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

[1]  B. Koop,et al.  Genomics of sablefish (Anoplopoma fimbria): expressed genes, mitochondrial phylogeny, linkage map and identification of a putative sex gene , 2013, BMC Genomics.

[2]  J. A. Luckenbach,et al.  Molecular cloning, characterization, and sexually dimorphic expression of five major sex differentiation-related genes in a Scorpaeniform fish, sablefish (Anoplopoma fimbria). , 2013, Comparative biochemistry and physiology. Part B, Biochemistry & molecular biology.

[3]  V. Loeschcke,et al.  Permanent Genetic Resources added to Molecular Ecology Resources Database 1 August 2012 – 30 September 2012 , 2013, Molecular ecology resources.

[4]  R. Guyomard,et al.  The sexually dimorphic on the Y-chromosome gene (sdY) is a conserved male-specific Y-chromosome sequence in many salmonids , 2012, Evolutionary applications.

[5]  A. Meyer,et al.  Horizontal Transfers of Tc1 Elements between Teleost Fishes and Their Vertebrate Parasites, Lampreys , 2012, Genome biology and evolution.

[6]  R. Guyomard,et al.  An Immune-Related Gene Evolved into the Master Sex-Determining Gene in Rainbow Trout, Oncorhynchus mykiss , 2012, Current Biology.

[7]  Peter C. Wainwright,et al.  Resolution of ray-finned fish phylogeny and timing of diversification , 2012, Proceedings of the National Academy of Sciences.

[8]  F. J. García‐de‐León,et al.  Population structure of sablefish Anoplopoma fimbria using genetic variability and geometric morphometric analysis , 2012 .

[9]  S. Brenner,et al.  A Trans-Species Missense SNP in Amhr2 Is Associated with Sex Determination in the Tiger Pufferfish, Takifugu rubripes (Fugu) , 2012, PLoS genetics.

[10]  A. Fujiyama,et al.  Tracing the Emergence of a Novel Sex-Determining Gene in Medaka, Oryzias luzonensis , 2012, Genetics.

[11]  R. Phillips,et al.  The sablefish (Anoplopoma fimbria) karyotype including the location of 5S and 18S rDNA and information on cell culture conditions , 2012 .

[12]  J. I. Fernandino,et al.  A Y-linked anti-Müllerian hormone duplication takes over a critical role in sex determination , 2012, Proceedings of the National Academy of Sciences.

[13]  C. Saski,et al.  Isolation and characterization of 12 microsatellites for the commercially important sablefish, Anoplopoma fimbria , 2012, Conservation Genetics Resources.

[14]  M. Luo,et al.  A Second Generation Integrated Map of the Rainbow Trout (Oncorhynchus mykiss) Genome: Analysis of Conserved Synteny with Model Fish Genomes , 2012, Marine Biotechnology.

[15]  C. Couch,et al.  A Microsatellite Linkage Map of Striped Bass (Morone saxatilis) Reveals Conserved Synteny with the Three-Spined Stickleback (Gasterosteus aculeatus) , 2012, Marine Biotechnology.

[16]  S. Omholt,et al.  A dense SNP-based linkage map for Atlantic salmon (Salmo salar) reveals extended chromosome homeologies and striking differences in sex-specific recombination patterns , 2011, BMC Genomics.

[17]  B. Koop,et al.  Assessment of population structure in Pacific Lepeophtheirus salmonis (Krøyer) using single nucleotide polymorphism and microsatellite genetic markers , 2011 .

[18]  Xianhu Zheng,et al.  A genetic linkage map and comparative genome analysis of common carp (Cyprinus carpio L.) using microsatellites and SNPs , 2011, Molecular Genetics and Genomics.

[19]  A. Amores,et al.  Stacks: Building and Genotyping Loci De Novo From Short-Read Sequences , 2011, G3: Genes | Genomes | Genetics.

[20]  A. Amores,et al.  Genome Evolution and Meiotic Maps by Massively Parallel DNA Sequencing: Spotted Gar, an Outgroup for the Teleost Genome Duplication , 2011, Genetics.

[21]  M. Blaxter,et al.  Genome-wide genetic marker discovery and genotyping using next-generation sequencing , 2011, Nature Reviews Genetics.

