DNA metabarcoding of Neotropical ichthyoplankton: Enabling high accuracy with lower cost

Detalhes bibliográficos
Autor(a) principal: Nobile, André B.
Data de Publicação: 2019
Outros Autores: Freitas-Souza, Diogo, Ruiz-Ruano, Francisco J., Nobile, Maria Lígia MO., Costa, Gabriela O., De Lima, Felipe P., Camacho, Juan Pedro M., Foresti, Fausto, Oliveira, Claudio
Tipo de documento: Artigo
Idioma: eng
Título da fonte: Repositório Institucional da UNESP
Texto Completo: http://dx.doi.org/10.3897/mbmg.3.35060
http://hdl.handle.net/11449/205143
Resumo: Knowledge of ichthyoplankton dynamics is extremely important for conservation management as it can provide information about preferential spawning sites, reproductive period, migratory routes and recruitment success, which can be used to guide management and conservation efforts. However, identification of the eggs and larvae of Neotropical freshwater fish is a difficult task. DNA barcodes have emerged as an alternative and highly accurate approach for species identification, but DNA barcoding can be time-consuming and costly. To solve this problem, we aimed to develop a simple protocol based on DNA metabarcoding, to investigate whether it is possible to detect and quantify all species present in a pool of organisms. To do this, 230 larvae were cut in half, one half was sequenced by the Sanger technique and the other half was used to compose six arrays with a pool of larvae that were sequenced using a next-generation technique (NGS). The results of the Sanger sequencing allowed the identification of almost all larvae at species level, and the results from NGS showed high accuracy in species detection, ranging from 83% to 100%, with an average of 95% in all samples. No false positives were detected. The frequency of organisms in the two methods was positively correlated (Pearson), with low variation among species. In conclusion, this protocol represents a considerable advance in ichthyoplankton studies, allowing a rapid, cost-effective, quali-quantitative approach that improves the accuracy of identification.
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spelling DNA metabarcoding of Neotropical ichthyoplankton: Enabling high accuracy with lower costDNA BarcodingFisheries managementIchthyofaunaUpper Paraná RiverKnowledge of ichthyoplankton dynamics is extremely important for conservation management as it can provide information about preferential spawning sites, reproductive period, migratory routes and recruitment success, which can be used to guide management and conservation efforts. However, identification of the eggs and larvae of Neotropical freshwater fish is a difficult task. DNA barcodes have emerged as an alternative and highly accurate approach for species identification, but DNA barcoding can be time-consuming and costly. To solve this problem, we aimed to develop a simple protocol based on DNA metabarcoding, to investigate whether it is possible to detect and quantify all species present in a pool of organisms. To do this, 230 larvae were cut in half, one half was sequenced by the Sanger technique and the other half was used to compose six arrays with a pool of larvae that were sequenced using a next-generation technique (NGS). The results of the Sanger sequencing allowed the identification of almost all larvae at species level, and the results from NGS showed high accuracy in species detection, ranging from 83% to 100%, with an average of 95% in all samples. No false positives were detected. The frequency of organisms in the two methods was positively correlated (Pearson), with low variation among species. In conclusion, this protocol represents a considerable advance in ichthyoplankton studies, allowing a rapid, cost-effective, quali-quantitative approach that improves the accuracy of identification.Laboratório de Biologia e Genética de Peixes Departamento de MorfologiaEvolutionary Genetics group Department of Genetics University of GranadaDepartment of Ecology and Genetics Evolutionary Biology Centre Uppsala UniversityUniversidade Estadual Paulista (Unesp)University of GranadaUppsala UniversityNobile, André B.Freitas-Souza, DiogoRuiz-Ruano, Francisco J.Nobile, Maria Lígia MO.Costa, Gabriela O.De Lima, Felipe P.Camacho, Juan Pedro M.Foresti, FaustoOliveira, Claudio2021-06-25T10:10:31Z2021-06-25T10:10:31Z2019-09-05info:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/article69-76http://dx.doi.org/10.3897/mbmg.3.35060Metabarcoding and Metagenomics, v. 3, p. 69-76.2534-9708http://hdl.handle.net/11449/20514310.3897/mbmg.3.350602-s2.0-85082304487Scopusreponame:Repositório Institucional da UNESPinstname:Universidade Estadual Paulista (UNESP)instacron:UNESPengMetabarcoding and Metagenomicsinfo:eu-repo/semantics/openAccess2021-10-23T10:40:59Zoai:repositorio.unesp.br:11449/205143Repositório InstitucionalPUBhttp://repositorio.unesp.br/oai/requestopendoar:29462024-08-05T14:38:11.588782Repositório Institucional da UNESP - Universidade Estadual Paulista (UNESP)false
dc.title.none.fl_str_mv DNA metabarcoding of Neotropical ichthyoplankton: Enabling high accuracy with lower cost
title DNA metabarcoding of Neotropical ichthyoplankton: Enabling high accuracy with lower cost
spellingShingle DNA metabarcoding of Neotropical ichthyoplankton: Enabling high accuracy with lower cost
Nobile, André B.
