title: Extensive local gene duplication and functional divergence among paralogs in Atlantic salmon.
abstract: Many organisms can generate alternative phenotypes from the same genome, enabling individuals to exploit diverse and variable environments. A prevailing hypothesis is that such adaptation has been favored by gene duplication events, which generate redundant genomic material that may evolve divergent functions. Vertebrate examples of recent whole-genome duplications are sparse although one example is the salmonids, which have undergone a whole-genome duplication event within the last 100 Myr. The life-cycle of the Atlantic salmon, Salmo salar, depends on the ability to produce alternating phenotypes from the same genome, to facilitate migration and maintain its anadromous life history. Here, we investigate the hypothesis that genome-wide and local gene duplication events have contributed to the salmonid adaptation. We used high-throughput sequencing to characterize the transcriptomes of three key organs involved in regulating migration in S. salar: Brain, pituitary, and olfactory epithelium. We identified over 10,000 undescribed S. salar sequences and designed an analytic workflow to distinguish between paralogs originating from local gene duplication events or from whole-genome duplication events. These data reveal that substantial local gene duplications took place shortly after the whole-genome duplication event. Many of the identified paralog pairs have either diverged in function or become noncoding. Future functional genomics studies will reveal to what extent this rich source of divergence in genetic sequence is likely to have facilitated the evolution of extreme phenotypic plasticity required for an anadromous life-cycle.
authors.affiliation: School of Biological Sciences, University of Bristol, United Kingdom ianawarren.work@gmail.com.
authors.forename: Ian A
authors.initials: IA
authors.lastname: Warren
authors.affiliation: School of Biological Sciences, University of Bristol, United KingdomInstitute of Zoology, Zoological Society of London, London, United Kingdom.
authors.forename: Kate L
authors.initials: KL
authors.lastname: Ciborowski
authors.affiliation: Institute of Biological and Environmental Sciences, University of Aberdeen, United Kingdom.
authors.forename: Elisa
authors.initials: E
authors.lastname: Casadei
authors.affiliation: Institute of Biological and Environmental Sciences, University of Aberdeen, United KingdomDepartment of Arctic and Marine Biology, Faculty of BioSciences Fisheries & Economy, University of Tromsø, Norway.
authors.forename: David G
authors.initials: DG
authors.lastname: Hazlerigg
authors.affiliation: Institute of Biological and Environmental Sciences, University of Aberdeen, United Kingdom.
authors.forename: Sam
authors.initials: S
authors.lastname: Martin
authors.affiliation: Institute of Zoology, Zoological Society of London, London, United Kingdom.
authors.forename: William C
authors.initials: WC
authors.lastname: Jordan
authors.affiliation: School of Biological Sciences, University of Bristol, United KingdomInstitute of Zoology, Zoological Society of London, London, United Kingdom.
authors.forename: Seirian
authors.initials: S
authors.lastname: Sumner
mesh_terms: D000818:Animals; D030541:Databases, Genetic; D020440:Gene Duplication; D014644:Genetic Variation; D010641:Phenotype; D020317:Salmo salar / Q000235:genetics*
keywords: Atlantic salmon; gene duplication; genome evolution; transcriptome; whole-genome duplication