The chicken is one of humanity’s closest and oldest allies. With a worldwide population in the billions, this former jungle fowl is one of the most important domesticated animals on Earth. In the February issue of G3, Warren et al. further our understanding of this familiar bird, presenting a new and substantially improved chicken genome assembly (Gallus_gallus-5.0).

The new resource is a great boon for avian geneticists, providing a gain of 183 Mb over the prior draft genome, including three autosomes missing in the older version. Warren et al. were also able to improve base accuracy over the previous draft by using the Illumina error-correction process. These advances will help researchers studying natural and artificial selection and those working on trait mapping in the chicken.

Most notably, Warren et al.’s assembly has 4,679 more annotated genes than the previous draft. Still, Gallus_gallus-5.0 lacks many genes, 232 of which are not present in any of the over 60 avian genomes in NCBI, and 129 of which have been found in other bird genomes but not in the chicken.

A significant area of improvement in Gallus_gallus-5.0 is on chromosome 16, which is known to harbor many important immune system-related genes. Having a correct, complete assembly in this region is crucial to research on avian immunity and disease—a topic of major relevance to farm productivity and human health.

Despite the important findings presented by Warren et al., the chicken genome assembly remains incomplete. Through the application of newer techniques, such as those based on long single-molecule sequencing chemistries or chromatin proximity mapping, even greater improvements in the chicken genome assembly will soon be possible.

CITATION:

Warren, W.; Hillier, L.; Tomlinson, C.; Minx, P.; Kremitzki, M.; Graves, T.; Markovic, C.; Bouk, N.; Pruitt, K.; Thibaud-Nissen, F.; Schneider, V.; Mansour, T.; Brown, C.; Zimin, A.; Hawken, R.; Abrahamsen, M.; Pyrkosz, A.; Morisson, M.; Fillon, V.; Vignal, A.; Chow, W.; Howe, K.; Fulton, J.; Miller, M.; Lovell, P.; Mello, C.; Wirthlin, M.; Mason, A.; Kuo, R.; Burt, D.; Dodgson, J.; Cheng, H. A New Chicken Genome Assembly Provides Insight into Avian Genome Structure.
G3, 7(1), 109-117.
DOI: 10.1534/g3.116.035923
http://www.g3journal.org/content/7/1/109.full

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Nicole Haloupek is a freelance science writer and a recent graduate of UC Berkeley's molecular and cell biology PhD program.

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