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Transcriptome architecture and regulation at environmental transitions of the fish pathogen Flavobacterium psychrophilum: 5’-end RNA-Seq

ABSTRACT: Transcriptome architecture and regulation at environmental transitions of the fish pathogen Flavobacterium psychrophilum: 5’-end RNA-Seq

PROVIDER: PRJNA689479 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR13347860.fastq.gz	Fastqsanger.gz

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Transcriptome architecture and regulation at environmental transitions of the fish pathogen Flavobacterium psychrophilum: 5’-end RNA-Seq

Project description:In a context of fast development of aquaculture, infections by Flavobacterium psychrophilum, a member of the family Flavobacteriaceae, are a major sanitary concern for the salmonid farming industry worldwide. Several phenotypic traits related to pathogenesis have been documented for this bacterium, but molecular factors involved remain poorly characterized. Here, we conducted a global study of adaptation to outside- and within-host environments using a combination of in vitro transcriptomic and computational approaches. The repertoire of transcription start sites and transcriptional units was established using 5’-end and global RNA-Seq. Responses to environmental conditions were explored by expression profiling across conditions, including host-related stresses, exposure to fish mucus and plasma, growth on blood, osmotic changes or freshwater. Analysis of these data allowed to identify many new regulatory elements including alternative sigma-factors promoters, 5’ cis-encoded and trans-acting RNAs. It also revealed interconnected regulations linked to specific environmental conditions for a wide range of biological processes: proteolytic activity, iron acquisition, fatty acids metabolism, respiration under low-oxygen concentration, protein secretion and folding, efflux pumps as well as adhesion and spreading. Results reported here constitute an important resource for guiding basic and applied research on this important pathogen, and a dedicated website is provided to facilitate their exploration.

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