MobiSeq: De novo SNP discovery in model and non-model species through sequencing the flanking region of transposable elements
Alquezar-Planas, David E.
Ahlmann Nielsen, Anne
Bruhn Pedersen, Lene
Sinding, Mikkel-Holger S.
Fredensborg Rath, Martin
Gilbert, M. Thomas P.
Hansen, Anders Johannes
KAUST DepartmentBiological and Environmental Sciences and Engineering (BESE) Division
Pathogen Genomics Laboratory
Permanent link to this recordhttp://hdl.handle.net/10754/631662
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AbstractIn 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.
CitationRey-Iglesia A, Gopalakrishan S, Carøe C, Alquezar-Planas DE, Ahlmann Nielsen A, et al. (2019) MobiSeq: De novo SNP discovery in model and non-model species through sequencing the flanking region of transposable elements. Molecular Ecology Resources. Available: http://dx.doi.org/10.1111/1755-0998.12984.
SponsorsWe are grateful to all the people and institutions that have provided samples for this study, specifically Department of Environment Nunavut, Environment and Natural Resources Northwest Territories, and Lindsey Carmichael and David Coltman at University of Alberta (wolf samples); Frank Zachos (Natural History Museum in Vienna); Meirav Meiri (Tel Aviv University); Adrian Lister, Ian Barnes and Richard Sabin (Natural History Museum of London); Kristian Murphy Gregersen (Natural History Museum of Denmark); Rolf Langvatn (University Centre in Svalbard); and Gennady Baryshnikov (Russian Academy of Sciences, Moscow) (deer material). We also thank Lasse Vinner for experimental methodology discussions; Maria Asplund for discussion on data analysis in the early stages of the project; and The Danish National Advanced Technology Foundation. S.G. was funded by EU Marie Skłodowska-Curie Grant 655732 (Wherewolf).
JournalMolecular Ecology Resources