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

• Main Authors: Warren, Ian A., Ciborowski, Kate L., Casadei, Elisa, Hazlerigg, David G., Martin, Sam A. M., Sumner, Seirian, Jordan, William C.
• Format: Dataset
• Language: English
• Published: Dryad 2014
• Subjects: Gene duplication; Salmo salar; whole genome duplication; Genome evolution; Atlantic salmon
• Online Access: https://dx.doi.org/10.5061/dryad.h02b3; https://datadryad.org/stash/dataset/doi:10.5061/dryad.h02b3

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 ... : 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 ...