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G3 (Bethesda). 2017 Jan 5;7(1):109-117. doi: 10.1534/g3.116.035923.

A New Chicken Genome Assembly Provides Insight into Avian Genome Structure.

Author information

1
McDonnell Genome Institute, Washington University School of Medicine, St. Louis, Missouri 63108 wwarren@wustl.edu hcheng@msu.edu.
2
McDonnell Genome Institute, Washington University School of Medicine, St. Louis, Missouri 63108.
3
National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894.
4
University of California-Davis, California 95616.
5
Institute for Physical Sciences and Technology, University of Maryland, College Park, Maryland 20742.
6
Cobb-Vantress Inc., Siloam Springs, Arkansas 72761-1030.
7
United States Department of Agriculture-Agricultural Research Service, Avian Disease and Oncology, East Lansing, Michigan 48823.
8
Génétique Physiologie et Systèmes d'Elevage, Université de Toulouse, Institut National de la Recherche Agronomique, Auzeville Castanet Tolosan, France.
9
Wellcome Trust Sanger Institute, Cambridgeshire CB10 1SA, United Kingdom.
10
Hy-Line International, Dallas, Iowa 50063.
11
Beckman Research Institute, Duarte, California 91010-3000.
12
Department of Behavioral Neuroscience, Oregon Health and Science University, Portland, Oregon 97239-3098.
13
The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Midlothian EH25 9RG, United Kingdom.
14
Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan 48824.
15
United States Department of Agriculture-Agricultural Research Service, Avian Disease and Oncology, East Lansing, Michigan 48823 wwarren@wustl.edu hcheng@msu.edu.

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.

KEYWORDS:

Gallus gallus; MHC; genome assembly

PMID:
27852011
PMCID:
PMC5217101
DOI:
10.1534/g3.116.035923
[Indexed for MEDLINE]
Free PMC Article

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