Freshwater vertebrate metabarcoding on Illumina platforms using double-indexed primers of the mitochondrial 16S rRNA gene
| Autor(a) principal: | |
|---|---|
| Data de Publicação: | 2016 |
| Outros Autores: | , , , , , , , , , |
| Tipo de documento: | Artigo |
| Idioma: | eng |
| Título da fonte: | Repositório Institucional da UNESP |
| Texto Completo: | http://dx.doi.org/10.1007/s12686-016-0550-y http://hdl.handle.net/11449/161850 |
Resumo: | Metabarcoding is a promising tool for biodiversity inventories and other applications in conservation genetics. We developed a new pair of primers for efficient and affordable high-throughput analysis of a 250 base pair stretch of DNA from the mitochondrial 16S rRNA gene of vertebrates, especially amphibians and fishes. By adapting a double-indexed protocol for Illumina platforms, our approach allows pooling of hundreds of samples in a single sequencing run. We obtained high detection rates of 82-93 % for fish in two German streams, 70 % for mock mixes of DNA from amphibians and fishes, and could distinguish multiple gene copies in amphibians, probably caused by nuclear-mitochondrial transposed DNA or heteroplasmy. |
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Freshwater vertebrate metabarcoding on Illumina platforms using double-indexed primers of the mitochondrial 16S rRNA geneeDNADouble-indexed primersAmphibiansDiscoglossusNUMTMetabarcoding is a promising tool for biodiversity inventories and other applications in conservation genetics. We developed a new pair of primers for efficient and affordable high-throughput analysis of a 250 base pair stretch of DNA from the mitochondrial 16S rRNA gene of vertebrates, especially amphibians and fishes. By adapting a double-indexed protocol for Illumina platforms, our approach allows pooling of hundreds of samples in a single sequencing run. We obtained high detection rates of 82-93 % for fish in two German streams, 70 % for mock mixes of DNA from amphibians and fishes, and could distinguish multiple gene copies in amphibians, probably caused by nuclear-mitochondrial transposed DNA or heteroplasmy.Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)Braunschweig Univ Technol, Inst Zool, Mendelssohnstr 4, D-38106 Braunschweig, GermanyUniv Estadual Paulista, Inst Biociencias, Dept Zool, BR-13506900 Rio Claro, SP, BrazilUniv Trieste, Dept Life Sci, Genet Lab, Via Licio Giorgieri 5, I-34127 Trieste, ItalyHelmholtz Ctr Infect Res, Dept Genome Analyt, Braunschweig, GermanyUniv Estadual Paulista, Inst Biociencias, Dept Zool, BR-13506900 Rio Claro, SP, BrazilCAPES: 88881.062205/2014-01FAPESP: 2013/50741-7SpringerBraunschweig Univ TechnolUniversidade Estadual Paulista (Unesp)Univ TriesteHelmholtz Ctr Infect ResVences, MiguelLyra, Mariana L. [UNESP]Perl, R. G. BinaBletz, Molly C.Stankovic, DavidLopes, Carla Martins [UNESP]Jarek, MichaelBhuju, SabinGeffers, RobertHaddad, Celio F. B. [UNESP]Steinfartz, Sebastian2018-11-26T16:56:29Z2018-11-26T16:56:29Z2016-09-01info:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/article323-327application/pdfhttp://dx.doi.org/10.1007/s12686-016-0550-yConservation Genetics Resources. Dordrecht: Springer, v. 8, n. 3, p. 323-327, 2016.1877-7252http://hdl.handle.net/11449/16185010.1007/s12686-016-0550-yWOS:000382116900027WOS000382116900027.pdfWeb of Sciencereponame:Repositório Institucional da UNESPinstname:Universidade Estadual Paulista (UNESP)instacron:UNESPengConservation Genetics Resources0,430info:eu-repo/semantics/openAccess2024-01-19T06:27:29Zoai:repositorio.unesp.br:11449/161850Repositório InstitucionalPUBhttp://repositorio.unesp.br/oai/requestopendoar:29462024-01-19T06:27:29Repositório Institucional da UNESP - Universidade Estadual Paulista (UNESP)false |
| dc.title.none.fl_str_mv |
Freshwater vertebrate metabarcoding on Illumina platforms using double-indexed primers of the mitochondrial 16S rRNA gene |
| title |
Freshwater vertebrate metabarcoding on Illumina platforms using double-indexed primers of the mitochondrial 16S rRNA gene |
| spellingShingle |
Freshwater vertebrate metabarcoding on Illumina platforms using double-indexed primers of the mitochondrial 16S rRNA gene Vences, Miguel eDNA Double-indexed primers Amphibians Discoglossus NUMT |
| title_short |
Freshwater vertebrate metabarcoding on Illumina platforms using double-indexed primers of the mitochondrial 16S rRNA gene |
