Plant & Animal Genomes XVI Conference

January 12-16, 2008
Town & Country Convention Center
San Diego, CA

Toward A Sheep Genome Assembly

Brian P Dalrymple^1,9 , John McEwan² , Richard Gibbs³ , George Weinstock³ , V Hutton Oddy^4,9 , Frank Nicholas^5,9 , James Kijas^1,9 , Jillian F Maddox^6,9 , Noelle E Cockett^7,9 , Ewen F Kirkness⁸ , Abhirami Ratnakumar¹ , Wesley C Barris¹ , Sean McWilliam¹ , International Sheep Genomics Consortium⁹

¹  CSIRO Livestock Industries, Brisbane, Queensland 4067, Australia

²  AgResearch, Invermay Agricultural Centre PB 50034, Mosgiel, NZ

³  BCM-Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, USA

⁴  University of New England, Armidale, NSW 2350, Australia

⁵  Reprogen and sheepGenomics, University of Sydney, NSW, 2006, Australia

⁶  University of Melbourne, Pakville, VIC 3010, Australia

⁷  Utah State University, Logan, UT 84322-4800, USA

⁸  TIGR, Rockville, MD 20850, USA

⁹  http://www.sheephapmap.org

As a first step towards the assembly of a sheep genome sequence we have built a virtual sheep genome (VSG). The VSG is a reordering and reorientation of segments of the human genome into the most likely order of the conserved syntenic segments in the sheep genome. Segments were defined by mapping the 179,047 CHORI-243 sheep BAC-end sequences onto the human, dog and bovine genome assemblies and converting the dog and cow coordinates to the human genome coordinates. By using sensitive BLAST parameters and filtering based on the orientation and distance apart of the two ends of each BAC, almost half of the sheep BACs were positioned on the human genome. The 1172 segments of the human genome were then ordered using the sheep linkage map and conserved synteny at several levels, across vertebrates, mammals and especially cow. Version 2 of the VSG is being built on the framework of the latest assembly of the bovine genome applying an equivalent strategy to version 1. Mapping of the sheep BACs to the bovine genome has identified local rearrangements in the sheep genome within regions of overall synteny. Version 2 will use the new ovine RH map that includes the results from the first sheep SNP-chip, an updated linkage map and physical mapping data for around 700 ovine coding sequences to enhance ordering of segments. It will also incorporate assembled sheep sequence being generated as part of sequencing six animals each at 0.5 X coverage and the small number of sequenced sheep BACs.