Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| ERR4676922.fasta.gz | Fasta.gz | |||
| ERR4676922_1.fastq.gz | Fastqsanger.gz | |||
| ERR4676922_2.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 3 of 3 |
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Project description:Transcriptomes of organisms reveal differentiation associated with the use of different habitats. However, this leaves open how much of the observed differentiation can be attributed to genetic differences or to transcriptional plasticity. In this study, we disentangle causes of differential gene expression in larvae of the European fire salamander from the Kottenforst forest in Germany. Larvae inhabit permanent streams and ephemeral ponds and represent an example of a young evolutionary split associated with contrasting ecological conditions. We found ample evidence for differentiation among larvae occupying different habitats in nature with 2800 out of 11797 genes being differentially expressed based on transcriptome data from salamander sampled in their natural habitat (see GEO Series GSE100819). We then quantified transcriptional plasticity towards temperature and genetic differentiation based on controlled temperature laboratory experiments. Gene-by-environment interactions modelling revealed that 28 % of the gene expression divergence observed among samples in nature could be attributed to plasticity related to water temperature. Expression patterns of only a small number of 101 genes were affected by the genotype. Our analysis demonstrates that effects of environmental factors must be taken into account to explain variation of gene expression in salamanders in nature. Notwithstanding, it provides first evidence that genetic factors determined gene expression divergence between pond and stream ecotypes and could be involved in adaptive evolution.
2018-04-24 | GSE113525 | GEO
Project description:Effect of temperature on salamander gut microbiome
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Project description:Antimicrobial peptides have been widely identified from amphibian skins except salamanders. A novel antimicrobial peptide (CFBD) was isolated and characterized from skin secretions of the salamander, Cynops fudingensis. The cDNA encoding CFBD precursor was cloned from the skin cDNA library of C. fudingensis. The precursor was composed of three domains: signal peptide of 17 residues, mature peptide of 41 residues and intervening propeptide of 3 residues. There are six cysteines in the sequence of mature CFBD peptide, which possibly form three disulfide-bridges. CFBD showed antimicrobial activities against Staphylococcus aureus, Bacillus subtilis, Candida albicans and Escherichia coli. This peptide could be classified into family of β-defensin based on its sequence similarity with β-defensins from other vertebrates. Evolution analysis indicated that CFBD was close to fish β-defensin. As far as we know, CFBD is the first β-defensin antimicrobial peptide from salamanders.
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Project description:The responses of individual salamander L-cones to light steps of moderate intensity (bleaching 0.3-3% of the total photopigment) and duration (between 5 and 90 s) were recorded using suction electrodes. Light initially suppressed the circulating current, which partially recovered or "sagged" over several seconds. The sensitivity of the cone to dim flashes decreased rapidly after light onset and approached a minimum within 500 ms. Background light did not affect the rising phase of the dim flash response, a measure of the initial gain of phototransduction. When the light was extinguished, the circulating current transiently exceeded or "overshot" its level in darkness. During the overshoot, the sensitivity of the cone required several seconds to recover. The sag and overshoot remained in voltage-clamped cones. Comparison with theory suggests that three mechanisms cause the sag, overshoot, and slow recovery of sensitivity after the light step: a gradual increase in the rate of inactivation of the phototransduction cascade during the light step, residual activity of the transduction cascade after the step is extinguished, and an increase in guanylate cyclase activity during the light step that persists after the light is extinguished.
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Project description:When related species meet upon postglacial range expansion, hybrid zones are frequently formed. Theory predicts that such zones may move over the landscape until equilibrium conditions are reached. One hybrid zone observed to be moving in historical times (1950-1979) is that of the pond-breeding salamanders Triturus cristatus and Triturus marmoratus in western France. We identified the ecological correlates of the species hybrid zone as elevation, forestation, and hedgerows favoring the more terrestrial T. marmoratus and pond density favoring the more aquatic T. cristatus. The past movement of the zone of ca. 30 km over three decades has probably been driven by the drastic postwar reduction of the "bocage" hedgerow landscape, favoring T. cristatus over T. marmoratus. No further hybrid zone movement was observed from 1979 to the present. To explain the changing dynamics of the hybrid zone, we propose that it stalled, either because an equilibrium was found at an altitude of ca. 140 m a.s.l. or due to pond loss and decreased population densities. While we cannot rule out the former explanation, we found support for the latter. Under agricultural intensification, ponds in the study area are lost at an unprecedented rate of 5.5% per year, so that remaining Triturus populations are increasingly isolated, hampering dispersal and further hybrid zone movement.
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Project description:Identification and characterization of known and novel microRNAs in liver tissues of Chinese giant salamander base on deep sequencing approach Raw sequence reads
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