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We used a bath challenge approach to profile the transcriptome responses of <jats:italic>M. viscosa<\/jats:italic>-infected Atlantic salmon skin at the lesion (Mv-At) and away from the lesion (Mv-Aw) sites. <jats:italic>M. viscosa<\/jats:italic> infection was confirmed through RNA-based qPCR assays. RNA-Seq identified 5212 and 2911 transcripts differentially expressed in the Mv-At compared to no-infection control and Mv-Aw groups, respectively. Also, there were 563 differentially expressed transcripts when comparing the Mv-Aw to control samples. Our results suggest that <jats:italic>M. viscosa<\/jats:italic> caused massive and strong, but largely infection site-focused, transcriptome dysregulations in Atlantic salmon skin, and its effects beyond the skin lesion site were comparably subtle. The <jats:italic>M. viscosa<\/jats:italic>-induced transcripts of Atlantic salmon were mainly involved in innate and adaptive immune response-related pathways, whereas the suppressed transcripts by this pathogen were largely connected to developmental and cellular processes. As validated by qPCR, <jats:italic>M. viscosa<\/jats:italic> dysregulated transcripts encoding receptors, signal transducers, transcription factors and immune effectors playing roles in TLR- and IFN-dependent pathways as well as immunoregulation, antigen presentation and T-cell development. This study broadened the current understanding of molecular pathways underlying <jats:italic>M. viscosa<\/jats:italic>-triggered responses of Atlantic salmon, and identified biomarkers that may assist to diagnose\u00a0and combat this pathogen.<\/jats:p>","DOI":"10.1038\/s41598-022-08341-7","type":"journal-article","created":{"date-parts":[[2022,3,17]],"date-time":"2022-03-17T16:33:41Z","timestamp":1647534821000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":18,"title":["Global gene expression responses of Atlantic salmon skin to Moritella viscosa"],"prefix":"10.1038","volume":"12","author":[{"given":"Khalil","family":"Eslamloo","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Surendra","family":"Kumar","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xi","family":"Xue","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kathleen S.","family":"Parrish","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sara L.","family":"Purcell","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mark D.","family":"Fast","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Matthew L.","family":"Rise","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2022,3,17]]},"reference":[{"key":"8341_CR1","unstructured":"FAO. 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