Construction of Ultradense Linkage Maps with Lep-MAP2: Stickleback F2 Recombinant Crosses as an Example
暂无分享,去创建一个
Pasi Rastas | Juha Merilä | Baocheng Guo | F. Calboli | P. Rastas | Baocheng Guo | J. Merilä | T. Shikano | Federico C F Calboli | Takahito Shikano | Federico C. F. Calboli
[1] Xiaowu Wang,et al. Construction and Analysis of High-Density Linkage Map Using High-Throughput Sequencing Data , 2014, PloS one.
[2] Richard Durbin,et al. Sequence analysis Fast and accurate short read alignment with Burrows – Wheeler transform , 2009 .
[3] Anete P. Souza,et al. OneMap: software for genetic mapping in outcrossing species. , 2007, Hereditas.
[4] C. Peichel,et al. Turnover of sex chromosomes and speciation in fishes , 2011, Environmental Biology of Fishes.
[5] Loretta Auvil,et al. Breakpoint regions and homologous synteny blocks in chromosomes have different evolutionary histories. , 2009, Genome research.
[6] Janna L. Fierst,et al. Using linkage maps to correct and scaffold de novo genome assemblies: methods, challenges, and computational tools , 2015, Front. Genet..
[7] L. Holm,et al. Flight‐induced changes in gene expression in the Glanville fritillary butterfly , 2015, Molecular ecology.
[8] Steven J. M. Jones,et al. Circos: an information aesthetic for comparative genomics. , 2009, Genome research.
[9] J. Merilä,et al. Molecular sexing and population genetic inference using a sex-linked microsatellite marker in the nine-spined stickleback (Pungitius pungitius) , 2011, BMC Research Notes.
[10] A. Meyer,et al. A Hybrid Genetic Linkage Map of Two Ecologically and Morphologically Divergent Midas Cichlid Fishes (Amphilophus spp.) Obtained by Massively Parallel DNA Sequencing (ddRADSeq) , 2013, G3: Genes | Genomes | Genetics.
[11] R. Hudson,et al. Inferring the evolutionary histories of the Adh and Adh-dup loci in Drosophila melanogaster from patterns of polymorphism and divergence. , 1991, Genetics.
[12] Katsutoshi Watanabe,et al. A RAD-based linkage map and comparative genomics in the gudgeons (genus Gnathopogon, Cyprinidae) , 2013, BMC Genomics.
[13] T. Lenormand. The evolution of sex dimorphism in recombination. , 2003, Genetics.
[14] A. Amores,et al. Rapid and cost-effective polymorphism identification and genotyping using restriction site associated DNA (RAD) markers. , 2007, Genome research.
[15] J. Slate,et al. Gene mapping in the wild with SNPs: guidelines and future directions , 2009, Genetica.
[16] W. Cresko,et al. Extensive linkage disequilibrium and parallel adaptive divergence across threespine stickleback genomes , 2012, Philosophical Transactions of the Royal Society B: Biological Sciences.
[17] R. Myers,et al. The Master Sex-Determination Locus in Threespine Sticklebacks Is on a Nascent Y Chromosome , 2004, Current Biology.
[18] S. Brenner,et al. Integration of the Genetic Map and Genome Assembly of Fugu Facilitates Insights into Distinct Features of Genome Evolution in Teleosts and Mammals , 2011, Genome biology and evolution.
[19] J. Mank,et al. Evolutionary Diversity and Turn-Over of Sex Determination in Teleost Fishes , 2009, Sexual Development.
[20] D. Absher,et al. A role for a neo-sex chromosome in stickleback speciation , 2009, Nature.
[21] J. V. Ooijen,et al. Multipoint maximum likelihood mapping in a full-sib family of an outbreeding species. , 2011 .
[22] J. Taggart,et al. A simplified protocol for routine total DNA isolation from salmonid fishes , 1992 .
[23] V. Bafna,et al. Evidence for large inversion polymorphisms in the human genome from HapMap data. , 2007, Genome research.
[24] Petri Auvinen,et al. Lep-MAP: fast and accurate linkage map construction for large SNP datasets , 2013, Bioinform..
[25] P. Etter,et al. RAD paired-end sequencing for local de novo assembly and SNP discovery in non-model organisms. , 2012, Methods in molecular biology.
[26] J. Volff,et al. Governing Sex Determination in Fish: Regulatory Putsches and Ephemeral Dictators , 2007, Sexual Development.
[27] A. Auton,et al. Recombination rate estimation in the presence of hotspots. , 2007, Genome research.