[22]  Robert J. Elshire,et al.  A Robust, Simple Genotyping-by-Sequencing (GBS) Approach for High Diversity Species , 2011, PloS one.

[23]  Carl Kingsford,et al.  A fast, lock-free approach for efficient parallel counting of occurrences of k-mers , 2011, Bioinform..

[24]  F. Le Gac,et al.  The gsdf gene locus harbors evolutionary conserved and clustered genes preferentially expressed in fish previtellogenic oocytes. , 2011, Gene.

[25]  S. Kalinowski,et al.  Permanent Genetic Resources added to Molecular Ecology Resources Database 1 August 2010 – 30 September 2010 , 2011, Molecular ecology resources.

[26]  Mary Goldman,et al.  The UCSC Genome Browser database: update 2011 , 2010, Nucleic Acids Res..

[27]  Y. Izutsu,et al.  Opposite roles of DMRT1 and its W-linked paralogue, DM-W, in sexual dimorphism of Xenopus laevis: implications of a ZZ/ZW-type sex-determining system , 2010, Development.

[28]  Huanming Yang,et al.  De novo assembly of human genomes with massively parallel short read sequencing. , 2010, Genome research.

[29]  Dan G. Bock,et al.  Permanent Genetic Resources added to Molecular Ecology Resources Database 1 August 2009–30 September 2009 , 2010, Molecular ecology resources.

[30]  Feng Liu,et al.  A consensus linkage map of the grass carp (Ctenopharyngodon idella) based on microsatellites and SNPs , 2010, BMC Genomics.

[31]  J. Inoue,et al.  Divergence time of the two regional medaka populations in Japan as a new time scale for comparative genomics of vertebrates , 2009, Biology Letters.

[32]  A. Sinclair,et al.  The avian Z-linked gene DMRT1 is required for male sex determination in the chicken , 2009, Nature.

[33]  Z. Sha,et al.  Construction of Genetic Linkage Maps and Comparative Genome Analysis of Catfish Using Gene-Associated Markers , 2009, Genetics.

[34]  M. Miya,et al.  Stickleback phylogenies resolved: evidence from mitochondrial genomes and 11 nuclear genes. , 2009, Molecular phylogenetics and evolution.

[35]  M. Shapiro,et al.  Turnover of Sex Chromosomes in the Stickleback Fishes (Gasterosteidae) , 2009, PLoS genetics.

[36]  Y. Palti,et al.  A second generation genetic map for rainbow trout (Oncorhynchus mykiss) , 2008, BMC Genetics.

[37]  Richard A. Moore,et al.  A salmonid EST genomic study: genes, duplications, phylogeny and microarrays , 2008, BMC Genomics.

[38]  J. Inoue,et al.  Interrelationships of the 11 gasterosteiform families (sticklebacks, pipefishes, and their relatives): a new perspective based on whole mitogenome sequences from 75 higher teleosts. , 2008, Molecular phylogenetics and evolution.

[39]  S. Omholt,et al.  A linkage map of the Atlantic salmon (Salmo salar) based on EST-derived SNP markers , 2008, BMC Genomics.

[40]  E. Sarropoulou,et al.  Linking the Genomes of Nonmodel Teleosts Through Comparative Genomics , 2008, Marine Biotechnology.

[41]  T. Kocher,et al.  Comparative Genomics and Positional Cloning , 2007 .

[42]  B. Koop,et al.  Bursts and horizontal evolution of DNA transposons in the speciation of pseudotetraploid salmonids , 2007, BMC Genomics.

[43]  M. Reith,et al.  A Genetic Linkage Map of Atlantic Halibut (Hippoglossus hippoglossus L.) , 2007, Genetics.

[44]  David Haussler,et al.  The UCSC genome browser database: update 2007 , 2006, Nucleic Acids Res..

[45]  Zhanjiang Liu Aquaculture genome technologies , 2007 .

[46]  G. Yoshizaki,et al.  A novel transforming growth factor-beta superfamily member expressed in gonadal somatic cells enhances primordial germ cell and spermatogonial proliferation in rainbow trout (Oncorhynchus mykiss). , 2007, Developmental biology.

