Conserved and divergent arms of the antiviral response in the duplicated genomes of salmonid fishes

• Published in: Genomics
• Main Authors: Clark, Thomas, C, Naseer, Shahmir, Gundappa, Manu, Kumar, Laurent, Audrey, Perquis, Aline, Collet, Bertrand, Macqueen, Daniel, J, Martin, Samuel A.M., Boudinot, Pierre
• Other Authors: Virologie et Immunologie Moléculaires (VIM (UR 0892)), Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Université Paris-Saclay-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), University of Aberdeen, University of Edinburgh (Edin.), Laboratoire de Physiologie et Génomique des Poissons = Fish Physiology and Genomics Institute (LPGP), Structure Fédérative de Recherche en Biologie et Santé de Rennes (Biosit : Biologie - Santé - Innovation Technologique)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), This work was funded by the European Union’s Horizon 2020 research and innovation program under grant agreement No 817923 (AQUAFAANG), by ANR (ANR-21-E35-0019, LipofishVac), by the Eranet ICRAD-Nucnanofish (ANR_13001498 and BBSRC_ICRAD BB/V019902/1), by the BBSRC Institutional strategic programme award(BBS/E/D/20002174) and by institutional grants from INRAE., ANR-21-CE35-0019,LipoFishVac,Vaccins liponanoparticulaires mARN et ADN pour les poissons, couplés à des adjuvants immunomodulateurs(2021), ANR-21-ICRD-0009,NucNanoFish,Nucleic NanoVaccines for Fish(2021), European Project: 817923,H2020,H2020-EU.3.2.1.1., H2020-EU.3.2.3.1.,AQUA-FAANG(2019)
• Format: Article in Journal/Newspaper
• Language: English
• Published: HAL CCSD 2023
• Subjects: [SDV]Life Sciences [q-bio]; [SDV.IMM]Life Sciences [q-bio]/Immunology; Atlantic salmon
• Online Access: https://hal.inrae.fr/hal-04172440; https://hal.inrae.fr/hal-04172440v1/document; https://hal.inrae.fr/hal-04172440v1/file/clark-2023-genomics.pdf; https://doi.org/10.1016/j.ygeno.2023.110663

International audience Antiviral innate immunity is orchestrated by the interferon system, which appeared in ancestors of jawed vertebrates. Interferon upregulation induces hundreds of interferon-stimulated-genes (ISGs) with effector or regulatory functions. Here we investigated the evolutionary diversification of ISG responses through comparison of two salmonid fishes, accounting for the impact of sequential whole genome duplications ancestral to teleosts and salmonids. We analysed the transcriptomic response of the IFN pathway in the head kidney of rainbow trout and Atlantic salmon, which separated 25-30 Mya. We identified a large set of ISGs conserved in both species and cross-referenced them with zebrafish and human ISGs. In contrast, around one-third of salmonid ISG lacked orthologs in human, mouse, chicken or frog, and often between rainbow trout and Atlantic salmon, revealing a fast-evolving, lineage-specific arm of the antiviral response. This study also provides a key resource for in-depth functional analysis of ISGs in salmonids of commercial significance.