PT  - JOURNAL ARTICLE
AU  - Alba Rey-Iglesia
AU  - Shyam Gopalakrishan
AU  - Christian Carøe
AU  - David E. Alquezar-Planas
AU  - Anne Ahlmann Nielsen
AU  - Timo Röder
AU  - Lene Bruhn Pedersen
AU  - Christina Næsborg-Nielsen
AU  - Mikkel-Holger S. Sinding
AU  - Martin Fredensborf Rath
AU  - Zhipeng Li
AU  - Bent Petersen
AU  - M. Thomas P. Gilbert
AU  - Michael Bunce
AU  - Tobias Mourier
AU  - Anders Johannes Hansen
TI  - MobiSeq: De Novo SNP discovery in model and non-model species through sequencing the flanking region of transposable elements
AID  - 10.1101/349290
DP  - 2018 Jan 01
TA  - bioRxiv
PG  - 349290
4099  - http://biorxiv.org/content/early/2018/06/17/349290.short
4100  - http://biorxiv.org/content/early/2018/06/17/349290.full
AB  - In recent years, the availability of reduced representation library (RRL) methods has catalysed an expansion of genome-scale studies to characterize both model and non-model organisms. Most of these methods rely on the use of restriction enzymes to obtain DNA sequences at a genome-wide level. These approaches have been widely used to sequence thousands of markers across individuals for many organisms at a reasonable cost, revolutionizing the field of population genomics. However, there are still some limitations associated with these methods, in particular, the high molecular weight DNA required as starting material, the reduced number of common loci among investigated samples, and the short length of the sequenced site-associated DNA. Here, we present MobiSeq, a RRL protocol exploiting simple laboratory techniques, that generates genomic data based on PCR targeted-enrichment of transposable elements and the sequencing of the associated flanking region. We validate its performance across 103 DNA extracts derived from three mammalian species: grey wolf (Canis lupus), red deer complex (Cervus sp.), and brown rat (Rattus norvegicus). MobiSeq enables the sequencing of hundreds of thousands loci across the genome, and performs SNP discovery with relatively low rates of clonality. Given the ease and flexibility of MobiSeq protocol, the method has the potential to be implemented for marker discovery and population genomics across a wide range of organisms – enabling the exploration of diverse evolutionary and conservation questions.