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

BMC Genomics

Research Article

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

[1] Department of Biology, Centre for Biomedical Research, University of Victoria, V8W 3N5, Victoria, British Columbia, Canada;Sablefish Canada Ltd, 335 Walkers Hook Rd, V8K 1N7, Salt Spring Island, British Columbia, Canada;

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

DOI  :  10.1186/1471-2164-14-452

 received in 2013-02-21, accepted in 2013-06-18,  发布年份 2013

来源: Springer

【 摘 要 】

BackgroundThe 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.ResultsA 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.ConclusionsThe 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.

【 授权许可】

Unknown   
© Rondeau et al.; licensee BioMed Central Ltd. 2013. This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.