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

Abstract

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.

An improved genome assembly uncovers prolific tandem repeats in Atlantic cod

“…The assemblies created in this study all span approximately 650 Mbp, which is similar to the ALLPATHS-LG estimation. 650 Mbp is 71% of the earlier estimation based on Feulgen Image Analysis Densitometry, and in line with similar results in platyfish (70–89% of earlier estimations) [47] and in northern pike (64–100%) [48]. In addition, CEGMA [38] and BUSCO [39] find 89-93% of conserved genes (Table 1), likely reflecting the approximate completeness of the genome assembly.…”

Functional Divergence of Type 2 Deiodinase Paralogs in the Atlantic Salmon

“…Members of the dio2 family encode selective, outer ring deiodinases responsible for conversion of thyroxine (T4) to active triiodothyronine (T3) within TH target tissues. The presence of only a single dio2 gene in the Northern pike (Esox lucius), which represents the closely related sister group to salmonids, the Ecosiformes [8], indicates that salmon dio2a and dio2b diverged following WGD within the salmonid lineage. Members of the dio3 family serve the converse function to dio2, encoding selective, inner ring deiodinases responsible for tissue conversion of T4 to inactive reverse T3 (rT3), or inactivating T3 by converting it further to diiodothyronine (T2).…”

The Atlantic salmon genome provides insights into rediploidization

“…As this analysis required calibration against an outgroup, we included only homeologous pairs having an orthologue in the Northern pike (Esox lucius), a member of the closest related diploid sister-group to salmonids 23 . Our results suggest ~100-80 Mya as a lower boundary for the Ss4R and that the Salmo-Oncorhynchus divergence occurred ~21 Mya ( Fig.…”