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Multi-platform next-generation sequencing of the domestic Turkey (Meleagris gallopavo): Genome assembly and analysis
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نویسنده
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dalloul r.a. ,long j.a. ,zimin a.v. ,aslam l. ,beal k. ,blomberg l.a. ,bouffard p. ,burt d.w. ,crasta o. ,crooijmans r.p.m.a. ,cooper k. ,coulombe r.a. ,de s. ,delany m.e. ,dodgson j.b. ,dong j.j. ,evans c. ,frederickson k.m. ,flicek p. ,florea l. ,folkerts o. ,groenen m.a.m. ,harkins t.t. ,herrero j. ,hoffmann s. ,megens h.-j. ,jiang a. ,de jong p. ,kaiser p. ,kim h. ,kim k.-w. ,kim s. ,langenberger d. ,lee m.-k. ,lee t. ,mane s. ,marcais g. ,marz m. ,mcelroy a.p. ,modise t. ,nefedov m. ,notredame c. ,paton i.r. ,payne w.s. ,pertea g. ,prickett d. ,puiu d. ,qioa d. ,raineri e. ,ruffier m. ,salzberg s.l. ,schatz m.c. ,scheuring c. ,schmidt c.j. ,schroeder s. ,searle s.m.j. ,smith e.j. ,smith j. ,sonstegard t.s. ,stadler p.f. ,tafer h. ,tu z. ,van tassell c.p. ,vilella a.j. ,williams k.p. ,yorke j.a. ,zhang l. ,zhang h.-b. ,zhang x. ,zhang y. ,reed k.m.
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منبع
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plos biology - 2010 - دوره : 8 - شماره : 9
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چکیده
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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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آدرس
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avian immunobiology laboratory,department of animal and poultry sciences,virginia tech,blacksburg,va, United States, animal biosciences and biotechnology laboratory,usda agricultural research service,beltsville,md, United States, institute for physical science and technology,university of maryland,college park,md, United States, animal breeding and genomics centre,wageningen university,wageningen, Netherlands, european bioinformatics institute,wellcome trust genome campus,hinxton,cambridge, United States, animal biosciences and biotechnology laboratory,usda agricultural research service,beltsville,md, United States, roche applied science,indianapolis,in, United States, the roslin institute and royal (dick) school of veterinary studies,university of edinburgh,roslin,midlothian, United Kingdom, virginia bioinformatics institute,virginia tech,blacksburg,va,united states,chromatin inc.,champaign,il, United States, animal breeding and genomics centre,wageningen university,wageningen, Netherlands, virginia bioinformatics institute,virginia tech,blacksburg,va, United States, department of veterinary sciences,utah state university,logan,ut, United States, gene expression and genomics unit,national institute on aging,national institutes of health,baltimore,md, United States, department of animal science,university of california,davis,ca, United States, department of microbiology and molecular genetics,michigan state university,east lansing,mi, United States, department of soil and crop sciences,texas a and m university,college station,tx, United States, virginia bioinformatics institute,virginia tech,blacksburg,va, United States, roche applied science,indianapolis,in, United States, european bioinformatics institute,wellcome trust genome campus,hinxton,cambridge, United States, center for bioinformatics and computational biology,university of maryland,college park,maryland, United States, virginia bioinformatics institute,virginia tech,blacksburg,va,united states,chromatin inc.,champaign,il, United States, animal breeding and genomics centre,wageningen university,wageningen, Netherlands, roche applied science,indianapolis,in, United States, european bioinformatics institute,wellcome trust genome campus,hinxton,cambridge, United States, department of computer science and interdisciplinary center for bioinformatics,university of leipzig,leipzig,germany,university of leipzig,leipzig, Germany, animal breeding and genomics centre,wageningen university,wageningen, Netherlands, department of animal science,university of california,davis,ca, United States, children's hospital and research center at oakland,oakland,ca, United States, institute for animal health,compton,berkshire, United Kingdom, laboratory of bioinformatics and population genetics,department of agricultural biotechnology,seoul national university,seoul, South Korea, laboratory of bioinformatics and population genetics,department of agricultural biotechnology,seoul national university,seoul, South Korea, avian immunobiology laboratory,department of animal and poultry sciences,virginia tech,blacksburg,va, United States, department of computer science and interdisciplinary