Plant & Animal Genomes XVII Conference

January 10-14, 2009
Town & Country Convention Center
San Diego, CA

Large-Scale Chromosomal Rearrangements In The Cattle Lineage And Their Association With Segmental Duplications And Repetitive Elements

Denis M. Larkin¹ , Greg Pape² , Ravikiran Donthu¹ , Loretta Auvil² , Lin Chen³ , Michael Welge² , Evan Eichler³ , Harris A. Lewin^1,4

¹  Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, USA

²  National Center for Supercomputing Applications, University of Illinois at Urbana-Champaign, Urbana, IL

³  Department of Genome Sciences, and Howard Hughes Medical Institute University of Washington, Seattle, WA, USA

⁴  Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA

The chromosomal coordinates of cattle BAC-end sequences (BESs) with unique BLASTn hits in human, macaque, dog, mouse chromosomes were used to build pair-wise homologous synteny blocks (HSBs). Cattle-pig HSBs were defined in the cattle genome using an integrated pig physical map that incorporated pig BESs. We found 124 evolutionary breakpoint regions (EBRs) in the cattle lineage: 100 that are cattle/ruminant-specific and 24 artiodactyl-specific. Ten additional EBRs were assigned to the ferungulate lineage, of which four are located in BTA16, suggesting that the region corresponding to HSA1:183-214 Mbp was actively rearranged before the Artiodactyla-Carnivora split. Segmental duplications (SDs) represent 11.7% and 23% of base-pairs in cattle/ruminant-specific EBRs and artiodactyl-specific EBRs, respectively. In the remainder of the genome, the equivalent fraction is significantly smaller (1.7%; P<e^-12), suggesting that SDs play a role in promoting chromosomal rearrangements, and that a significant fraction of SDs observed in the cattle genome occurred before the Ruminant-Suina split. The density of ancient mammalian repeats (LINE-L2, SINE-MIR), SINE-BovA and tRNA^Glu-derived SINEs is significantly lower in cattle/ruminant EBRs than in the rest of the genome. Cattle/ruminant EBRs are enriched for recently appearing LINE-L1 elements whereas artiodactyl EBRs are enriched for tRNA^Glu-derived SINEs. Our work suggests that specific repeat families played an important role in promoting chromosomal rearrangements in the artiodacyl and ruminant lineages by promoting segmental duplications. On the basis of our previous findings, we propose a common, repeat-dependent mechanism for chromosome rearrangements in different mammalian lineages that involves different repeat families and SDs in the different lineages.