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Genomic Signatures of Freshwater Adaptation in Pacific Herring (Clupea pallasii)

Pacific herring (Clupea pallasii) is an essential target of commercial fishing in the North Pacific Ocean. Previous studies have suggested the existence of marine and lake ecological forms of this species within its range. The lake ecological form of herring has a shortened life cycle, spending the...

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Autores principales: Nedoluzhko, Artem, Orlova, Svetlana Yu., Kurnosov, Denis S., Orlov, Alexei M., Galindo-Villegas, Jorge, Rastorguev, Sergey M.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9601299/
https://www.ncbi.nlm.nih.gov/pubmed/36292743
http://dx.doi.org/10.3390/genes13101856
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author Nedoluzhko, Artem
Orlova, Svetlana Yu.
Kurnosov, Denis S.
Orlov, Alexei M.
Galindo-Villegas, Jorge
Rastorguev, Sergey M.
author_facet Nedoluzhko, Artem
Orlova, Svetlana Yu.
Kurnosov, Denis S.
Orlov, Alexei M.
Galindo-Villegas, Jorge
Rastorguev, Sergey M.
author_sort Nedoluzhko, Artem
collection PubMed
description Pacific herring (Clupea pallasii) is an essential target of commercial fishing in the North Pacific Ocean. Previous studies have suggested the existence of marine and lake ecological forms of this species within its range. The lake ecological form of herring has a shortened life cycle, spending the winter and spawning in brackish waters near the shoreline without long migrations for feeding; it also has a relatively smaller body size than the marine form. Genetic-based studies have shown that brackish water Pacific herring not only can be distinguished as a separate lake ecological form but possibly has its genetic legacy. Here, as part of an ongoing study, using ddRAD-sequencing data for marine and lake ecological forms from a total of 54 individuals and methods of comparative bioinformatics, we describe genomic signatures of freshwater adaptivity in Pacific herring. In total, 253 genes containing discriminating SNPs were found, and part of those genes was organized into genome clusters, also known as “genomic islands of divergence”. Moreover, the Tajima’s D test showed that these loci are under directional selection in the lake populations of the Pacific herring. Yet, most discriminating loci between the lake and marine ecological forms of Pacific herring do not intersect (by gene name) with those in other known marine fish species with known freshwater/brackish populations. However, some are associated with the same physiological trait—osmoregulation.
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spelling pubmed-96012992022-10-27 Genomic Signatures of Freshwater Adaptation in Pacific Herring (Clupea pallasii) Nedoluzhko, Artem Orlova, Svetlana Yu. Kurnosov, Denis S. Orlov, Alexei M. Galindo-Villegas, Jorge Rastorguev, Sergey M. Genes (Basel) Article Pacific herring (Clupea pallasii) is an essential target of commercial fishing in the North Pacific Ocean. Previous studies have suggested the existence of marine and lake ecological forms of this species within its range. The lake ecological form of herring has a shortened life cycle, spending the winter and spawning in brackish waters near the shoreline without long migrations for feeding; it also has a relatively smaller body size than the marine form. Genetic-based studies have shown that brackish water Pacific herring not only can be distinguished as a separate lake ecological form but possibly has its genetic legacy. Here, as part of an ongoing study, using ddRAD-sequencing data for marine and lake ecological forms from a total of 54 individuals and methods of comparative bioinformatics, we describe genomic signatures of freshwater adaptivity in Pacific herring. In total, 253 genes containing discriminating SNPs were found, and part of those genes was organized into genome clusters, also known as “genomic islands of divergence”. Moreover, the Tajima’s D test showed that these loci are under directional selection in the lake populations of the Pacific herring. Yet, most discriminating loci between the lake and marine ecological forms of Pacific herring do not intersect (by gene name) with those in other known marine fish species with known freshwater/brackish populations. However, some are associated with the same physiological trait—osmoregulation. MDPI 2022-10-14 /pmc/articles/PMC9601299/ /pubmed/36292743 http://dx.doi.org/10.3390/genes13101856 Text en © 2022 by the authors. https://creativecommons.org/licenses/by/4.0/Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
Nedoluzhko, Artem
Orlova, Svetlana Yu.
Kurnosov, Denis S.
Orlov, Alexei M.
Galindo-Villegas, Jorge
Rastorguev, Sergey M.
Genomic Signatures of Freshwater Adaptation in Pacific Herring (Clupea pallasii)
title Genomic Signatures of Freshwater Adaptation in Pacific Herring (Clupea pallasii)
title_full Genomic Signatures of Freshwater Adaptation in Pacific Herring (Clupea pallasii)
title_fullStr Genomic Signatures of Freshwater Adaptation in Pacific Herring (Clupea pallasii)
title_full_unstemmed Genomic Signatures of Freshwater Adaptation in Pacific Herring (Clupea pallasii)
title_short Genomic Signatures of Freshwater Adaptation in Pacific Herring (Clupea pallasii)
title_sort genomic signatures of freshwater adaptation in pacific herring (clupea pallasii)
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9601299/
https://www.ncbi.nlm.nih.gov/pubmed/36292743
http://dx.doi.org/10.3390/genes13101856
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