title: Complex haplotypes, copy number polymorphisms and coding variation in two recently divergent mouse strains.
abstract: Inbred mouse strains provide the foundation for mouse genetics. By selecting for phenotypic features of interest, inbreeding drives genomic evolution and eliminates individual variation, while fixing certain sets of alleles that are responsible for the trait characteristics of the strain. Mouse strains 129Sv (129S5) and C57BL/6J, two of the most widely used inbred lines, diverged from common ancestors within the last century, yet very little is known about the genomic differences between them. By comparative genomic hybridization and sequence analysis of 129S5 short insert libraries, we identified substantial structural variation, a complex fine-scale haplotype pattern with a continuous distribution of diversity blocks, and extensive nucleotide variation, including nonsynonymous coding SNPs and stop codons. Collectively, these genomic changes denote the level and direction of allele fixation that has occurred during inbreeding and provide a basis for defining what makes these mouse strains unique.
authors.affiliation: The Wellcome Trust Sanger Institute, Hinxton, Cambs, CB10 1SA, UK.
authors.forename: David J
authors.initials: DJ
authors.lastname: Adams
authors.forename: Emmanouil T
authors.initials: ET
authors.lastname: Dermitzakis
authors.forename: Tony
authors.initials: T
authors.lastname: Cox
authors.forename: James
authors.initials: J
authors.lastname: Smith
authors.forename: Rob
authors.initials: R
authors.lastname: Davies
authors.forename: Ruby
authors.initials: R
authors.lastname: Banerjee
authors.forename: James
authors.initials: J
authors.lastname: Bonfield
authors.forename: James C
authors.initials: JC
authors.lastname: Mullikin
authors.forename: Yeun Jun
authors.initials: YJ
authors.lastname: Chung
authors.forename: Jane
authors.initials: J
authors.lastname: Rogers
authors.forename: Allan
authors.initials: A
authors.lastname: Bradley
mesh_terms: D000818:Animals; D018628:Gene Dosage; D014644:Genetic Variation; D016678:Genome; D006239:Haplotypes; D051379:Mice; D008810:Mice, Inbred C57BL; D008969:Molecular Sequence Data; D011110:Polymorphism, Genetic