Friday, February 23, 2018

GRCg6: Curation of the chicken reference genome assembly transfers to the GRC

The GRC announces the release of the latest chicken reference genome assembly, GRCg6.

The chicken reference assembly defines a standard upon which other avian whole genome studies are based. Providing the best representation of the chicken genome is essential for facilitating continued progress in understanding and improving human health as this species serves as a model organism similar to mouse, zebrafish and other vertebrates.

The chicken reference genome project began as an international research collaboration coordinated by the McDonnell Genome Institute with past funding from the National Institutes of Health (NIH) and U.S. Department of Agriculture whose shared goals were to determine the sequence of the chicken chromosomes and annotate all possible chicken genes. The initial genome reference was completed and published in Nature in 2004 and has since evolved in quality. The reference experienced a major upgrade in 2016, termed Gallus_gallus-5.0 (GCA_000002315.3), as a result of long read sequencing technology and added transcriptome data. In 2017, responsibility for the management of chicken genome assembly updates transferred to the Genome Reference Consortium (GRC). The generation of additional sequence coverage comprised of long read data, in particular average read lengths of 12kb, as well as improvements to de novo assembly algorithms has resulted in another upgrade, GRCg6, that has now been released for immediate community use. Manual annotation of de novo assembled contigs that have been integrated with finished BAC clones have produced an assembly with superior metrics of quality, such as N50 contig size of 18Mb and much lower gap counts.

Visit the chicken homepage at the GRC website for assembly notifications, report assembly issues or contact us with questions.

The GRCg6 assembly will be available in all major genome browsers, and will be annotated by both the NCBI eukaryotic genome annotation pipeline and Ensembl.

* Photo courtesy of Dr. Jerry Dodgson