Abstract
| Original language | English |
|---|---|
| Journal | Molecular Ecology Resources |
| Volume | 19 |
| Issue number | 2 |
| Pages (from-to) | 512-525 |
| Number of pages | 14 |
| ISSN | 1755-098X |
| DOIs | |
| Publication status | Published - 2019 |
Keywords
- TE
- SNP discovery
- Genotyping
- Population genomics
- Reduced representation library
- Transposable elements
Cite this
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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 journal › Journal article › Research › peer-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 -