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Bovine: the companion papers for the publication of the bovine genome sequence

Collection published: 24 April 2009

Last updated: 23 February 2011

The cow (Bos taurus) is an important model organism for biomedical research and development, in addition to being agriculturally important. This special series of companion papers includes work from both the Bovine Genome Sequencing and Analysis Consortium and the Bovine HapMap Consortium.

		Research article Genomic characteristics of cattle copy number variations Yali Hou, George E Liu, Derek M Bickhart, Maria Cardone, Kai Wang, Eui-soo Kim, Lakshmi K Matukumalli, Mario Ventura, Jiuzhou Song, Paul M VanRaden, Tad S Sonstegard, Curt P Van Tassell BMC Genomics 2011, 12:127 (23 February 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
		Research Whole genome sequencing of a single Bos taurus animal for single nucleotide polymorphism discovery Sebastian H Eck, Anna Benet-Pagès, Krzysztof Flisikowski, Thomas Meitinger, Ruedi Fries, Tim M Strom Genome Biology 2009, 10:R82 (6 August 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The next generation sequencing of a single cow genome with low-to-medium coverage has revealed 2.44 million new SNPs.
		Research article Characterization of the prohormone complement in cattle using genomic libraries and cleavage prediction approaches Bruce R Southey, Sandra L Rodriguez-Zas, Jonathan V Sweedler BMC Genomics 2009, 10:228 (16 May 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
		Research article Bos taurus genome sequence reveals the assortment of immunoglobulin and surrogate light chain genes in domestic cattle Anna Ekman, Mikael Niku, Jenni Liljavirta, Antti Iivanainen BMC Immunology 2009, 10:22 (30 April 2009) Abstract \| Full text \| PDF \| PubMed
		Research The bovine lactation genome: insights into the evolution of mammalian milk Danielle G Lemay, David J Lynn, William F Martin, Margaret C Neville, Theresa M Casey, Gonzalo Rincon, Evgenia V Kriventseva, Wesley C Barris, Angie S Hinrichs, Adrian J Molenaar, Katherine S Pollard, Nauman J Maqbool, Kuljeet Singh, Regan Murney, Evgeny M Zdobnov, Ross L Tellam, Juan F Medrano, J Bruce German, Monique Rijnkels Genome Biology 2009, 10:R43 (24 April 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Comparison of milk protein and mammary genes in the bovine genome with those from other mammals gives insights into the evolution of lactation.
		Research article Gene synteny comparisons between different vertebrates provide new insights into breakage and fusion events during mammalian karyotype evolution Claus Kemkemer, Matthias Kohn, David N Cooper, Lutz Froenicke, Josef Högel, Horst Hameister, Hildegard Kehrer-Sawatzki BMC Evolutionary Biology 2009, 9:84 (24 April 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
		Commentary Unlocking the bovine genome Ross L Tellam, Danielle G Lemay, Curtis P Van Tassell, Harris A Lewin, Kim C Worley, Christine G Elsik BMC Genomics 2009, 10:193 (24 April 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary An extensive collaboration involving over 300 scientists from 25 different countries has analyzed the draft genome sequence of cattle, yielding insights into ruminant evolution and domestication and providing an invaluable research resource for the beef and dairy industries.
		Research article Genomic analysis reveals extensive gene duplication within the bovine TRB locus Timothy Connelley, Jan Aerts, Andy Law, W Ivan Morrison BMC Genomics 2009, 10:192 (24 April 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
		Research article Genomic organization and classification of the bovine WC1 genes and expression by peripheral blood gamma delta T cells Carolyn TA Herzig, Cynthia L Baldwin BMC Genomics 2009, 10:191 (24 April 2009) Abstract \| Full text \| PDF \| PubMed
		Research article Transcriptional reprogramming of gene expression in bovine somatic cell chromatin transfer embryos Nelida Rodriguez-Osorio, Zhongde Wang, Poothappillai Kasinathan, Grier P Page, James M Robl, Erdogan Memili BMC Genomics 2009, 10:190 (24 April 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
		Research article High-resolution haplotype block structure in the cattle genome Rafael Villa-Angulo, Lakshmi K Matukumalli, Clare A Gill, Jungwoo Choi, Curtis P Van Tassell, John J Grefenstette BMC Genetics 2009, 10:19 (24 April 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The haplotype block structure of beef and dairy breeds of cattle are unexpectedly similar and estimates of effective population sizes reflect ancient cattle domestication and more recent population bottlenecks.