center for bioinformatics,university of leipzig,leipzig, Germany, department of soil and crop sciences,texas a and m university,college station,tx, United States, laboratory of bioinformatics and population genetics,department of agricultural biotechnology,seoul national university,seoul, South Korea, virginia bioinformatics institute,virginia tech,blacksburg,va, United States, institute for physical science and technology,university of maryland,college park,md, United States, department of computer science and interdisciplinary center for bioinformatics,university of leipzig,leipzig,germany,philipps-universität marburg,pharmazeutische chemie,marburg, Germany, avian immunobiology laboratory,department of animal and poultry sciences,virginia tech,blacksburg,va, United States, virginia bioinformatics institute,virginia tech,blacksburg,va, United States, children's hospital and research center at oakland,oakland,ca, United States, comparative bioinformatics,centre for genomic regulation (crg),universitat pompeus fabre,barcelona, Spain, the roslin institute and royal (dick) school of veterinary studies,university of edinburgh,roslin,midlothian, United Kingdom, department of microbiology and molecular genetics,michigan state university,east lansing,mi, United States, center for bioinformatics and computational biology,university of maryland,college park,maryland, United States, institute for animal health,compton,berkshire, United Kingdom, center for bioinformatics and computational biology,university of maryland,college park,maryland, United States, department of computer science,virginia tech,blacksburg,va, United States, comparative bioinformatics,centre for genomic regulation (crg),universitat pompeus fabre,barcelona, Spain, wellcome trust sanger institute,wellcome trust genome campus,hinxton,cambridge, United Kingdom, center for bioinformatics and computational biology,department of computer science,university of maryland,college park,md, United States, center for bioinformatics and computational biology,department of computer science,university of maryland,college park,md, United States, department of soil and crop sciences,texas a and m university,college station,tx, United States, department of animal and food sciences,university of delaware,newark,delaware, United States, bovine functional genomics laboratory,usda agricultural research service,beltsville agricultural research center,beltsville,md, United States, wellcome trust sanger institute,wellcome trust genome campus,hinxton,cambridge, United Kingdom, avian immunobiology laboratory,department of animal and poultry sciences,virginia tech,blacksburg,va, United States, the roslin institute and royal (dick) school of veterinary studies,university of edinburgh,roslin,midlothian, United Kingdom, bovine functional genomics laboratory,usda agricultural research service,beltsville agricultural research center,beltsville,md, United States, department of computer science and interdisciplinary center for bioinformatics,university of leipzig,leipzig,germany,max planck institute for mathematics in the sciences,leipzig,germany,fraunhofer institut für zelltherapie und immunologie,leipzig,germany,department of theoretical chemistry,university of vienna,vienna,austria,santa fe institute,santa fe,nm, United States, department of computer science and interdisciplinary center for bioinformatics,university of leipzig,leipzig,germany,department of theoretical chemistry,university of vienna,vienna, Austria, department of biochemistry,virginia tech,blacksburg,va, United States, bovine functional genomics laboratory,usda agricultural research service,beltsville agricultural research center,beltsville,md,united states,animal improvement programs laboratory,usda agricultural research service,beltsville agricultural research center,beltsville,md, United States, european bioinformatics institute,wellcome trust genome campus,hinxton,cambridge, United States, virginia bioinformatics institute,virginia tech,blacksburg,va, United States, institute for physical science and technology,university of maryland,college park,md, United States, department of computer science,virginia tech,blacksburg,va, United States, department of soil and crop sciences,texas a and m university,college station,tx, United States, department of soil and crop sciences,texas a and m university,college station,tx, United States, department of soil and crop sciences,texas a and m university,college station,tx, United States, department of veterinary and biomedical sciences,college of veterinary medicine,university of minnesota,st. paul,mn, United States
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Authors
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