GNAS2009 Abstract #8 - Tellam, Ross
Annotation of the Bos taurus genome - the easy and the difficult
Ross Tellam1 and Chris Elsik2 on behalf of the Bovine Genome Sequencing, Annotation and Analysis Consortium
1CSIRO Livestock Industries, Brisbane, QLD, Australia. 2Department of Biology, Georgetown University, Washington, USA.
Bos taurus (domesticated cattle) is one of the world' s most important food animal species and also among the most biologically interesting due to its unique digestive, reproductive and immune system physiology. Furthermore, cattle represent an important clade for the annotation of human genes and evolutionary studies. As a major step toward understanding the biology and evolution of cattle and other mammals, the cow genome (Hereford female) was sequenced to 7.1X coverage using a combined whole genome shotgun and BAC skim approach. The scaffold N50 size was 2.19 Mbp. A dispersed community-based gene annotation effort was employed to annotate the genome with gene model submissions coordinated in a central database. The major effort employed the Apollo genome annotation viewer and editor, which was complemented by annotations from the Hinxton Annotation Jamboree. Approximately 4,000 genes were physically annotated. The overall effort was supported by strong bioinformatics expertise. The process required a high level of organization but importantly it engaged those who are likely to interact with and exploit the genome sequence in the future. In addition, this annotation strategy provided an initial discovery framework using experts in various fields of biology. A description of the overall process will be presented with specific comments on the major annotation effort using the Apollo genome annotation viewer and editor. A number of examples highlighting annotation difficulties and anomalies will be discussed.