		Research article Cross-species mapping of bidirectional promoters enables prediction of unannotated 5' UTRs and identification of species-specific transcripts Helen Piontkivska, Mary Q Yang, Denis M Larkin, Harris A Lewin, James Reecy, Laura Elnitski BMC Genomics 2009, 10:189 (24 April 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Genes arranged head-to-head and sharing a common bi-directional promoter region display a conserved intergenic architecture in cows, humans and other mammals, which will help to identify regulatory regions and unrecognized genes in other mammals’ genomes.
		Research article Analysis of the complement and molecular evolution of tRNA genes in cow Dave TP Tang, Evgeny A Glazov, Sean M McWilliam, Wesley C Barris, Brian P Dalrymple BMC Genomics 2009, 10:188 (24 April 2009) Abstract \| Full text \| PDF \| PubMed
		Research article Characterization of the bovine type I IFN locus: rearrangements, expansions, and novel subfamilies Angela M Walker, R Michael Roberts BMC Genomics 2009, 10:187 (24 April 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
		Research article Novel transcripts discovered by mining genomic DNA from defined regions of bovine chromosome 6 Rosemarie Weikard, Tom Goldammer, Annett Eberlein, Christa Kuehn BMC Genomics 2009, 10:186 (24 April 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
		Research article Characterization of the bovine pregnancy-associated glycoprotein gene family – analysis of gene sequences, regulatory regions within the promoter and expression of selected genes Bhanu Telugu, Angela M Walker, Jonathan A Green BMC Genomics 2009, 10:185 (24 April 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
		Research article QTL global meta-analysis: are trait determining genes clustered? Hanni Salih, David L Adelson BMC Genomics 2009, 10:184 (24 April 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
		Research article Functional genomics of HMGN3a and SMARCAL1 in early mammalian embryogenesis Alper Uzun, Nelida Rodriguez-Osorio, Abdullah Kaya, Hongfeng Wang, John J Parrish, Valentin A Ilyin, Erdogan Memili BMC Genomics 2009, 10:183 (24 April 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
		Research article A high resolution RH map of the bovine major histocompatibility complex Candice L Brinkmeyer-Langford, Christopher P Childers, Krista L Fritz, Ashley L Gustafson-Seabury, Marian Cothran, Terje Raudsepp, James E Womack, Loren C Skow BMC Genomics 2009, 10:182 (24 April 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
		Research article An examination of positive selection and changing effective population size in Angus and Holstein cattle populations (Bos taurus) using a high density SNP genotyping platform and the contribution of ancient polymorphism to genomic diversity in Domestic cattle Sean MacEachern, Ben Hayes, John McEwan, Mike Goddard BMC Genomics 2009, 10:181 (24 April 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
		Research article Bos taurus genome assembly Yue Liu, Xiang Qin, Xing-Zhi Song, Huaiyang Jiang, Yufeng Shen, K James Durbin, Sigbjørn Lien, Matthew Kent, Marte Sodeland, Yanru Ren, Lan Zhang, Erica Sodergren, Paul Havlak, Kim C Worley, George M Weinstock, Richard A Gibbs BMC Genomics 2009, 10:180 (24 April 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The assembly of the bovine genome used both bacterial artificial chromosome (BAC) and whole genome shotgun (WGS) sequences, exploiting the strengths of each to provide a more accurate and comprehensive coverage of the genome.
		Research article A high density linkage map of the bovine genome Juan A Arias, Mike Keehan, Paul Fisher, Wouter Coppieters, Richard Spelman BMC Genetics 2009, 10:18 (24 April 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
		Research article Molecular evolution of the Bovini tribe (Bovidae, Bovinae): Is there evidence of rapid evolution or reduced selective constraint in Domestic cattle? Sean MacEachern, John McEwan, Alan McCulloch, Andrew Mather, Keith Savin, Mike Goddard BMC Genomics 2009, 10:179 (24 April 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
		Research article Genome wide signatures of positive selection: The comparison of independent samples and the identification of regions associated to traits William Barendse, Blair E Harrison, Rowan J Bunch, Merle B Thomas, Lex B Turner BMC Genomics 2009, 10:178 (24 April 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
		Research article Phylogenetic reconstruction and the identification of ancient polymorphism in the Bovini tribe (Bovidae, Bovinae) Sean MacEachern, John McEwan, Mike Goddard BMC Genomics 2009, 10:177 (24 April 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
		Research article Two-stage genome-wide association study identifies integrin beta 5 as having potential role in bull fertility Jean M Feugang, Abdullah Kaya, Grier P Page, Lang Chen, Tapan Mehta, Kashif Hirani, Lynne Nazareth, Einko Topper, Richard Gibbs, Erdogan Memili BMC Genomics 2009, 10:176 (24 April 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central

		Research article Genomic characteristics of cattle copy number variations Yali Hou, George E Liu, Derek M Bickhart, Maria Cardone, Kai Wang, Eui-soo Kim, Lakshmi K Matukumalli, Mario Ventura, Jiuzhou Song, Paul M VanRaden, Tad S Sonstegard, Curt P Van Tassell BMC Genomics 2011, 12:127 (23 February 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
		Research Whole genome sequencing of a single Bos taurus animal for single nucleotide polymorphism discovery Sebastian H Eck, Anna Benet-Pagès, Krzysztof Flisikowski, Thomas Meitinger, Ruedi Fries, Tim M Strom Genome Biology 2009, 10:R82 (6 August 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The next generation sequencing of a single cow genome with low-to-medium coverage has revealed 2.44 million new SNPs.
