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ABSTRACT: Pathogenic infection and immune-related gene expression of Chinese sturgeon (Acipenser Sinensis) challenged by Citrobacter freundii

PROVIDER: PRJNA639973 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR12039170_1.fastq.gz	Fastqsanger.gz
	SRR12039170_2.fastq.gz	Fastqsanger.gz
	SRR12039171_1.fastq.gz	Fastqsanger.gz
	SRR12039171_2.fastq.gz	Fastqsanger.gz
	SRR12039172_1.fastq.gz	Fastqsanger.gz

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Project description:The Chinese sturgeon (Acipenser sinensis) is anadromous fish distributed in Yangtze River and East China Sea. In this study, we reported cleft-palate Chinese sturgeons in artificial population for the first time. In order to explore the genetic basis of palate malformation in A. sinensis, Illumina RNA-seq technology was used to analyze the transcriptome data of normal and cleft-palate individuals in farmed Chinese sturgeons. Raw reads were obtained and assembled into 808,612 unigenes, with an average length of 509.33 bp and an N50 of 574 bp. Sequence similarity analyses against four public databases (Nr, Uniprot, KEGG and COGs) found 158,642 unigenes that can be annotated. GABAergic synapse and TGF-β signal pathway were the most two enriched pathways with high Richfactor in the analyses of different expressed genes. In these two signal pathways, six genes (GABRA4, GS, GNS, S6K, PITX2, and BMP8) were found as cleft-palate genes in Chinese sturgeon. These findings contribute to our understanding of the genetic basis of cleft palate in sturgeon, while simultaneously adding to our knowledge about craniofacial development.

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Transcriptome profiles in the spleen of the Chinese giant salamander (Andrias davidianus) challenged with Citrobacter freundii

Project description:The Chinese giant salamander (Andrias davidianus) is one of the most important ecological breeding species with distinct characteristics and is cultured in many locations throughout China. In the present study, the transcriptome of A. davidianus spleen tissue, that had challenged with Citrobacter freundii, was analyzed using Illumina sequencing technology. The result was compared to a heathy control group. After assembly and annotation, 128,540 transcripts were generated with a median length of 349 bp. Comparative expression analysis indicated 1,995 differentially expressed genes (DEGs), 812 of which were up-regulated and 1,183 were down-regulated. Furthermore, DEGs were classified into three gene ontology categories, 535 of which were annotated to 237 KEGG pathways. Finally, six immune-related DEGs involved in the immune-related pathways were randomly selected for scrutinization. This work provides valuable data for an improved understanding the defense mechanisms of A. davidianus against bacterial pathogens at the transcriptional level.

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Transcriptome profiling reveals cleft palate-related genes in Chinese sturgeon (Acipenser sinensis)

Project description:Transcriptome profiling reveals cleft palate-related genes in Chinese sturgeon (Acipenser sinensis)

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iTRAQ-based comparative proteomic of bullfrog Lithobates catesbeianus Spleen challenged with Citrobacter freundii, a red-leg syndrome associated pathogen in raniculture

Project description:study the protein expression profile of immune response in the spleen of bullfrog after infection of Citrobacter freundii

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Transcriptome profiles in the spleen of the Chinese giant salamander (Andrias davidianus) challenged with Citrobacter freundii

Project description:Transcriptome profiles in the spleen of the Chinese giant salamander (Andrias davidianus) challenged with Citrobacter freundii

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Project description:Conjugative plasmids are the main vehicle for the horizontal spread of antimicrobial resistance (AMR). Although AMR plasmids provide advantages to their hosts under antibiotic pressure, they can also disrupt the cell’s regulatory network, impacting the fitness of their hosts. Despite the importance of plasmid-bacteria interactions on the evolution of AMR, the effects of plasmid carriage on host physiology has remained underexplored, and most studies have focused on model bacteria and plasmids that lack clinical relevance. Here, we analyzed the transcriptional response of 11 clinical enterobacterial strains (2 Escherichia coli, 1 Citrobacter freundii and 8 Klebsiella spp.) and the laboratory-adapted E. coli MG1655 to carriage of pOXA-48, one of the most widely spread carbapenem-resistance plasmids. Our analyses revealed that pOXA-48 produces variable responses on their hosts, but commonly affects processes related to metabolism, transport, response to stimulus, cellular organization and motility. More notably, the presence of pOXA-48 caused an increase in the expression of a small chromosomal operon of unknown function in Klebsiella spp. and C. freundii, which is not present in E. coli. Phylogenetic analysis suggested that this operon has been horizontally mobilized across different Proteobacteria species. We demonstrate that a pOXA-48-encoded LysR transcriptional regulator controls the expression of the operon in Klebsiella spp. and C. freundii. In summary, our results highlight a crosstalk between pOXA-48 and the chromosome of its natural hosts.

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