[47]  H. Imamura,et al.  Revisiting recent phylogenetic studies of “Scorpaeniformes” , 2007, Ichthyological Research.

[48]  L. Bargelloni,et al.  A Genetic Linkage Map of the Hermaphrodite Teleost Fish Sparus aurata L. , 2006, Genetics.

[49]  Robert K. Jansen,et al.  Automatic annotation of organellar genomes with DOGMA , 2004, Bioinform..

[50]  Charles E. Chapple,et al.  Genome duplication in the teleost fish Tetraodon nigroviridis reveals the early vertebrate proto-karyotype , 2004, Nature.

[51]  J. F. Cordes,et al.  DNA marker technologies and their applications in aquaculture genetics. , 2004 .

[52]  R. Myers,et al.  The Master Sex-Determination Locus in Threespine Sticklebacks Is on a Nascent Y Chromosome , 2004, Current Biology.

[53]  Ward C Wheeler,et al.  Polyphyly of the mail-cheeked fishes (Teleostei: Scorpaeniformes): evidence from mitochondrial and nuclear sequence data. , 2004, Molecular phylogenetics and evolution.

[54]  J. Schein,et al.  Development and application of a salmonid EST database and cDNA microarray: data mining and interspecific hybridization characteristics. , 2004, Genome research.

[55]  Z. Liua,et al.  DNA marker technologies and their applications in aquaculture genetics , 2004 .

[56]  G. Barlow,et al.  Fishes of the world , 2004, Environmental Biology of Fishes.

[57]  S. Lukyanov,et al.  Suppression subtractive hybridization. , 2004, Methods in molecular biology.

[58]  Tadashi Sato,et al.  Oryzias curvinotus Has DMY, a Gene That Is Required for Male Development in the Medaka, O. latipes , 2003, Zoological science.

[59]  M. Yabe,et al.  Demise of the Scorpaeniformes (Actinopterygii: Percomorpha):An Alternative Phylogenetic Hypothesis , 2002 .

[60]  Tom H. Pringle,et al.  The human genome browser at UCSC. , 2002, Genome research.

[61]  Shuichi Asakawa,et al.  DMY is a Y-specific DM-domain gene required for male development in the medaka fish , 2002, Nature.

[62]  J. Postlethwait,et al.  Sex-specific recombination rates in zebrafish (Danio rerio). , 2002, Genetics.

[63]  R. Voorrips MapChart: software for the graphical presentation of linkage maps and QTLs. , 2002, The Journal of heredity.

[64]  S. L. Pereira Mitochondrial genome organization and vertebrate phylogenetics , 2000 .

[65]  S Rozen,et al.  Primer3 on the WWW for general users and for biologist programmers. , 2000, Methods in molecular biology.

[66]  M. Miya,et al.  Organization of the Mitochondrial Genome of a Deep-Sea Fish, Gonostoma gracile (Teleostei: Stomiiformes): First Example of Transfer RNA Gene Rearrangements in Bony Fishes , 1999, Marine Biotechnology.

[67]  G. Benson,et al.  Tandem repeats finder: a program to analyze DNA sequences. , 1999, Nucleic acids research.

[68]  P. Green,et al.  Base-calling of automated sequencer traces using phred. I. Accuracy assessment. , 1998, Genome research.

[69]  P Green,et al.  Base-calling of automated sequencer traces using phred. II. Error probabilities. , 1998, Genome research.

[70]  T. Crease,et al.  Identification of two QTL influencing upper temperature tolerance in three rainbow trout (Oncorhynchus mykiss) half-sib families , 1998, Heredity.

[71]  S. Lukyanov,et al.  An improved PCR method for walking in uncloned genomic DNA. , 1995, Nucleic acids research.

[72]  D. F. Alderdice,et al.  Preliminary trials on incubation of sablefish eggs (Anoplopoma fimbria) , 1988 .

[73]  M. Allen,et al.  Atlas and zoogeography of common fishes in the Bering Sea and Northeastern Pacific , 1988 .

[74]  J. Sambrook,et al.  Molecular Cloning: A Laboratory Manual , 2001 .