		Research article Characterization of the prohormone complement in cattle using genomic libraries and cleavage prediction approaches Bruce R Southey, Sandra L Rodriguez-Zas, Jonathan V Sweedler BMC Genomics 2009, 10:228 (16 May 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
		Research article Bos taurus genome sequence reveals the assortment of immunoglobulin and surrogate light chain genes in domestic cattle Anna Ekman, Mikael Niku, Jenni Liljavirta, Antti Iivanainen BMC Immunology 2009, 10:22 (30 April 2009) Abstract \| Full text \| PDF \| PubMed
		Research The bovine lactation genome: insights into the evolution of mammalian milk Danielle G Lemay, David J Lynn, William F Martin, Margaret C Neville, Theresa M Casey, Gonzalo Rincon, Evgenia V Kriventseva, Wesley C Barris, Angie S Hinrichs, Adrian J Molenaar, Katherine S Pollard, Nauman J Maqbool, Kuljeet Singh, Regan Murney, Evgeny M Zdobnov, Ross L Tellam, Juan F Medrano, J Bruce German, Monique Rijnkels Genome Biology 2009, 10:R43 (24 April 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Comparison of milk protein and mammary genes in the bovine genome with those from other mammals gives insights into the evolution of lactation.
		Research article Gene synteny comparisons between different vertebrates provide new insights into breakage and fusion events during mammalian karyotype evolution Claus Kemkemer, Matthias Kohn, David N Cooper, Lutz Froenicke, Josef Högel, Horst Hameister, Hildegard Kehrer-Sawatzki BMC Evolutionary Biology 2009, 9:84 (24 April 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
		Commentary Unlocking the bovine genome Ross L Tellam, Danielle G Lemay, Curtis P Van Tassell, Harris A Lewin, Kim C Worley, Christine G Elsik BMC Genomics 2009, 10:193 (24 April 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary An extensive collaboration involving over 300 scientists from 25 different countries has analyzed the draft genome sequence of cattle, yielding insights into ruminant evolution and domestication and providing an invaluable research resource for the beef and dairy industries.
		Research article Genomic analysis reveals extensive gene duplication within the bovine TRB locus Timothy Connelley, Jan Aerts, Andy Law, W Ivan Morrison BMC Genomics 2009, 10:192 (24 April 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
		Research article Genomic organization and classification of the bovine WC1 genes and expression by peripheral blood gamma delta T cells Carolyn TA Herzig, Cynthia L Baldwin BMC Genomics 2009, 10:191 (24 April 2009) Abstract \| Full text \| PDF \| PubMed
		Research article Transcriptional reprogramming of gene expression in bovine somatic cell chromatin transfer embryos Nelida Rodriguez-Osorio, Zhongde Wang, Poothappillai Kasinathan, Grier P Page, James M Robl, Erdogan Memili BMC Genomics 2009, 10:190 (24 April 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
		Research article High-resolution haplotype block structure in the cattle genome Rafael Villa-Angulo, Lakshmi K Matukumalli, Clare A Gill, Jungwoo Choi, Curtis P Van Tassell, John J Grefenstette BMC Genetics 2009, 10:19 (24 April 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The haplotype block structure of beef and dairy breeds of cattle are unexpectedly similar and estimates of effective population sizes reflect ancient cattle domestication and more recent population bottlenecks.
