1. Vervet Monkey Genomics: Genome Canada and Génome Québec Physical Map Project J. Wasserscheid, G. Leveque, C. Nagy, C. Pinsonnault, and K. Dewar, McGill University and Génome Québec Innovation Center A. Jasinska and N. Freimer, Center for Neurobehavioral Genetics, UCLA This work is funded by Genome Canada, Génome Québec and CIHR. Please visit our website at http://www.genomequebec.mcgill.ca/compgen/submit_db/vervet_project While still early in the project, our vervet comparative physical map is proving useful for genetic mapping studies of behavioural traits (Freimer et al., PNAS, 2007) and for identifying and investigating intriguing aspects of genome evolution. We are now extending our analysis to all chromosomes to build a genome wide scaffold and physical map. Genomic rearrangements Genomic rearrangements The vervet monkey is an important biomedical model for the study of complex traits and diseases. Due to its high chromosome number (2n = 60) and recent divergence time from rhesus (~ 10-12 million years ago), it allows us to identify and characterize genome rearrangements. We are generating a genome physical map and comparing it to human, chimpanzee, and rhesus. Gaps as indicators of progress Gap closure status Compared to human, vervet BACs cover 84% of the genome in orthologous co-linear segments. The remaining 16% represent “holes” in the map, as well as complex orthologies due to centromeric, telomeric, and large segmental duplication regions. Hum 8 Ver 8 Hum 3 Different levels of genome rearrangements Hum 6 Different chromosomes display varying levels of rearrangement complexity. BAC end sequence results correlate with existing microsatellite results (Jasinska et al., Mammalian Genome, 2007). Chromosome overviews Human chromosome 18 local inversion #5 Rhesus chromosome 18: co-linearity with vervet genome Expanded view of an inversion Vervet results indicate a 730 Kb local inversion compared to human (rearrangement 5). The same clones display regional co-linearity on rhesus, indicating that the rearrangement predates the vervet:rhesus divergence. The occurrence of vervet BAC clones containing centromeric sequence motifs (ALRs) can be used to help map the positions of neo-centromeres. Our vervet chr18 prediction agrees with the placement of a rhesus neo-centromere (Ventura et al., Science, 2007). Evolutionary new centromeres H18R18V18 Formation of new centromeres in rhesus and vervet chromosome 18  Our genome maps are built from paired end sequences from vervet BAC clones (bacterial artificial chromosomes, ~ 170 Kb in length)  As of September 30, 2007: Paired end sequences for 112,404 BAC clones were deposited in NCBI/GenBank, representing 5X coverage of the vervet genome. Our goal is to achieve > 8X coverage. DNA sequencing Estimation of genome coverage Introduction Project progress Project progress Conclusion and next steps Deviations from co-linearity We have identified 2,842 vervet BACs displaying non-colinearity to human, or rhesus, or both. Non-colinearity can be detected by inappropriate clone lengths, improper end sequence orientations, and/or pairs of BAC ends aligning to separate chromosomes. As a relative measure of the rate of genome evolution: 46% (1,292) of the vervet BACs are discordant on human but concordant on rhesus 33% (950) are discordant on human and rhesus 21% (600) are concordant on human but discordant on rhesus We are localizing concordant and discordant vervet BACs on the human, chimp, and rhesus genome assemblies in order to identify and characterize genome rearrangements. humanvervetrhesus 46%21%33% Of the vervet/human co-linear BACs, 93% (80,061) are also co-linear with rhesus. The identification of genomic regions of co-linearity aids genetic mapping and can be used to immediately infer gene content and organization for the vervet. Co-linearity with human and rhesus Of all vervet BAC clones sequenced,  76% (85,766 clones) display co-linearity to human  21% cannot be evaluated (poor alignments of one or both ends)  3% display deviations from co-linearity Discordant mapped BACs 3%4 Un-mappable BACs 6%3 Single end mapped BACs 15%2 Concordant mapped BACs 76%1 AB C D A : centromere motifs B : gaps C : concordant BACs D : discordant BACs 1 : p-arm inversion (seen in vervet and rhesus) 2 : 1.3 Mb inversion (seen in vervet and rhesus) 3 : neo-centromere (seen in vervet and rhesus) 4 : 450 Kb inversion (seen only in vervet) 5 : 730 Kb inversion (seen in vervet and rhesus) 6 : 290 Kb inversion (seen in vervet and rhesus) 7 : 250 Kb inversion (seen only in vervet) Untangling chromosome 18 Characterization of chr18 Chromosome 18 statistics: 75.6 Mb covered in BACs (>99%) 17 gaps remaining smallest gap: 39 bp largest gap: 102 Kb largest contiguous region: 13.7 Mb 4 regions of > 10 Mb (60% chr18) 1 1 2 4 5 6 7 H18R18V18 4 5 6 7 4 5 6 7 1 2 2 33