PROPOSAL TO SEQUENCE THE GENOME OF THE CHICKEN
John D. McPherson, Washington University,
Genome Sequencing Center
Jerry Dodgson, Michigan State University
Robb Krumlauf, Stowers Institute
Olivier Pourquié, Stowers Institute
I. Overview and Rationale of the Sequencing Strategy.
The chicken genome has a haploid content of 1.2 x 109 base pairs (bp) of DNA;
approximately 40% that of either mouse or human. The strategy that will be employed to
sequence this genome is to assemble 6-fold whole-genome shotgun coverage of the
genome and to order and orient the resulting sequence scaffolds by alignment to end-
sequences of BACs in a comprehensive contig map. This is in contrast to the BAC-by-
BAC approach used by the Human Genome Project laboratories to sequence the human
genome but is similar to the first phase of the strategy currently being used to sequence
the mouse genome. Initial analysis of an assembly of available 5-fold mouse whole-
genome shotgun sequence indicates that approximately 98% coverage of the genome has
been achieved in reads and about 90% is covered in assembled bases. These scaffolds are
aligned to a BAC contig map using corresponding BAC end-sequences. The sequence
continuity and quality of the resulting mouse sequence supports the proposed strategy
and level of whole-genome shotgun coverage for the chicken genome. The resulting
sequence will provide an invaluable tool for the chicken, and other research communities.
The generation of finished sequence for selected regions will be readily achievable
utilizing the combined BAC map and sequence. In addition, they will provide a suitable
basis for generating a complete finished sequence of this genome in the future.
II. Biological Rationales for the Utility of the Chicken Genome Sequence.
Chicken as a model for studies of health/disease and biology. The chicken is the
premier non-mammalian vertebrate model organism. It one of the primary models for
embryology and development as its embryonic