation, and inoculated plants after four days of incubation. cDNA libraries were prepared and paired-end sequencing performed using Illumina Hiseq 2000. Transcriptome profiles, GO enrichment and KEGG pathway analysis indicate that defence response related genes are differentially expressed between incubated non-inoculated and incubated inoculated conditions both within resistant and susceptible genotypes. A significant up-regulation of defence related genes as well as genes involved in cell wall cellulose metabolic processes and aryl-alcohol dehydrogenase (NADP+) activity was observed in the resistant genotype. The candidate genes identified in this study might be potential molecular marker resources for breeding perennial ryegrass cultivars with improved resistance to pink snow mould.
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Project description:Salmon infected with an ectoparasitic marine copepod, the salmon louse Lepeophtheirus salmonis, incur a wide variety of consequences depending upon host sensitivity. Juvenile pink salmon (Oncorhynchus gorbuscha) migrate from natal freshwater systems to the ocean at a young age relative to other Pacific salmon, and require rapid development of appropriate defences against marine pathogens. We analyzed the early transcriptomic responses of naïve juvenile pink salmon of sizes 0.3g (no scales), 0.7g (mid-scale development) and 2.4g (scales fully developed) to a low-level laboratory exposure with early moult stage L. salmonis. All infected size groups exhibited unique transcriptional profiles. Inflammation and inhibition of cell proliferation was identified in the smallest size class (0.3g), while increased glucose absorption and retention was identified in the middle size class (0.7g). Tissue-remodelling genes were also up-regulated in both the 0.3g and 0.7g size groups. Profiles of the 2.4g size class indicated cell-mediated immunity and possibly parasite-induced growth augmentation. Understanding a size-based threshold of resistance to L. salmonis is important for fisheries management. This work characterizes molecular responses reflecting the gradual development of innate immunity to L. salmonis between the susceptible (0.3g) and refractory (2.4g) pink salmon size classes.
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Project description:Abstract The pink sea fan, Eunicella verrucosa (Pallas, 1766), inhabits rocky substrates across the northeast Atlantic and the western Mediterranean. Across much of its range it has been detrimentally affected by fishing. DNA from 17 E. verrucosa specimens was amplified by phi29-induced rolling circle amplification. Following purification by sodium acetate-ethanol precipitation, the circular genomic DNA was sequenced on an Illumina MiSeq v2. Specimens originated from sites along the west coast of Ireland, southwest Wales, southwest/southern England, northwest France, southern Portugal, and the Mediterranean coast of northeast Spain. All samples had identical mitochondrial genome sequences of 19,267 bp and included 14 protein-coding genes (including the mutS gene), two ribosomal RNA subunits (12S and 16S) and one methionine tRNA gene. Two genes (nad2 and nad5) overlapped by 13 bp; all other genes were separated by non-coding intergenic regions. All protein-coding genes had the same start codon (ATG) and a TAA or TAG stop codon, except for cox1 that terminated with the incomplete stop codon T--. The mitochondrial genome of E. verrucosa (MW588805) showed 99.72% similarity with that of a related sea fan species, Eunicella cavolini, with six SNPs and a 49 bp deletion between nad5 and nad4 in E. verrucosa distinguishing the two.
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