The genome and linkage map of the northern pike (Esox lucius): conserved synteny revealed between the salmonid sister group and the Neoteleostei

PLoS One. 2014 Jul 28;9(7):e102089. doi: 10.1371/journal.pone.0102089. eCollection 2014.

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.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Esocidae / classification
  • Esocidae / genetics*
  • Genetic Linkage*
  • Genome*
  • Molecular Sequence Data
  • Phylogeny
  • Transcriptome

Associated data

  • GENBANK/AZJR00000000
  • GENBANK/GATF00000000

Grant support

This study was primarily supported by a grant from the Natural Sciences and Engineering Research Council of Canada (www.nserc-crsng.gc.ca) to BFK; additional resources were provided by the University of Victoria (www.uvic.ca). Support was provided by NSERC through a postgraduate scholarship to EBR and by the government of British Columbia to support DRM. Compute Canada (www.computecanada.ca) contributed computing resources. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.