DOI: 10.5061/dryad.3p545
title: Data from: Divergent immunity and energetic programs in the gills of migratory and resident Oncorhynchus mykiss

description: Divergent life history strategies occur in steelhead or rainbow trout
 Oncorhynchus mykiss, and many populations produce both migrant (anadromous
 fish that move to the ocean after rearing) and resident (do not migrate
 and remain in fresh water) individuals. Mechanisms leading to each type
 are only partially understood; while the general tendency of a population
 is heritable, individual tendency may be plastic, influenced by local
 environment. Steelhead hatchery programmes aim to mitigate losses in wild
 stocks by producing trout that will migrate to the ocean and not compete
 with wild trout for limited freshwater resources. To increase our
 understanding of gill function in these migratory or resident phenotypes,
 here we compare gill transcriptome profiles of hatchery-released fish
 either at the release site (residents) or five river kilometres downstream
 while still in full fresh water (migrants). To test whether any of these
 genes can be used as predictive markers for smoltification, we compared
 these genes between migrant-like and undifferentiated trout while still in
 the hatchery in a common environment (prerelease). Results confirmed the
 gradual process of smoltification, and the importance of energetics, gill
 remodelling and ion transport capacity for migrants. Additionally,
 residents overexpressed transcripts involved in antiviral defences,
 potentially for immune surveillance via dendritic cells in the gills. The
 best smoltification marker candidate was protein s100a4, expression of
 which was highly correlated with Na(+) , K(+) ATPase (NKA) activity and
 smolt-like morphology in pre- and postrelease trout gills.
description: photosArchive of photographs
 of each individual fish in *.jpg format. Fish identification numbers
 correspond to Table S1.Table S1. Sample
 informationLength, weight,
 smoltscale, sex and NKA activity for every fish sampled. Individuals
 included in the microarray analysis and incorporated into the microarray
 reference pool are identified. Numbers assigned to each sample during RNA
 purification, and names used for each sample in the Gene Expression
 Omnibus accession are also listed.resub_tableS1.xlsxTable S2. Primer table.qPCR targets, primers, amplicon sizes (bases) and efficiency percentages from Oncorhynchus mykiss standard curve.resub_tableS2.docxTable S3. Gene Ontology enrichment in migrants or residents.Trimmed GO enrichment for the day eight migrant compared to resident gene lists (GO Trimming performed with an 0.80 soft trim threshold). BP = Biological Process; CC = Cellular Component; MF = Molecular Function.resub_tableS3.docxAdditional File 1. Total differential gene lists.Total differential gene lists for day 8 migrant compared to resident, pre-release smoltscale 3 compared to smoltscale 2, and resident day 48 compared to resident day 8.resub_additional_file1.xlsxFigure S1. Correlation between qPCR and microarray.(a) R2 and slope for each gene measured by microarray and qPCR (i.e., log2(qPCR) against log2(microarray)), and two example correlation plots (b) s100a4 and (c) irf1.resub_figS1.pdfresub_readme2Readme file associated with all files in this package.