[28] J. B. Walsh,et al. Effects of linkage on rates of molecular evolution. , 1988, Proceedings of the National Academy of Sciences of the United States of America.
[29] J. Ott,et al. Strategies for multilocus linkage analysis in humans. , 1984, Proceedings of the National Academy of Sciences of the United States of America.
[30] John H Postlethwait,et al. The zebrafish gene map defines ancestral vertebrate chromosomes. , 2005, Genome research.
[31] K. H. Wolfe,et al. Rearrangement rate following the whole-genome duplication in teleosts. , 2006, Molecular biology and evolution.
[32] Gonçalo R. Abecasis,et al. The Sequence Alignment/Map format and SAMtools , 2009, Bioinform..
[33] Richard G. F. Visser,et al. SMOOTH: a statistical method for successful removal of genotyping errors from high-density genetic linkage data , 2005, Theoretical and Applied Genetics.
[34] J. Merilä. Nine‐spined stickleback (Pungitius pungitius): an emerging model for evolutionary biology research , 2013, Annals of the New York Academy of Sciences.
[35] L. Feuk,et al. Discovery of Human Inversion Polymorphisms by Comparative Analysis of Human and Chimpanzee DNA Sequence Assemblies , 2005, PLoS genetics.
[36] J. Vilkki,et al. Genetic Architecture of Parallel Pelvic Reduction in Ninespine Sticklebacks , 2013, G3: Genes, Genomes, Genetics.
[37] Chunfa Tong,et al. A hidden Markov model approach to multilocus linkage analysis in a full-sib family , 2010, Tree Genetics & Genomes.
[38] F. Huntingford,et al. Biology of the Three-Spined Stickleback , 2006 .
[39] Ian Mayer,et al. The Molecular Genetics of Evolutionary Change in Sticklebacks , 2006 .
[40] R. Wootton. The Darwinian stickleback Gasterosteus aculeatus: a history of evolutionary studies. , 2009, Journal of fish biology.
[41] P. Hedrick. SEX: DIFFERENCES IN MUTATION, RECOMBINATION, SELECTION, GENE FLOW, AND GENETIC DRIFT , 2007, Evolution; international journal of organic evolution.
[42] Heini M. Natri,et al. Progressive Recombination Suppression and Differentiation in Recently Evolved Neo-sex Chromosomes , 2013, Molecular biology and evolution.
[43] J. Dutheil,et al. Recombination Difference between Sexes: A Role for Haploid Selection , 2005, PLoS biology.
[44] D. Weigel,et al. Genetic linkage map of the guppy, Poecilia reticulata, and quantitative trait loci analysis of male size and colour variation , 2009, Proceedings of the Royal Society B: Biological Sciences.
[45] Richard G. F. Visser,et al. RECORD: a novel method for ordering loci on a genetic linkage map , 2005, Theoretical and Applied Genetics.
[46] M. Schartl,et al. Sex Determination and Sex Chromosome Evolution: Insights from Medaka , 2009, Sexual Development.
[47] Alex A. Pollen,et al. The genomic basis of adaptive evolution in threespine sticklebacks , 2012, Nature.
[48] S. Khoo,et al. A microsatellite linkage map of rainbow trout (Oncorhynchus mykiss) characterized by large sex-specific differences in recombination rates. , 2000, Genetics.
[49] W. G. Hill,et al. The effect of linkage on limits to artificial selection. , 1966, Genetical research.
[50] M. Kirkpatrick. How and Why Chromosome Inversions Evolve , 2010, PLoS biology.
[51] Richard G. F. Visser,et al. RECORD: a novel method for ordering loci on a genetic linkage map , 2005, Theoretical and Applied Genetics.
[52] Fumiko Ohta,et al. The medaka draft genome and insights into vertebrate genome evolution , 2007, Nature.
[53] B. May,et al. Breeding new strains of tilapia : development of an artificial center of origin and linkage map based on AFLP and microsatellite loci , 2000 .
[54] Frédéric J. J. Chain,et al. Genomic divergence between nine- and three-spined sticklebacks , 2013, BMC Genomics.
[55] M. Matz,et al. Construction of a high-resolution genetic linkage map and comparative genome analysis for the reef-building coral Acropora millepora , 2009, Genome Biology.
[56] Raed I. Seetan,et al. A radiation hybrid map of chromosome 1D reveals synteny conservation at a wheat speciation locus , 2013, Functional & Integrative Genomics.
[57] M. Kendall. A NEW MEASURE OF RANK CORRELATION , 1938 .
[58] J C Murray,et al. Pediatrics and , 1998 .
