ARS | Publication request: A PHYSICAL MAP OF THE CHICKEN GENOME

Submitted to: Nature Magazine
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: September 17, 2004
Publication Date: December 9, 2004
Citation: Wallis, J.W., Aerts, J., Groenen, M., Crooijmans, R., Layman, D., Graves, T.A., Scheer, D., Kremitzki, C., Fedele, M., Mudd, N., Cardenas, M., Higginbotham, J., Carter, J., McGrane, R., Gaige, T., Mead, K., Walker, J., Albracht, D., Davito, J., Yang, S., Leong, S., Chinwalla, A., Sekhon, M., Wylie, K., Dodgson, J., Romanov, M., Cheng, H.H., deJong, P., Osoegawa, K., Nefedov, M., Zhang, H., McPherson, J., Krzywinski, M., Schein, J., Hillier, L., Mardis, E., Wilson, R., Warren, W. 2004. A physical map of the chicken genome. Nature Magazine. 432:761-764.

Interpretive Summary: Physical contig maps form the framework for whole genome shotgun sequencing. In this paper, a physical map was generated for the chicken genome. As a result, the chicken genome sequence could be readily assembled. In addition, this physical map provides the ability for scientists to readily develop genetic markers, clone important genes, etc. Combined with the chicken genome sequence, these provide tools describe the complete list of genes and proteins used to generate a chicken. This information will greatly enhance the ability of scientists to identify agricultural important genes and biological pathways, which will ultimately help the US poultry industry and consumers.

Technical Abstract: Strategies for analyzing large, complex genomes have evolved over the past few years such that a combination of whole genome shotgun sequencing and hierarchal map-assisted sequencing is now often used. A fingerprint clone (FPC) map, based upon complete restriction enzyme digests of clones and the subsequent determination of clone overlap by comparing fragment sizes, can be linked to a sequence to identify local mis-assemblies, supply long-range linking of assembly supercontigs, anchor sequence contigs to the genetic map, and provide templates for closing gaps in draft sequence assemblies. In addition, fingerprint maps are a critical resource for numerous functional genomic studies. In an accompanying paper, we describe the draft sequence of the chicken, Gallus gallus, the first species sequenced that is both a model organism and global food source. Here we present a clone map of the chicken genome at 20-fold coverage, containing 260 contigs of overlapping clones. This map represents approximately 95% of the genome.