| title_full |
Freshwater vertebrate metabarcoding on Illumina platforms using double-indexed primers of the mitochondrial 16S rRNA gene |
| title_fullStr |
Freshwater vertebrate metabarcoding on Illumina platforms using double-indexed primers of the mitochondrial 16S rRNA gene |
| title_full_unstemmed |
Freshwater vertebrate metabarcoding on Illumina platforms using double-indexed primers of the mitochondrial 16S rRNA gene |
| title_sort |
Freshwater vertebrate metabarcoding on Illumina platforms using double-indexed primers of the mitochondrial 16S rRNA gene |
| author |
Vences, Miguel |
| author_facet |
Vences, Miguel Lyra, Mariana L. [UNESP] Perl, R. G. Bina Bletz, Molly C. Stankovic, David Lopes, Carla Martins [UNESP] Jarek, Michael Bhuju, Sabin Geffers, Robert Haddad, Celio F. B. [UNESP] Steinfartz, Sebastian |
| author_role |
author |
| author2 |
Lyra, Mariana L. [UNESP] Perl, R. G. Bina Bletz, Molly C. Stankovic, David Lopes, Carla Martins [UNESP] Jarek, Michael Bhuju, Sabin Geffers, Robert Haddad, Celio F. B. [UNESP] Steinfartz, Sebastian |
| author2_role |
author author author author author author author author author author |
| dc.contributor.none.fl_str_mv |
Braunschweig Univ Technol Universidade Estadual Paulista (Unesp) Univ Trieste Helmholtz Ctr Infect Res |
| dc.contributor.author.fl_str_mv |
Vences, Miguel Lyra, Mariana L. [UNESP] Perl, R. G. Bina Bletz, Molly C. Stankovic, David Lopes, Carla Martins [UNESP] Jarek, Michael Bhuju, Sabin Geffers, Robert Haddad, Celio F. B. [UNESP] Steinfartz, Sebastian |
| dc.subject.por.fl_str_mv |
eDNA Double-indexed primers Amphibians Discoglossus NUMT |
| topic |
eDNA Double-indexed primers Amphibians Discoglossus NUMT |
| description |
Metabarcoding is a promising tool for biodiversity inventories and other applications in conservation genetics. We developed a new pair of primers for efficient and affordable high-throughput analysis of a 250 base pair stretch of DNA from the mitochondrial 16S rRNA gene of vertebrates, especially amphibians and fishes. By adapting a double-indexed protocol for Illumina platforms, our approach allows pooling of hundreds of samples in a single sequencing run. We obtained high detection rates of 82-93 % for fish in two German streams, 70 % for mock mixes of DNA from amphibians and fishes, and could distinguish multiple gene copies in amphibians, probably caused by nuclear-mitochondrial transposed DNA or heteroplasmy. |
| publishDate |
2016 |
| dc.date.none.fl_str_mv |
2016-09-01 2018-11-26T16:56:29Z 2018-11-26T16:56:29Z |
| dc.type.status.fl_str_mv |
info:eu-repo/semantics/publishedVersion |
| dc.type.driver.fl_str_mv |
info:eu-repo/semantics/article |
| format |
article |
| status_str |
publishedVersion |
| dc.identifier.uri.fl_str_mv |
http://dx.doi.org/10.1007/s12686-016-0550-y Conservation Genetics Resources. Dordrecht: Springer, v. 8, n. 3, p. 323-327, 2016. 1877-7252 http://hdl.handle.net/11449/161850 10.1007/s12686-016-0550-y WOS:000382116900027 WOS000382116900027.pdf |
| url |
http://dx.doi.org/10.1007/s12686-016-0550-y http://hdl.handle.net/11449/161850 |
| identifier_str_mv |
Conservation Genetics Resources. Dordrecht: Springer, v. 8, n. 3, p. 323-327, 2016. 1877-7252 10.1007/s12686-016-0550-y WOS:000382116900027 WOS000382116900027.pdf |
| dc.language.iso.fl_str_mv |
eng |
| language |
eng |
| dc.relation.none.fl_str_mv |
Conservation Genetics Resources 0,430 |
| dc.rights.driver.fl_str_mv |
info:eu-repo/semantics/openAccess |
| eu_rights_str_mv |
openAccess |
| dc.format.none.fl_str_mv |
323-327 application/pdf |
| dc.publisher.none.fl_str_mv |
Springer |
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Springer |
| dc.source.none.fl_str_mv |
Web of Science reponame:Repositório Institucional da UNESP instname:Universidade Estadual Paulista (UNESP) instacron:UNESP |
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Universidade Estadual Paulista (UNESP) |
| instacron_str |
UNESP |
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UNESP |
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Repositório Institucional da UNESP |
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Repositório Institucional da UNESP |
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Repositório Institucional da UNESP - Universidade Estadual Paulista (UNESP) |
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