[59] K. Crandall,et al. Recombination in evolutionary genomics. , 2002, Annual review of genetics.
[60] Andreas R. Pfenning,et al. Comparative genomics reveals insights into avian genome evolution and adaptation , 2014, Science.
[61] M. Shapiro,et al. The Genetic Architecture of Skeletal Convergence and Sex Determination in Ninespine Sticklebacks , 2009, Current Biology.
[62] P. J. Park,et al. The World's Oldest Fossil Threespine Stickleback Fish , 2009, Copeia.
[63] G. Coop,et al. Scrambling Eggs: Meiotic Drive and the Evolution of Female Recombination Rates , 2011, Genetics.
[64] Leonid Kruglyak,et al. The use of a genetic map of biallelic markers in linkage studies , 1997, Nature Genetics.
[65] G. Martin,et al. High density molecular linkage maps of the tomato and potato genomes. , 1992, Genetics.
[66] J. V. van Ooijen. Multipoint maximum likelihood mapping in a full-sib family of an outbreeding species. , 2011, Genetics research.
[67] B. Charlesworth. Sex Determination: Primitive Y Chromosomes in Fish , 2004, Current Biology.
[68] S. Otto,et al. Evolution of sex: Resolving the paradox of sex and recombination , 2002, Nature Reviews Genetics.
[69] M. Shapiro,et al. Turnover of Sex Chromosomes in the Stickleback Fishes (Gasterosteidae) , 2009, PLoS genetics.
[70] P. Nosil,et al. Theoretical models of the influence of genomic architecture on the dynamics of speciation , 2014, Molecular ecology.
[71] J. Postlethwait,et al. Sex-specific recombination rates in zebrafish (Danio rerio). , 2002, Genetics.
[72] F B Christiansen,et al. Population genetic perspectives on the evolution of recombination. , 1996, Annual review of genetics.
[73] M. Goddard,et al. Mapping genes for complex traits in domestic animals and their use in breeding programmes , 2009, Nature Reviews Genetics.
[74] S. Xu,et al. Meiosis and the evolution of recombination at low mutation rates. , 2000, Genetics.
[75] D. Rokhsar,et al. Genome Assembly Improvement and Mapping Convergently Evolved Skeletal Traits in Sticklebacks with Genotyping-by-Sequencing , 2015, G3: Genes, Genomes, Genetics.
[76] Riccardo Velasco,et al. Genetic Mapping in the Presence of Genotyping Errors , 2007, Genetics.
[77] Rob J. Kulathinal,et al. The Genomics of Speciation in Drosophila: Diversity, Divergence, and Introgression Estimated Using Low-Coverage Genome Sequencing , 2009, PLoS genetics.
[78] G. Bell,et al. Sex differences in recombination , 1991 .
[79] J. Mank,et al. Evolution of alternative sex-determining mechanisms in teleost fishes , 2006 .
[80] D. Absher,et al. Population genomics of parallel phenotypic evolution in stickleback across stream–lake ecological transitions , 2012, Proceedings of the Royal Society B: Biological Sciences.
[81] J. Vilkki,et al. Quantitative trait loci for growth and body size in the nine‐spined stickleback Pungitius pungitius L. , 2013, Molecular ecology.
[82] Jonathan Flint,et al. Genetic architecture of quantitative traits in mice, flies, and humans. , 2009, Genome research.
[83] Heini M. Natri,et al. High degree of sex chromosome differentiation in stickleback fishes , 2011, BMC Genomics.
[84] Eric S. Lander,et al. Resolution of quantitative traits into Mendelian factors by using a complete linkage map of restriction fragment length polymorphisms , 1988, Nature.
[85] S. Yeaman. Genomic rearrangements and the evolution of clusters of locally adaptive loci , 2013, Proceedings of the National Academy of Sciences.
[86] S. Foster,et al. The Evolutionary biology of the threespine stickleback , 1995 .
[87] J. Merilä,et al. Utility of sequenced genomes for microsatellite marker development in non-model organisms: a case study of functionally important genes in nine-spined sticklebacks (Pungitius pungitius) , 2010, BMC Genomics.
[88] H. Rundle,et al. Speciation in nature : the threespine stickleback model systems , 2002 .
[89] K. Ocalewicz,et al. Heteromorphic sex chromosomes in the ninespine stickleback Pungitius pungitius , 2008 .
[90] M. Miya,et al. Stickleback phylogenies resolved: evidence from mitochondrial genomes and 11 nuclear genes. , 2009, Molecular phylogenetics and evolution.