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Data from: Extensive local gene duplication and functional divergence among paralogs in Atlantic salmon

Citation

Warren, Ian A. et al. (2020), Data from: Extensive local gene duplication and functional divergence among paralogs in Atlantic salmon, Dryad, Dataset, https://doi.org/10.5061/dryad.h02b3

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 favoured 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 million years. 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 characterise 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 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 non-coding. 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.

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References

  • This dataset is supplement to https://doi.org/10.1093/gbe/evu131
  • This dataset is supplemented by urn: NCBIShortReadsArchive:SRR1435393
  • This dataset is supplemented by urn: NCBIShortReadsArchive:SRR1435329
  • This dataset is supplemented by urn: NCBIShortReadsArchive:SRR1435483