A New Chicken Genome Assembly Provides Insight into Avian Genome Structure

G3 (Bethesda). 2016 Nov 14. pii: g3.116.035923. doi: 10.1534/g3.116.035923. [Epub ahead of print]


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 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.


Warren WC1, Hillier LW2, Tomlinson C2, Minx P2, Kremitzki M2, Graves T2, Markovic C2, Bouk N3, Pruitt KD3, Thibaud-Nissen F3, Schneider V3, Mansour TA4, Brown CT4, Zimin A5, Hawken R6, Abrahamsen M6, Pyrkosz AB7, Morisson M8, Fillon V8, Vignal A8, Chow W9, Howe K9, Fulton JE10, Miller MM11, Lovell P12, Mello CV12, Wirthlin M12, Mason AS13, Kuo R13, Burt DW13, Dodgson JB14, Cheng HH7.