Open Access Highly Accessed Research article

Genomics of sablefish (Anoplopoma fimbria): expressed genes, mitochondrial phylogeny, linkage map and identification of a putative sex gene

Eric B Rondeau1, Amber M Messmer1, Dan S Sanderson1, Stuart G Jantzen1, Kristian R von Schalburg1, David R Minkley1, Jong S Leong1, Graham M Macdonald1, Amanda E Davidsen1, William A Parker1, Rosetta SA Mazzola1, Briony Campbell2 and Ben F Koop1*

Author Affiliations

1 Department of Biology, Centre for Biomedical Research, University of Victoria, Victoria, British Columbia V8W 3N5, Canada

2 Sablefish Canada Ltd, 335 Walkers Hook Rd., Salt Spring Island, British Columbia V8K 1N7, Canada

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BMC Genomics 2013, 14:452  doi:10.1186/1471-2164-14-452

Published: 6 July 2013

Abstract

Background

The sablefish (order: Scorpaeniformes) is an economically important species in commercial fisheries of the North Pacific and an emerging species in aquaculture. Aside from a handful of sequences in NCBI and a few published microsatellite markers, little is known about the genetics of this species. The development of genetic tools, including polymorphic markers and a linkage map will allow for the successful development of future broodstock and mapping of phenotypes of interest. The significant sexual dimorphism between females and males makes a genetic test for early identification of sex desirable.

Results

A full mitochondrial genome is presented and the resulting phylogenetic analysis verifies the placement of the sablefish within the Scorpaeniformes. Nearly 35,000 assembled transcript sequences are used to identify genes and obtain polymorphic SNP and microsatellite markers. 360 transcribed polymorphic loci from two sablefish families produce a map of 24 linkage groups. The sex phenotype maps to sablefish LG14 of the male map. We show significant conserved synteny and conservation of gene-order between the threespine stickleback Gasterosteus aculeatus and sablefish. An additional 1843 polymorphic SNP markers are identified through next-generation sequencing techniques. Sex-specific markers and sequence insertions are identified immediately upstream of the gene gonadal-soma derived factor (gsdf), the master sex determinant locus in the medaka species Oryzias luzonensis.

Conclusions

The first genomic resources for sablefish provide a foundation for further studies. Over 35,000 transcripts are presented, and the genetic map represents, as far as we can determine, the first linkage map for a member of the Scorpaeniformes. The observed level of conserved synteny and comparative mapping will allow the use of the stickleback genome in future genetic studies on sablefish and other related fish, particularly as a guide to whole-genome assembly. The identification of sex-specific insertions immediately upstream of a known master sex determinant implicates gsdf as an excellent candidate for the master sex determinant for sablefish.

Keywords:
Sablefish; Black cod; Microsatellite; SNP; Linkage map; Conserved synteny; Threespine stickleback; Sex-specific sequences; Gonadal soma-derived factor