A New Chicken Genome Assembly Provides Insight into Avian Genome Structure

Wesley C Warren, LaDeana W Hillier, Chad Tomlinson, Patrick Minx, Milinn Kremitzki, Tina Graves, Chris Markovic, Nathan Bouk, Kim D Pruitt, Francoise Thibaud-Nissen, Valerie Schneider, Tamer A Mansour, C Titus Brown, Aleksey Zimin, Rachel Hawken, Mitch Abrahamsen, Alexis B Pyrkosz, Mireille Morisson, Valerie Fillon, Alain Vignal, William Chow, Kerstin Howe, Janet E Fulton, Marcia M Miller, Peter Lovell, Claudio V Mello, Morgan Wirthlin, Andrew S Mason, Richard Kuo, David W Burt, Jerry B Dodgson, Hans H Cheng

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.