title: A New Chicken Genome Assembly Provides Insight into Avian Genome Structure.
abstract: The importance of the Gallus gallus (chicken) as a model organism and agricultural animal merits a continuation of sequence assembly improvement efforts. We present a new version of the chicken genome assembly (Gallus_gallus-5.0; GCA_000002315.3), built from combined long single molecule sequencing technology, finished BACs, and improved physical maps. In overall assembled bases, we see a gain of 183 Mb, including 16.4 Mb in placed chromosomes with a corresponding gain in the percentage of intact repeat elements characterized. Of the 1.21 Gb genome, we include three previously missing autosomes, GGA30, 31, and 33, and improve sequence contig length 10-fold over the previous Gallus_gallus-4.0. Despite the significant base representation improvements made, 138 Mb of sequence is not yet located to chromosomes. When annotated for gene content, Gallus_gallus-5.0 shows an increase of 4679 annotated genes (2768 noncoding and 1911 protein-coding) over those in Gallus_gallus-4.0. We also revisited the question of what genes are missing in the avian lineage, as assessed by the highest quality avian genome assembly to date, and found that a large fraction of the original set of missing genes are still absent in sequenced bird species. Finally, our new data support a detailed map of MHC-B, encompassing two segments: one with a highly stable gene copy number and another in which the gene copy number is highly variable. The chicken model has been a critical resource for many other fields of study, and this new reference assembly will substantially further these efforts.
authors.affiliation: McDonnell Genome Institute, Washington University School of Medicine, St. Louis, Missouri 63108 wwarren@wustl.edu hcheng@msu.edu.
authors.forename: Wesley C
authors.initials: WC
authors.lastname: Warren
authors.affiliation: McDonnell Genome Institute, Washington University School of Medicine, St. Louis, Missouri 63108.
authors.forename: LaDeana W
authors.initials: LW
authors.lastname: Hillier
authors.affiliation: McDonnell Genome Institute, Washington University School of Medicine, St. Louis, Missouri 63108.
authors.forename: Chad
authors.initials: C
authors.lastname: Tomlinson
authors.affiliation: McDonnell Genome Institute, Washington University School of Medicine, St. Louis, Missouri 63108.
authors.forename: Patrick
authors.initials: P
authors.lastname: Minx
authors.affiliation: McDonnell Genome Institute, Washington University School of Medicine, St. Louis, Missouri 63108.
authors.forename: Milinn
authors.initials: M
authors.lastname: Kremitzki
authors.affiliation: McDonnell Genome Institute, Washington University School of Medicine, St. Louis, Missouri 63108.
authors.forename: Tina
authors.initials: T
authors.lastname: Graves
authors.affiliation: McDonnell Genome Institute, Washington University School of Medicine, St. Louis, Missouri 63108.
authors.forename: Chris
authors.initials: C
authors.lastname: Markovic
authors.affiliation: National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894.
authors.forename: Nathan
authors.initials: N
authors.lastname: Bouk
authors.affiliation: National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894.
authors.forename: Kim D
authors.initials: KD
authors.lastname: Pruitt
authors.affiliation: National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894.
authors.forename: Francoise
authors.initials: F
authors.lastname: Thibaud-Nissen
authors.affiliation: National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894.
authors.forename: Valerie
authors.initials: V
authors.lastname: Schneider
authors.affiliation: University of California-Davis, California 95616.
authors.forename: Tamer A
authors.initials: TA
authors.lastname: Mansour
authors.affiliation: University of California-Davis, California 95616.
authors.forename: C Titus
authors.initials: CT
authors.lastname: Brown
authors.affiliation: Institute for Physical Sciences and Technology, University of Maryland, College Park, Maryland 20742.
authors.forename: Aleksey
authors.initials: A
authors.lastname: Zimin
authors.affiliation: Cobb-Vantress Inc., Siloam Springs, Arkansas 72761-1030.
authors.forename: Rachel
authors.initials: R
authors.lastname: Hawken
authors.affiliation: Cobb-Vantress Inc., Siloam Springs, Arkansas 72761-1030.
authors.forename: Mitch
authors.initials: M
authors.lastname: Abrahamsen
authors.affiliation: United States Department of Agriculture-Agricultural Research Service, Avian Disease and Oncology, East Lansing, Michigan 48823.
authors.forename: Alexis B
authors.initials: AB
authors.lastname: Pyrkosz
authors.affiliation: Génétique Physiologie et Systèmes d'Elevage, Université de Toulouse, Institut National de la Recherche Agronomique, Auzeville Castanet Tolosan, France.
authors.forename: Mireille
authors.initials: M
authors.lastname: Morisson
authors.affiliation: Génétique Physiologie et Systèmes d'Elevage, Université de Toulouse, Institut National de la Recherche Agronomique, Auzeville Castanet Tolosan, France.
authors.forename: Valerie
authors.initials: V
authors.lastname: Fillon
authors.affiliation: Génétique Physiologie et Systèmes d'Elevage, Université de Toulouse, Institut National de la Recherche Agronomique, Auzeville Castanet Tolosan, France.
authors.forename: Alain
authors.initials: A
authors.lastname: Vignal
authors.affiliation: Wellcome Trust Sanger Institute, Cambridgeshire CB10 1SA, United Kingdom.
authors.forename: William
authors.initials: W
authors.lastname: Chow
authors.affiliation: Wellcome Trust Sanger Institute, Cambridgeshire CB10 1SA, United Kingdom.
authors.forename: Kerstin
authors.initials: K
authors.lastname: Howe
authors.affiliation: Hy-Line International, Dallas, Iowa 50063.
authors.forename: Janet E
authors.initials: JE
authors.lastname: Fulton
authors.affiliation: Beckman Research Institute, Duarte, California 91010-3000.
authors.forename: Marcia M
authors.initials: MM
authors.lastname: Miller
authors.affiliation: Department of Behavioral Neuroscience, Oregon Health and Science University, Portland, Oregon 97239-3098.
authors.forename: Peter
authors.initials: P
authors.lastname: Lovell
authors.affiliation: Department of Behavioral Neuroscience, Oregon Health and Science University, Portland, Oregon 97239-3098.
authors.forename: Claudio V
authors.initials: CV
authors.lastname: Mello
authors.affiliation: Department of Behavioral Neuroscience, Oregon Health and Science University, Portland, Oregon 97239-3098.
authors.forename: Morgan
authors.initials: M
authors.lastname: Wirthlin
authors.affiliation: The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Midlothian EH25 9RG, United Kingdom.
authors.forename: Andrew S
authors.initials: AS
authors.lastname: Mason
authors.affiliation: The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Midlothian EH25 9RG, United Kingdom.
authors.forename: Richard
authors.initials: R
authors.lastname: Kuo
authors.affiliation: The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Midlothian EH25 9RG, United Kingdom.
authors.forename: David W
authors.initials: DW
authors.lastname: Burt
authors.affiliation: Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan 48824.
authors.forename: Jerry B
authors.initials: JB
authors.lastname: Dodgson
authors.affiliation: United States Department of Agriculture-Agricultural Research Service, Avian Disease and Oncology, East Lansing, Michigan 48823 wwarren@wustl.edu hcheng@msu.edu.
authors.forename: Hans H
authors.initials: HH
authors.lastname: Cheng
mesh_terms: D000818:Animals; D002645:Chickens / Q000235:genetics*; D022202:Chromosomes, Artificial, Bacterial; D019295:Computational Biology; D020451:Contig Mapping; D016678:Genome / Q000235:genetics*; D058977:Molecular Sequence Annotation; D017422:Sequence Analysis, DNA
keywords: Gallus gallus; MHC; genome assembly