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

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dc.contributor.authorRondeau, Eric B
dc.contributor.authorMessmer, Amber M
dc.contributor.authorSanderson, Dan S
dc.contributor.authorJantzen, Stuart G
dc.contributor.authorSchalburg, Kristian R von
dc.contributor.authorMinkley, David R
dc.contributor.authorLeong, Jong S
dc.contributor.authorMacdonald, Graham M
dc.contributor.authorDavidsen, Amanda E
dc.contributor.authorParker, William A
dc.contributor.authorMazzola, Rosetta SA
dc.contributor.authorCampbell, Briony
dc.contributor.authorKoop, Ben F
dc.date.accessioned2015-03-27T19:50:48Z
dc.date.available2015-03-27T19:50:48Z
dc.date.copyright2013en_US
dc.date.issued2013-07-06
dc.descriptionBioMed Centralen_US
dc.description.abstractBackground: 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.en_US
dc.description.reviewstatusRevieweden_US
dc.description.scholarlevelFacultyen_US
dc.description.sponsorshipThis work was supported by Genome British Columbia, Sablefish Canada Ltd., the University of Victoria and NSERC Canada.en_US
dc.identifier.citationRondeau et al.: Genomics of sablefish (Anoplopoma fimbria): expressed genes, mitochondrial phylogeny, linkage map and identification of a putative sex gene. BMC Genomics 2013 14:452.en_US
dc.identifier.urihttp://www.biomedcentral.com/1471-2164/14/452
dc.identifier.urihttp://dx.doi.org/10.1186/1471-2164-14-452
dc.identifier.urihttp://hdl.handle.net/1828/5936
dc.language.isoenen_US
dc.publisherBMC Genomicsen_US
dc.rights.tempAttribution-NonCommercial-NoDerivs 2.5 Canada*
dc.rights.urihttp://creativecommons.org/licenses/by-nc-nd/2.5/ca/*
dc.subjectSablefish
dc.subjectBlack cod
dc.subjectMicrosatellite
dc.subjectSNP
dc.subjectLinkage map
dc.subjectConserved synteny
dc.subjectThreespine stickleback
dc.subjectSex-specific sequences
dc.subjectGonadal soma-derived factor
dc.subjectCentre for Biomedical Research
dc.subject.departmentDepartment of Biology
dc.titleGenomics of sablefish (Anoplopoma fimbria): expressed genes, mitochondrial phylogeny, linkage map and identification of a putative sex geneen_US
dc.typeArticleen_US

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