		Research article Cross-species mapping of bidirectional promoters enables prediction of unannotated 5' UTRs and identification of species-specific transcripts Helen Piontkivska, Mary Q Yang, Denis M Larkin, Harris A Lewin, James Reecy, Laura Elnitski BMC Genomics 2009, 10:189 (24 April 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Genes arranged head-to-head and sharing a common bi-directional promoter region display a conserved intergenic architecture in cows, humans and other mammals, which will help to identify regulatory regions and unrecognized genes in other mammals’ genomes.
		Research article Analysis of the complement and molecular evolution of tRNA genes in cow Dave TP Tang, Evgeny A Glazov, Sean M McWilliam, Wesley C Barris, Brian P Dalrymple BMC Genomics 2009, 10:188 (24 April 2009) Abstract \| Full text \| PDF \| PubMed
		Research article Characterization of the bovine type I IFN locus: rearrangements, expansions, and novel subfamilies Angela M Walker, R Michael Roberts BMC Genomics 2009, 10:187 (24 April 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
		Research article Novel transcripts discovered by mining genomic DNA from defined regions of bovine chromosome 6 Rosemarie Weikard, Tom Goldammer, Annett Eberlein, Christa Kuehn BMC Genomics 2009, 10:186 (24 April 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
		Research article Characterization of the bovine pregnancy-associated glycoprotein gene family – analysis of gene sequences, regulatory regions within the promoter and expression of selected genes Bhanu Telugu, Angela M Walker, Jonathan A Green BMC Genomics 2009, 10:185 (24 April 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
		Research article QTL global meta-analysis: are trait determining genes clustered? Hanni Salih, David L Adelson BMC Genomics 2009, 10:184 (24 April 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
		Research article Functional genomics of HMGN3a and SMARCAL1 in early mammalian embryogenesis Alper Uzun, Nelida Rodriguez-Osorio, Abdullah Kaya, Hongfeng Wang, John J Parrish, Valentin A Ilyin, Erdogan Memili BMC Genomics 2009, 10:183 (24 April 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
		Research article A high resolution RH map of the bovine major histocompatibility complex Candice L Brinkmeyer-Langford, Christopher P Childers, Krista L Fritz, Ashley L Gustafson-Seabury, Marian Cothran, Terje Raudsepp, James E Womack, Loren C Skow BMC Genomics 2009, 10:182 (24 April 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
		Research article An examination of positive selection and changing effective population size in Angus and Holstein cattle populations (Bos taurus) using a high density SNP genotyping platform and the contribution of ancient polymorphism to genomic diversity in Domestic cattle Sean MacEachern, Ben Hayes, John McEwan, Mike Goddard BMC Genomics 2009, 10:181 (24 April 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
		Research article Bos taurus genome assembly Yue Liu, Xiang Qin, Xing-Zhi Song, Huaiyang Jiang, Yufeng Shen, K James Durbin, Sigbjørn Lien, Matthew Kent, Marte Sodeland, Yanru Ren, Lan Zhang, Erica Sodergren, Paul Havlak, Kim C Worley, George M Weinstock, Richard A Gibbs BMC Genomics 2009, 10:180 (24 April 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The assembly of the bovine genome used both bacterial artificial chromosome (BAC) and whole genome shotgun (WGS) sequences, exploiting the strengths of each to provide a more accurate and comprehensive coverage of the genome.
		Research article A high density linkage map of the bovine genome Juan A Arias, Mike Keehan, Paul Fisher, Wouter Coppieters, Richard Spelman BMC Genetics 2009, 10:18 (24 April 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
		Research article Molecular evolution of the Bovini tribe (Bovidae, Bovinae): Is there evidence of rapid evolution or reduced selective constraint in Domestic cattle? Sean MacEachern, John McEwan, Alan McCulloch, Andrew Mather, Keith Savin, Mike Goddard BMC Genomics 2009, 10:179 (24 April 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
		Research article Genome wide signatures of positive selection: The comparison of independent samples and the identification of regions associated to traits William Barendse, Blair E Harrison, Rowan J Bunch, Merle B Thomas, Lex B Turner BMC Genomics 2009, 10:178 (24 April 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
		Research article Phylogenetic reconstruction and the identification of ancient polymorphism in the Bovini tribe (Bovidae, Bovinae) Sean MacEachern, John McEwan, Mike Goddard BMC Genomics 2009, 10:177 (24 April 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
		Research article Two-stage genome-wide association study identifies integrin beta 5 as having potential role in bull fertility Jean M Feugang, Abdullah Kaya, Grier P Page, Lang Chen, Tapan Mehta, Kashif Hirani, Lynne Nazareth, Einko Topper, Richard Gibbs, Erdogan Memili BMC Genomics 2009, 10:176 (24 April 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central