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

Alba Rey-Iglesia, Shyam Gopalakrishan, Christian Carøe, David E. Alquezar-Planas, Anne Ahlmann Nielsen, Timo Röder, Lene Bruhn Pedersen, Christina Naesborg-Nielsen, Mikkel-Holger S. Sinding, Martin Fredensborg Rath, Zhipeng Li, Bent Petersen, M. Thomas P. Gilbert, Michael Bunce, Tobias Mourier, Anders Johannes Hansen*

*Corresponding author for this work

Research output: Contribution to journalJournal articleResearchpeer-review

Abstract

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

Keywords

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

Cite this

Rey-Iglesia, A., Gopalakrishan, S., Carøe, C., Alquezar-Planas, D. E., Nielsen, A. A., Röder, T., ... Hansen, A. J. (2019). MobiSeq: De Novo SNP discovery in model and non-model species through sequencing the flanking region of transposable elements. Molecular Ecology Resources, 19(2), 512-525. https://doi.org/10.1111/1755-0998.12984
Rey-Iglesia, Alba ; Gopalakrishan, Shyam ; Carøe, Christian ; Alquezar-Planas, David E. ; Nielsen, Anne Ahlmann ; Röder, Timo ; Bruhn Pedersen, Lene ; Naesborg-Nielsen, Christina ; Sinding, Mikkel-Holger S. ; Fredensborg Rath, Martin ; Li, Zhipeng ; Petersen, Bent ; Gilbert, M. Thomas P. ; Bunce, Michael ; Mourier, Tobias ; Hansen, Anders Johannes. / MobiSeq: De Novo SNP discovery in model and non-model species through sequencing the flanking region of transposable elements. In: Molecular Ecology Resources. 2019 ; Vol. 19, No. 2. pp. 512-525.
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abstract = "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.",
keywords = "TE, SNP discovery, Genotyping, Population genomics, Reduced representation library, Transposable elements",
author = "Alba Rey-Iglesia and Shyam Gopalakrishan and Christian Car{\o}e and Alquezar-Planas, {David E.} and Nielsen, {Anne Ahlmann} and Timo R{\"o}der and {Bruhn Pedersen}, Lene and Christina Naesborg-Nielsen and Sinding, {Mikkel-Holger S.} and {Fredensborg Rath}, Martin and Zhipeng Li and Bent Petersen and Gilbert, {M. Thomas P.} and Michael Bunce and Tobias Mourier and Hansen, {Anders Johannes}",
year = "2019",
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Rey-Iglesia, A, Gopalakrishan, S, Carøe, C, Alquezar-Planas, DE, Nielsen, AA, Röder, T, Bruhn Pedersen, L, Naesborg-Nielsen, C, Sinding, M-HS, Fredensborg Rath, M, Li, Z, Petersen, B, Gilbert, MTP, Bunce, M, Mourier, T & Hansen, AJ 2019, 'MobiSeq: De Novo SNP discovery in model and non-model species through sequencing the flanking region of transposable elements', Molecular Ecology Resources, vol. 19, no. 2, pp. 512-525. https://doi.org/10.1111/1755-0998.12984

MobiSeq: De Novo SNP discovery in model and non-model species through sequencing the flanking region of transposable elements. / Rey-Iglesia, Alba; Gopalakrishan, Shyam; Carøe, Christian; Alquezar-Planas, David E.; Nielsen, Anne Ahlmann; Röder, Timo; Bruhn Pedersen, Lene; Naesborg-Nielsen, Christina; Sinding, Mikkel-Holger S.; Fredensborg Rath, Martin; Li, Zhipeng; Petersen, Bent; Gilbert, M. Thomas P.; Bunce, Michael; Mourier, Tobias; Hansen, Anders Johannes.

In: Molecular Ecology Resources, Vol. 19, No. 2, 2019, p. 512-525.

Research output: Contribution to journalJournal articleResearchpeer-review

TY - JOUR

T1 - MobiSeq: De Novo SNP discovery in model and non-model species through sequencing the flanking region of transposable elements

AU - Rey-Iglesia, Alba

AU - Gopalakrishan, Shyam

AU - Carøe, Christian

AU - Alquezar-Planas, David E.

AU - Nielsen, Anne Ahlmann

AU - Röder, Timo

AU - Bruhn Pedersen, Lene

AU - Naesborg-Nielsen, Christina

AU - Sinding, Mikkel-Holger S.

AU - Fredensborg Rath, Martin

AU - Li, Zhipeng

AU - Petersen, Bent

AU - Gilbert, M. Thomas P.

AU - Bunce, Michael

AU - Mourier, Tobias

AU - Hansen, Anders Johannes

PY - 2019

Y1 - 2019

N2 - 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.

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. This article is protected by copyright. All rights reserved.

KW - TE

KW - SNP discovery

KW - Genotyping

KW - Population genomics

KW - Reduced representation library

KW - Transposable elements

U2 - 10.1111/1755-0998.12984

DO - 10.1111/1755-0998.12984

M3 - Journal article

VL - 19

SP - 512

EP - 525

JO - Molecular Ecology Resources

JF - Molecular Ecology Resources

SN - 1755-098X

IS - 2

ER -