A new chicken genome assembly provides insight into avian genome structure

Authors: WARREN, W - WASHINGTON UNIVERSITY SCHOOL OF MEDICINE; HILLIER, L - WASHINGTON UNIVERSITY SCHOOL OF MEDICINE; TOMLINSON, C - WASHINGTON UNIVERSITY SCHOOL OF MEDICINE; MINX, P - WASHINGTON UNIVERSITY SCHOOL OF MEDICINE; KREMITZKI, M - WASHINGTON UNIVERSITY SCHOOL OF MEDICINE; GRAVES, T - WASHINGTON UNIVERSITY SCHOOL OF MEDICINE; MARKOVIC, C - WASHINGTON UNIVERSITY SCHOOL OF MEDICINE; BOURK, N - NATIONAL INSTITUTES OF HEALTH (NIH); PRUITT, K - NATIONAL INSTITUTES OF HEALTH (NIH); THIBAUD-NISSEN, F - NATIONAL INSTITUTES OF HEALTH (NIH); SCHNEIDER, V - NATIONAL INSTITUTES OF HEALTH (NIH); MANSOUR, T - UC DAVIS MEDICAL CENTER; BROWN, C - UC DAVIS MEDICAL CENTER; ZIMIN, A - UNIVERSITY OF MARYLAND; HAWKEN, R - COBB-VANTRESS, INC.; ABRAHAMSEN, M - COBB-VANTRESS, INC.; BLACK PYRKOSZ, ALEXIS; MORRISON, M - INRA, GÉNÉTIQUE ANIMALE ET BIOLOGIE INTÉGRATIVE , JOUY-EN-JOSAS, FRANCE; FILLON, V - INRA, GÉNÉTIQUE ANIMALE ET BIOLOGIE INTÉGRATIVE , JOUY-EN-JOSAS, FRANCE; VIGNAL, A - INRA, GÉNÉTIQUE ANIMALE ET BIOLOGIE INTÉGRATIVE , JOUY-EN-JOSAS, FRANCE; CHOW, W - WELLCOME TRUST SANGER INSTITUTE; HOWE, K - WELLCOME TRUST SANGER INSTITUTE; FULTON, J - HY-LINE INTERNATIONAL; MILLER, M - CITY OF HOPE MEDICAL CENTER; LOVELL, P - OREGON HEALTH & SCIENCE UNIVERSITY; MELLO, C - OREGON HEALTH & SCIENCE UNIVERSITY; CHENG, HANS

Submitted to: G3, Genes/Genomes/Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 11/14/2016
Publication Date: 1/20/2017
Publication URL: http://handle.nal.usda.gov/10113/5661748
Citation: Warren, W.C., Hillier, L.W., Tomlinson, C., Minx, P., Kremitzki, M., Graves, T., Markovic, C., Bourk, N., Pruitt, K.D., Thibaud-Nissen, F., Schneider, V., Mansour, T.A., Brown, C.T., Zimin, A., Hawken, R., Abrahamsen, M., Black Pyrkosz, A.A., Morrison, M., Fillon, V., Vignal, A., Chow, W., Howe, K., Fulton, J.E., Miller, M.M., Lovell, P., Mello, C.V., Cheng, H.H. 2017. A new chicken genome assembly provides insight into avian genome structure. G3, Genes/Genomes/Genetics. 7(1):109-117. https://doi.org/10.1534/g3.116.035923.
DOI: https://doi.org/10.1534/g3.116.035923

Interpretive Summary: In the modern age of agriculture, having a complete and accurate genome sequence of the plant or animal of interest is essential. Although chicken is the first agricultural animal to have a genome sequence, that assembly contained many deficiencies including gaps and lack of entire sequences for several chromosomes. In this submission, the genome assembly has been improved to include more assembled sequence, reduce gaps, and add sequences that identify three more chromosomes. This enhanced tool will aid scientists both in academia and industry to identify genes and sequence variants that are critical for the agriculture including the production of affordable and more nutritious poultry products.

Technical 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. Gallus_gallus-5.0 when annotated for gene content shows an increase of 4,679 annotated genes, 2,768 non-coding and 1,911 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 most such 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.