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

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. Copyright © 2017 Warren et al.

Journal: G3
DOI: 10.1534/g3.116.035923
Year: 2017

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