MobiSeq: De novo SNP discovery in model and non-model species through sequencing the flanking region of transposable elements.

摘要: In recent years, the availability of reduced representation library (RRL) methods has catalysed an expansion genome-scale studies to characterize both model and non-model organisms. Most these rely on use restriction enzymes obtain DNA sequences at a genome-wide level. These approaches have been widely used sequence thousands markers across individuals for many organisms reasonable cost, revolutionizing field population genomics. However, there are still some limitations associated with methods, in particular high molecular weight required as starting material, number common loci among investigated samples, short length sequenced site-associated DNA. Here, we present MobiSeq, RRL protocol exploiting simple laboratory techniques, that generates genomic data based PCR targeted enrichment transposable elements sequencing flanking region. We validate its performance 103 extracts derived from three mammalian species: grey wolf (Canis lupus), red deer complex (Cervus sp.) brown rat (Rattus norvegicus). MobiSeq enables hundreds genome performs SNP discovery relatively low rates clonality. Given ease flexibility protocol, method potential be implemented marker genomics wide range organisms-enabling exploration diverse evolutionary conservation questions.