MobiSeq: De novo SNP discovery in model and non-model species through sequencing the flanking region of transposable elements
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...
| Main Authors: | , , , , , , , , , , , , , , , |
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| Format: | Journal Article |
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Wiley-Blackwell
2019
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| Online Access: | http://hdl.handle.net/20.500.11937/74699 |
| _version_ | 1848763348073578496 |
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| author | Rey-Iglesia, A. Gopalakrishan, S. Carøe, C. Alquezar-Planas, D. Ahlmann Nielsen, A. Röder, T. Bruhn Pedersen, L. Næsborg-Nielsen, C. Sinding, M. Fredensborg Rath, M. Li, Z. Petersen, B. Gilbert, M. Bunce, Michael Mourier, T. Hansen, A. |
| author_facet | Rey-Iglesia, A. Gopalakrishan, S. Carøe, C. Alquezar-Planas, D. Ahlmann Nielsen, A. Röder, T. Bruhn Pedersen, L. Næsborg-Nielsen, C. Sinding, M. Fredensborg Rath, M. Li, Z. Petersen, B. Gilbert, M. Bunce, Michael Mourier, T. Hansen, A. |
| author_sort | Rey-Iglesia, A. |
| building | Curtin Institutional Repository |
| collection | Online Access |
| description | 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. |
| first_indexed | 2025-11-14T11:02:02Z |
| format | Journal Article |
| id | curtin-20.500.11937-74699 |
| institution | Curtin University Malaysia |
| institution_category | Local University |
| last_indexed | 2025-11-14T11:02:02Z |
| publishDate | 2019 |
| publisher | Wiley-Blackwell |
| recordtype | eprints |
| repository_type | Digital Repository |
| spelling | curtin-20.500.11937-746992019-05-01T05:43:15Z MobiSeq: De novo SNP discovery in model and non-model species through sequencing the flanking region of transposable elements Rey-Iglesia, A. Gopalakrishan, S. Carøe, C. Alquezar-Planas, D. Ahlmann Nielsen, A. Röder, T. Bruhn Pedersen, L. Næsborg-Nielsen, C. Sinding, M. Fredensborg Rath, M. Li, Z. Petersen, B. Gilbert, M. Bunce, Michael Mourier, T. Hansen, A. 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. 2019 Journal Article http://hdl.handle.net/20.500.11937/74699 10.1111/1755-0998.12984 Wiley-Blackwell restricted |
| spellingShingle | Rey-Iglesia, A. Gopalakrishan, S. Carøe, C. Alquezar-Planas, D. Ahlmann Nielsen, A. Röder, T. Bruhn Pedersen, L. Næsborg-Nielsen, C. Sinding, M. Fredensborg Rath, M. Li, Z. Petersen, B. Gilbert, M. Bunce, Michael Mourier, T. Hansen, A. MobiSeq: De novo SNP discovery in model and non-model species through sequencing the flanking region of transposable elements |
| title | 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_short | 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 |
| url | http://hdl.handle.net/20.500.11937/74699 |