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

Research output: Contribution to journalJournal article – Annual report year: 2019Researchpeer-review

DOI

  • Author: Rey-Iglesia, Alba

    Natural History Museum of Denmark, Denmark

  • Author: Gopalakrishan, Shyam

    Natural History Museum of Denmark, Denmark

  • Author: Carøe, Christian

    Natural History Museum of Denmark, Denmark

  • Author: Alquezar-Planas, David E.

    Natural History Museum of Denmark, Denmark

  • Author: Nielsen, Anne Ahlmann

    Natural History Museum of Denmark, Denmark

  • Author: Röder, Timo

    Natural History Museum of Denmark, Denmark

  • Author: Bruhn Pedersen, Lene

    Natural History Museum of Denmark, Denmark

  • Author: Naesborg-Nielsen, Christina

    Natural History Museum of Denmark, Denmark

  • Author: Sinding, Mikkel Holger Strander

    Natural History Museum of Denmark, Denmark

  • Author: Fredensborg Rath, Martin

    University of Copenhagen, Denmark

  • Author: Li, Zhipeng

    Chinese Academy of Agricultural Sciences, China

  • Author: Petersen, Bent

    Department of Health Technology, Technical University of Denmark

  • Author: Gilbert, M. Thomas P.

    Natural History Museum of Denmark, Denmark

  • Author: Bunce, Michael

    Curtin University of Technology, Australia

  • Author: Mourier, Tobias

    Natural History Museum of Denmark, Denmark

  • Author: Hansen, Anders Johannes

    Natural History Museum of Denmark, Denmark

View graph of relations

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. This article is protected by copyright. All rights reserved.
Original languageEnglish
JournalMolecular Ecology Resources
Volume19
Issue number2
Pages (from-to)512-525
Number of pages14
ISSN1755-098X
DOIs
Publication statusPublished - 2019
CitationsWeb of Science® Times Cited: No match on DOI

    Research areas

  • TE, SNP discovery, Genotyping, Population genomics, Reduced representation library, Transposable elements

ID: 164225622