Browsing by Author "Burt, David W."

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    Multi-Platform Next-Generation Sequencing of the Domestic Turkey (Meleagris gallopavo): Genome Assembly and Analysis
    Dalloul, Rami A.; Long, Julie A.; Zimin, Aleksey V.; Aslam, Luqman; Beal, Kathryn; Blomberg, Le Ann; Bouffard, Pascal; Burt, David W.; Crasta, Oswald; Crooijmans, Richard P. M. A.; Cooper, Kristal; Coulombe, Roger A.; De, Supriyo; Delany, Mary E.; Dodgson, Jerry B.; Dong, Jennifer J.; Evans, Clive; Frederickson, Karin M.; Flicek, Paul; Florea, Liliana; Folkerts, Otto; Groenen, Martien A. M.; Harkins, Tim T.; Herrero, Javier; Hoffmann, Steve; Megens, Hendrik-Jan; Jiang, Andrew; de Jong, Pieter; Kaiser, Pete; Kim, Heebal; Kim, Kyu-Won; Kim, Sungwon; Langenberger, David; Lee, Mi-Kyung; Lee, Taeheon; Mane, Shrinivasrao P.; Marcais, Guillaume; Marz, Manja; McElroy, Audrey P.; Modise, Thero; Nefedov, Mikhail; Notredame, Cédric; Paton, Ian R.; Payne, William S.; Pertea, Geo; Prickett, Dennis; Puiu, Daniela; Qioa, Dan; Raineri, Emanuele; Ruffier, Magali; Salzberg, Steven L.; Schatz, Michael C.; Scheuring, Chantel; Schmidt, Carl J.; Schroeder, Steven; Searle, Stephen M. J.; Smith, Edward J.; Smith, Jacqueline; Sonstegard, Tad S.; Stadler, Peter F.; Tafer, Hakim; Tu, Zhijian Jake; Van Tassell, Curtis P.; Vilella, Albert J.; Williams, Kelly P.; Yorke, James A.; Zhang, Liqing; Zhang, Hong-Bin; Zhang, Xiaojun; Zhang, Yang; Reed, Kent M. (PLOS, 2010-09-01)
    A synergistic combination of two next-generation sequencing platforms with a detailed comparative BAC physical contig map provided a cost-effective assembly of the genome sequence of the domestic turkey (Meleagris gallopavo). Heterozygosity of the sequenced source genome allowed discovery of more than 600,000 high quality single nucleotide variants. Despite this heterozygosity, the current genome assembly (,1.1 Gb) includes 917 Mb of sequence assigned to specific turkey chromosomes. Annotation identified nearly 16,000 genes, with 15,093 recognized as protein coding and 611 as non-coding RNA genes. Comparative analysis of the turkey, chicken, and zebra finch genomes, and comparing avian to mammalian species, supports the characteristic stability of avian genomes and identifies genes unique to the avian lineage. Clear differences are seen in number and variety of genes of the avian immune system where expansions and novel genes are less frequent than examples of gene loss. The turkey genome sequence provides resources to further understand the evolution of vertebrate genomes and genetic variation underlying economically important quantitative traits in poultry. This integrated approach may be a model for providing both gene and chromosome level assemblies of other species with agricultural, ecological, and evolutionary interest.
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    Poultry genomics puts meat on the table.
    Smith, Edward J.; Pourquié, Olivier; Burt, David W. (2005)
    Why did the chicken cross the road, you ask? Because the draft sequence of its genome has been released, silly. So, along with other ‘bird enthusiasts’ and advocates, those long involved in chicken genetics and genetic studies of birds came to Cold Spring Harbor Laboratory (CSHL), 8–11 May 2005, for the 3rd Chicken Genomics Workshop to pat each other on the back for the recently released draft sequence (International Chicken Genome Sequencing Consortium, 2004), compare notes, review progress, and plan for the road ahead! Never mind that the meeting preceded, perhaps as a convenience or, to a cynic, just ‘being chicken’ (an inability to ‘stand alone’?), the annual ‘Biology of Genomes’ meeting: these scientists did not shy away from the ‘chicken jokes’ or from making a strong case for why their work ranks up there with other tractable biomedical models. Joking aside, many speakers at the chicken meeting also attended or were part of ‘Biology of Genomes’, so the chicken is now clearly recognized as a model genome and of great value in evolutionary comparisons. Scientific presentations included the usual staples at genome meetings, such as SNPs, sequence to function, QTL identification and expression profiling. They also included novel talks about gynandromorphs, endogenous viral elements, transgenesis, developmental mutants and signalling pathways. The gathering represented a culmination and a celebration of a vision that started with the partnership between Jerry Dodgson, Michigan State, and Lyman Crittenden, USDA–ARS, as well as the efforts of several European scientists, including the late Nat Bumstead, Martien Groenen (Wageningen) and Dave Burt (Roslin Institute). It was appropriate that the meeting ended with an exploration by the chicken community of ‘what now?