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United States Department of Agriculture

Agricultural Research Service

Title: Alignment Genomes Across Species

Authors
item Williams, John - ROSLIN INSTITUTE
item Hastings, Nicola - ROSLIN INSTITUTE
item Jann, Oliver - ROSLIN INSTITUTE
item Law, Andy - ROSLIN INSTITUTE
item Stone, Roger
item Snelling, Warren
item Connor, Erin
item Sonstegard, Tad
item Smith, Timothy

Submitted to: Plant and Animal Genome Conference
Publication Type: Abstract Only
Publication Acceptance Date: November 20, 2004
Publication Date: January 14, 2005
Citation: Williams, J.L., Hastings, N., Jann, O., Law, A., Stone, R.T., Snelling, W.M., Connor, E.E., Sonstegard, T.S., Smith, T.P. 2005. Alignment genomes across species [abstract]. Plant and Animal Genome XVII. p. 241.

Technical Abstract: At the gross level it is known the organisation of large regions of chromosomes are conserved between species, with extended chromosome segments containing many of the same genes in several species. However, as more detailed information on genome organisation becomes available in different species it has been shown that gene order can differ between species within apparently conserved segments. With the availability of human, mouse and rat genome sequence, and radiation hybrid panels for livestock species it is now possible explore the alignment of genomes and the degree of conservation of synteny between species at high resolution. PCR primers for EST markers were derived from publicly available sequences of bovine cDNA clones from libraries produced at MARC. The EST markers were genotyped on the Roslin 3000 rad cattle WGRH panel and chromosomal assignments of markers made by 2-point linkage analysis against markers which had been previously typed on the RH panel. Radiation hybrid maps were then built for all bovine chromosomes. In silico sequence analysis was carried out to localise othologues of the EST sequences on the human, mouse and rat genome sequences. This allowed alignment of the cattle map with human mouse and rat genomes. At low resolution blocks of conserved synteny were identified, while at high resolution gene order within and among blocks of conserved synteny was similar for some regions but showed considerable rearrangement in others. Thus care should be taken in using comparative mapping information to identify putative candidate genes at particular genomic locations.

Last Modified: 11/25/2014