Table 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

photos

Archive of photographs of each individual fish in *.jpg format. Fish identification numbers correspond to Table S1

Additional 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_readme2

Readme file associated with all files in this package

Table S1. Sample information

Length, 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

The Genome and Linkage Map of the Northern Pike (<i>Esox lucius</i>): Conserved Synteny Revealed between the Salmonid Sister Group and the Neoteleostei

<div><p>The northern pike is the most frequently studied member of the Esociformes, the closest order to the diverse and economically important Salmoniformes. The ancestor of all salmonids purportedly experienced a whole-genome duplication (WGD) event, making salmonid species ideal for studying the early impacts of genome duplication while complicating their use in wider analyses of teleost evolution. Studies suggest that the Esociformes diverged from the salmonid lineage prior to the WGD, supporting the use of northern pike as a pre-duplication outgroup. Here we present the first genome assembly, reference transcriptome and linkage map for northern pike, and evaluate the suitability of this species to provide a representative pre-duplication genome for future studies of salmonid and teleost evolution. The northern pike genome sequence is composed of 94,267 contigs (N50 = 16,909 bp) contained in 5,688 scaffolds (N50 = 700,535 bp); the total scaffolded genome size is 878 million bases. Multiple lines of evidence suggest that over 96% of the protein-coding genome is present in the genome assembly. The reference transcriptome was constructed from 13 tissues and contains 38,696 transcripts, which are accompanied by normalized expression data in all tissues. Gene-prediction analysis produced a total of 19,601 northern pike-specific gene models. The first-generation linkage map identifies 25 linkage groups, in agreement with northern pike's diploid karyotype of 2N = 50, and facilitates the placement of 46% of assembled bases onto linkage groups. Analyses reveal a high degree of conserved synteny between northern pike and other model teleost genomes. While conservation of gene order is limited to smaller syntenic blocks, the wider conservation of genome organization implies the northern pike exhibits a suitable approximation of a non-duplicated Protacanthopterygiian genome. This dataset will facilitate future studies of esocid biology and empower ongoing examinations of the Atlantic salmon and rainbow trout genomes by facilitating their comparison with other major teleost groups.</p></div

The percent similarities identified through transcriptome blastn comparisons.

<p>Blast results from non-redundant, repeat mask transcripts >300 bp with minimum 100 bp alignment. Results plotted by 1% intervals, grouped into bins. Results are graphed as A) within species (paralogues) and B) between species (Orthologues). Eluc  =  <i>Esox lucius</i>, Ssal  =  <i>Salmo salar</i>, Gacu  =  <i>Gasterosteus aculeatus</i>.</p

The northern pike merged linkage map: LG-21 to LG-25.

<p>Genomic scaffold identified by first 4 digit number, with multiple scaffold markers distinguished by final letter. Markers not mapped to a scaffold identified by “(EST)”; sex-specific linkage maps in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0102089#pone.0102089.s001" target="_blank">Figure S1</a>. Marker information in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0102089#pone.0102089.s009" target="_blank">Table S7</a>.</p

The northern pike merged linkage map: LG-11 to LG-20.

<p>Genomic scaffold identified by first 4 digit number, with multiple scaffold markers distinguished by final letter. Markers not mapped to a scaffold identified by “(EST)”; sex-specific linkage maps in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0102089#pone.0102089.s001" target="_blank">Figure S1</a>. Marker information in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0102089#pone.0102089.s009" target="_blank">Table S7</a>.</p

<i>Esox lucius</i> genome assembly statistics. Minimum contig and scaffold size ≥200 bp.

<p><i>Esox lucius</i> genome assembly statistics. Minimum contig and scaffold size ≥200 bp.</p