MobiSeq: De novo SNP discovery in model and non-model species through sequencing the flanking region of transposable elements
Type
ArticleAuthors
Rey-Iglesia, AlbaGopalakrishan, Shyam
Carøe, Christian
Alquezar-Planas, David E.
Ahlmann Nielsen, Anne
Röder, Timo
Bruhn Pedersen, Lene
Næsborg-Nielsen, Christina
Sinding, Mikkel-Holger S.
Fredensborg Rath, Martin
Li, Zhipeng
Petersen, Bent
Gilbert, M. Thomas P.
Bunce, Michael
Mourier, Tobias
Hansen, Anders Johannes
KAUST Department
Biological and Environmental Sciences and Engineering (BESE) DivisionPathogen Genomics Laboratory
Date
2018-12-21Online Publication Date
2019-02-06Print Publication Date
2019-03Embargo End Date
2019-12-21Permanent link to this record
http://hdl.handle.net/10754/631662
Metadata
Show full item recordAbstract
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.Citation
Rey-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.Sponsors
We 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).Publisher
WileyJournal
Molecular Ecology ResourcesAdditional Links
https://onlinelibrary.wiley.com/doi/full/10.1111/1755-0998.12984https://doi.org/10.1101/349290
ae974a485f413a2113503eed53cd6c53
10.1111/1755-0998.12984
Scopus Count
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