title: Long noncoding RNAs (lncRNAs) dynamics evidence immunomodulation during ISAV-Infected Atlantic salmon (Salmo salar).
abstract: Despite evidence for participation in the host response to infection, the roles of many long non-coding RNAs (lncRNAs) remain unknown. Therefore, the aims of this study were to identify lncRNAs in Atlantic salmon (Salmo salar) and evaluate their transcriptomic regulation during ISA virus (ISAV) infection, an Orthomyxoviridae virus associated with high mortalities in salmonid aquaculture. Using next-generation sequencing, whole-transcriptome analysis of the Salmo salar response to ISAV infection was performed, identifying 5,636 putative lncRNAs with a mean length of 695 base pairs. The transcriptional modulation evidenced a similar number of differentially expressed lncRNAs in the gills (3,294), head-kidney (3,275), and liver (3,325) over the course of the infection. Moreover, analysis of a subset of these lncRNAs showed the following: (i) Most were similarly regulated in response to ISA virus infection; (ii) The transcript subsets were uniquely modulated in each tissue (gills, liver, and head-kidney); and (iii) A subset of lncRNAs were upregulated for each tissue and time analysed, indicating potential markers for ISAV infection. These findings represent the first discovery of widespread differential expression of lncRNAs in response to virus infection in non-model species, suggesting that lncRNAs could be involved in regulating the host response during ISAV infection.
authors.affiliation: Laboratory of Biotechnology and Aquatic Genomics, Interdisciplinary Center for Aquaculture Research (INCAR), University of Concepción, Concepción, Chile.
authors.forename: Sebastian
authors.initials: S
authors.lastname: Boltaña
authors.affiliation: Laboratory of Biotechnology and Aquatic Genomics, Interdisciplinary Center for Aquaculture Research (INCAR), University of Concepción, Concepción, Chile.
authors.forename: Diego
authors.initials: D
authors.lastname: Valenzuela-Miranda
authors.affiliation: Laboratory of Biotechnology and Aquatic Genomics, Interdisciplinary Center for Aquaculture Research (INCAR), University of Concepción, Concepción, Chile.
authors.forename: Andrea
authors.initials: A
authors.lastname: Aguilar
authors.affiliation: Institute of Aquaculture, University of Stirling, Stirling, UK.
authors.forename: Simon
authors.initials: S
authors.lastname: Mackenzie
authors.affiliation: Laboratory of Biotechnology and Aquatic Genomics, Interdisciplinary Center for Aquaculture Research (INCAR), University of Concepción, Concepción, Chile.
authors.forename: Cristian
authors.initials: C
authors.lastname: Gallardo-Escárate
mesh_terms: D000818:Animals; D005393:Fish Diseases / Q000473:pathology* / Q000821:virology; D020869:Gene Expression Profiling; D005880:Gills / Q000473:pathology; D059014:High-Throughput Nucleotide Sequencing; D056747:Immunomodulation; D046829:Isavirus / Q000276:immunology* / Q000472:pathogenicity; D007668:Kidney / Q000473:pathology; D008099:Liver / Q000473:pathology; D009976:Orthomyxoviridae Infections / Q000473:pathology / Q000662:veterinary*; D062085:RNA, Long Noncoding / Q000032:analysis* / Q000235:genetics; D020317:Salmo salar; D017422:Sequence Analysis, DNA
chemical_list: D062085:RNA, Long Noncoding