the genomic landscape shaped by selection on transposable elements across 18 mouse strains基因组景观的选择在转座的元素在18日鼠标菌株.pdfVIP

Nellåker et al. Genome Biology 2012, 13:R45 /2012/13/6/R45 RESEARCH Open Access The genomic landscape shaped by selection on transposable elements across 18 mouse strains 1*† 2† 3 2 1,3 1,4,5 Christoffer Nellåker , Thomas M Keane , Binnaz Yalcin , Kim Wong , Avigail Agam , T Grant Belgard , 3 2 6 1,2* Jonathan Flint , David J Adams , Wayne N Frankel and Chris P Ponting Abstract Background: Transposable element (TE)-derived sequence dominates the landscape of mammalian genomes and can modulate gene function by dysregulating transcription and translation. Our current knowledge of TEs in laboratory mouse strains is limited primarily to those present in the C57BL/6J reference genome, with most mouse TEs being drawn from three distinct classes, namely short interspersed nuclear elements (SINEs), long interspersed nuclear elements (LINEs) and the endogenous retrovirus (ERV) superfamily. Despite their high prevalence, the different genomic and gene properties controlling whether TEs are preferentially purged from, or are retained by, genetic drift or positive selection in mammalian genomes remain poorly defined. Results: Using whole genome sequencing data from 13 classical laboratory and 4 wild-derived mouse inbred strains, we developed a comprehensive catalogue of 103,798 polymorphic TE variants. We employ this extensive data set to characterize TE variants across the Mus lineage, and to infer neutral and selective processes that have acted over 2 million years. Our results indicate that the majority of TE variants are introduced though the male germline and that onl