DOI: 10.5061/dryad.h02b3
title: Data from: Extensive local gene duplication and functional divergence among paralogs in Atlantic salmon

description: 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.
description: Assembly of 454 reads
 from the brainAssembly of the 454
 reads from the brains of Salmo salar parrDRYAD_Brain.zipAssembly of 454 reads from olfactory epitheliumAssembly of 454 reads from olfactory epithelium from Salmo salar at the parr stageDRYAD_OLF.zipAssembly of 454 reads from pituitary glandAssembly of 454 reads from pituitary gland of Salmo salar at the parr stageDRYAD_PIT.zipAssembly of 454 reads from all tissuesAssembly of 454 reads from brain, pituitary and olfactory epithelium of Salmo salar, at the parr stage.DRYAD_Pool.zipPython script for protein prediction and ka/ks calculationsdNCalc_tBLASTx_clustal_ORF.pyPython script for comparing duplicatesIncludes selection of random sequence pairs.duplicate_analysis_comparisons.pyPython script for identifying duplicate pairs in Salmo salarduplicate_search_3.pyPython script for carrying out a reciprocal BLAST searchreciprocalblast_allsteps.pyProcessed 454 reads for brain454 reads for brain from Salmo salar in the parr stage. Trimmed for quality and adaptors (see paper for detail)Processed 454 reads for pituitary454 reads for pituitary from Salmo salar at the parr stage. Trimmed for quality and adaptors (see paper for detail)Processed 454 reads for olfactory epitheliumProcessed 454 reads for olfactory epithelium from Salmo salar at the parr stage. Trimmed for quality and adaptors (see paper for detail)Python modules required for dNCalcs_tBLASTx_clustal_ORF.pyian_mods.py