MobiSeq: De novo SNP discovery in model and non‐model species through sequencing the flanking region of transposable elements
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 leve...
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Online Access: | http://dx.doi.org/10.1111/1755-0998.12984 https://api.wiley.com/onlinelibrary/tdm/v1/articles/10.1111%2F1755-0998.12984 https://onlinelibrary.wiley.com/doi/pdf/10.1111/1755-0998.12984 https://onlinelibrary.wiley.com/doi/full-xml/10.1111/1755-0998.12984 |
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crwiley:10.1111/1755-0998.12984 2024-06-23T07:51:59+00:00 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. 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 2019 http://dx.doi.org/10.1111/1755-0998.12984 https://api.wiley.com/onlinelibrary/tdm/v1/articles/10.1111%2F1755-0998.12984 https://onlinelibrary.wiley.com/doi/pdf/10.1111/1755-0998.12984 https://onlinelibrary.wiley.com/doi/full-xml/10.1111/1755-0998.12984 en eng Wiley http://onlinelibrary.wiley.com/termsAndConditions#vor Molecular Ecology Resources volume 19, issue 2, page 512-525 ISSN 1755-098X 1755-0998 journal-article 2019 crwiley https://doi.org/10.1111/1755-0998.12984 2024-06-06T04:22:44Z 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. Article in Journal/Newspaper Canis lupus Wiley Online Library Molecular Ecology Resources 19 2 512 525 |
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Open Polar |
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Wiley Online Library |
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crwiley |
language |
English |
description |
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. |
format |
Article in Journal/Newspaper |
author |
Rey‐Iglesia, Alba Gopalakrishan, 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 |
spellingShingle |
Rey‐Iglesia, Alba Gopalakrishan, 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 MobiSeq: De novo SNP discovery in model and non‐model species through sequencing the flanking region of transposable elements |
author_facet |
Rey‐Iglesia, Alba Gopalakrishan, 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 |
author_sort |
Rey‐Iglesia, Alba |
title |
MobiSeq: De novo SNP discovery in model and non‐model species through sequencing the flanking region of transposable elements |
title_short |
MobiSeq: De novo SNP discovery in model and non‐model species through sequencing the flanking region of transposable elements |
title_full |
MobiSeq: De novo SNP discovery in model and non‐model species through sequencing the flanking region of transposable elements |
title_fullStr |
MobiSeq: De novo SNP discovery in model and non‐model species through sequencing the flanking region of transposable elements |
title_full_unstemmed |
MobiSeq: De novo SNP discovery in model and non‐model species through sequencing the flanking region of transposable elements |
title_sort |
mobiseq: de novo snp discovery in model and non‐model species through sequencing the flanking region of transposable elements |
publisher |
Wiley |
publishDate |
2019 |
url |
http://dx.doi.org/10.1111/1755-0998.12984 https://api.wiley.com/onlinelibrary/tdm/v1/articles/10.1111%2F1755-0998.12984 https://onlinelibrary.wiley.com/doi/pdf/10.1111/1755-0998.12984 https://onlinelibrary.wiley.com/doi/full-xml/10.1111/1755-0998.12984 |
genre |
Canis lupus |
genre_facet |
Canis lupus |
op_source |
Molecular Ecology Resources volume 19, issue 2, page 512-525 ISSN 1755-098X 1755-0998 |
op_rights |
http://onlinelibrary.wiley.com/termsAndConditions#vor |
op_doi |
https://doi.org/10.1111/1755-0998.12984 |
container_title |
Molecular Ecology Resources |
container_volume |
19 |
container_issue |
2 |
container_start_page |
512 |
op_container_end_page |
525 |
_version_ |
1802643165730045952 |