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Ontology highlight
ABSTRACT:
PROVIDER: PRJEB80341 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| ERR13698331.fastq.gz | Fastqsanger.gz | |||
| ERR13698332.fastq.gz | Fastqsanger.gz | |||
| ERR13698333.fastq.gz | Fastqsanger.gz | |||
| ERR13698334.fastq.gz | Fastqsanger.gz | |||
| ERR13702789_1.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 8 |
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Project description:Pelophylax lessonae (pool frog), genomic and transcriptomic data
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Project description:Along with the prevalence of edible frog farming in China, the outbreak of a deadly infectious frog diseased, called frog meningitis (or cataracts and torticollis), has increased in frequency and geographical range dramatically. More than 10 bacterial species, belonging to 8 genera, has been reported as its potential pathogens. Diseased frogs typically manifest as torticollis, cataracts, edema and finally death, resulting in huge economic loss. Currently, the pathogenesis of this disease has not been investigated systematically. Here, we summarized the pathological stages of infected black-spotted frogs (Pelophylax nigromaculata) in Sichuan province according to their symptoms, typically progressing of pathological stage with only torticollis to stage with both torticollis and cataracts. On the basis, we analyzed the pathogenesis by a combination of comparative environmental analysis, microbiomics and transcriptomics. Results showed that more severely infected frog ponds tended to have lower water alkalinity. Elizabethkingia miricola was the only bacteria, whose abundance was positively correlated with the disease degree, and it has absolute dominance in the eyeball and brain of some torticollis-cataracts frogs. E. miricola and several other bacterial species, which belonged to pathogenic genera of meningitis, might be constitutively existed in the resident microbiome in frogs or their environment. Activations of infectious processes and immune responses related pathways were the major difference between health and diseased frogs at transcriptional level. Despite transcriptional activation of immunoglobulins was observed in both torticollis-only and torticollis-cataracts frogs, transcriptional activation of innate immune system (including MHC, toll-like receptor, and cathelicidins) in brain, inflammation system (including interleukins and receptors) in brain, and acute phase proteins (including transferrins and fibrinogens) in both liver and brain was only observed in torticollis-cataracts frogs. Activation of inflammation and the resulting higher vascular permeability in torticollis-cataracts frogs could explain the severe brain infection, cooccurrence of torticollis and cataracts, and systemic edema in torticollis-cataracts frogs. In addition, meningitis could also result in reduction in energy production in liver, and this was more severe in torticollis-cataracts frogs. In conclusion, our results suggested environment might have a role in susceptibility of frog meningitis. E. miricola was the most likely pathogen of meningitis of black-spotted frogs in Sichuan. Refer to the pathogenesis of human meningitis, excessive inflammation likely played a critical role in the progress of frog meningitis, and its resulted sepsis and organ failure might be the direct cause of infected frogs.
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Project description:The goal of this study was to compare the skin transcriptomes of non-irradiated and 30 Gy irradiated Pelophylax nigromaculatus and to find the polypeptide sequences that were changed before and after irradiation. Skin mRNA profiles of non-irradiated and 30Gy irradiated Pelophylax nigromaculatus were generated by deep sequencing,using Illumina HiSeq.The sequenced sequences were assembled into transcripts, and the transcripts were hierarchically clustered using the Corset program. Subsequent analysis was performed using the clustered sequences as references:CDS prediction, SNP and InDel analysis, gene expression level analysis, SSR analysis, RNA-seq overall quality assessment, differential expression analysis, differential gene GO enrichment analysis and KEGG enrichment analysis.Through differential analysis, 875 down-regulated mRNAs and 536 up-regulated mRNAs were identified, and 271 significant changes in peptides were found through the rank sum test, which provided the basis for the next study.
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Project description:First isolation of Brucella microti-like bacteria from Pelophylax ridibundus in a domestic frog farm in France
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Project description:Frogs are an ecologically diverse and phylogenetically ancient group of anuran amphibians that include important vertebrate cell and developmental model systems, notably the genus Xenopus. Here we report a high-quality reference genome sequence for the western clawed frog, Xenopus tropicalis, along with draft chromosome-scale sequences of three distantly related emerging model frog species, Eleutherodactylus coqui, Engystomops pustulosus and Hymenochirus boettgeri. Frog chromosomes have remained remarkably stable since the Mesozoic Era, with limited Robertsonian (i.e., centric) translocations and end-to-end fusions found among the smaller chromosomes. Conservation of synteny includes conservation of centromere locations, marked by centromeric tandem repeats associated with Cenp-a binding, surrounded by pericentromeric LINE/L1 elements. We explored chromosome structure across frogs, using a dense meiotic linkage map for X. tropicalis and chromatin conformation capture (Hi-C) data for all species. Abundant satellite repeats occupy the unusually long (~20 megabase) terminal regions of each chromosome that coincide with high rates of recombination. Both embryonic and differentiated cells show reproducible association of centromeric chromatin, and of telomeres, reflecting a Rabl-like configuration. Our comparative analyses reveal 13 conserved ancestral anuran chromosomes from which contemporary frog genomes were constructed.
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