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.
Highlights
IntroductionOf the nine currently available teleost genome assemblies (www. ensembl.org), all fall into either the Neoteleostei or the Ostariophysi [1]
Of the nine currently available teleost genome assemblies, all fall into either the Neoteleostei or the Ostariophysi [1]
This work represents the largest currently available collection of genomic data for a member of the Esociformes and the first genome assembly for a non-salmonid member of the Protacanthopterygii, an economically important superorder which bridges the evolutionary gap between the Ostariophysi and Neoteleostei
Summary
Of the nine currently available teleost genome assemblies (www. ensembl.org), all fall into either the Neoteleostei or the Ostariophysi [1]. Ensembl.org), all fall into either the Neoteleostei or the Ostariophysi [1]. This is not necessarily surprising as combined these two clades comprise more than 70% of the approximately 26,840 extant teleost species [2]. Other groups contain a number of commercially important species and receive a significant amount of scientific attention. This observation is true of the Protacanthopterygii (the salmonids, esocids and marine smelts) [2]. The Protacanthopterygii are placed in an interesting evolutionary position, having diverged from the Neoteleostei approximately 200 million years ago (MYA). The generation of a genome sequence representing the Protacanthopterygii provides an intermediate phylogenetic branch of significant scientific interest
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