DNA Barcoding
Fisheries management
Ichthyofauna
Upper Paraná River
title_short DNA metabarcoding of Neotropical ichthyoplankton: Enabling high accuracy with lower cost
title_full DNA metabarcoding of Neotropical ichthyoplankton: Enabling high accuracy with lower cost
title_fullStr DNA metabarcoding of Neotropical ichthyoplankton: Enabling high accuracy with lower cost
title_full_unstemmed DNA metabarcoding of Neotropical ichthyoplankton: Enabling high accuracy with lower cost
title_sort DNA metabarcoding of Neotropical ichthyoplankton: Enabling high accuracy with lower cost
author Nobile, André B.
author_facet Nobile, André B.
Freitas-Souza, Diogo
Ruiz-Ruano, Francisco J.
Nobile, Maria Lígia MO.
Costa, Gabriela O.
De Lima, Felipe P.
Camacho, Juan Pedro M.
Foresti, Fausto
Oliveira, Claudio
author_role author
author2 Freitas-Souza, Diogo
Ruiz-Ruano, Francisco J.
Nobile, Maria Lígia MO.
Costa, Gabriela O.
De Lima, Felipe P.
Camacho, Juan Pedro M.
Foresti, Fausto
Oliveira, Claudio
author2_role author
author
author
author
author
author
author
author
dc.contributor.none.fl_str_mv Universidade Estadual Paulista (Unesp)
University of Granada
Uppsala University
dc.contributor.author.fl_str_mv Nobile, André B.
Freitas-Souza, Diogo
Ruiz-Ruano, Francisco J.
Nobile, Maria Lígia MO.
Costa, Gabriela O.
De Lima, Felipe P.
Camacho, Juan Pedro M.
Foresti, Fausto
Oliveira, Claudio
dc.subject.por.fl_str_mv DNA Barcoding
Fisheries management
Ichthyofauna
Upper Paraná River
topic DNA Barcoding
Fisheries management
Ichthyofauna
Upper Paraná River
description Knowledge of ichthyoplankton dynamics is extremely important for conservation management as it can provide information about preferential spawning sites, reproductive period, migratory routes and recruitment success, which can be used to guide management and conservation efforts. However, identification of the eggs and larvae of Neotropical freshwater fish is a difficult task. DNA barcodes have emerged as an alternative and highly accurate approach for species identification, but DNA barcoding can be time-consuming and costly. To solve this problem, we aimed to develop a simple protocol based on DNA metabarcoding, to investigate whether it is possible to detect and quantify all species present in a pool of organisms. To do this, 230 larvae were cut in half, one half was sequenced by the Sanger technique and the other half was used to compose six arrays with a pool of larvae that were sequenced using a next-generation technique (NGS). The results of the Sanger sequencing allowed the identification of almost all larvae at species level, and the results from NGS showed high accuracy in species detection, ranging from 83% to 100%, with an average of 95% in all samples. No false positives were detected. The frequency of organisms in the two methods was positively correlated (Pearson), with low variation among species. In conclusion, this protocol represents a considerable advance in ichthyoplankton studies, allowing a rapid, cost-effective, quali-quantitative approach that improves the accuracy of identification.
publishDate 2019
dc.date.none.fl_str_mv 2019-09-05
2021-06-25T10:10:31Z
2021-06-25T10:10:31Z
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/10.3897/mbmg.3.35060
Metabarcoding and Metagenomics, v. 3, p. 69-76.
2534-9708
http://hdl.handle.net/11449/205143
10.3897/mbmg.3.35060
2-s2.0-85082304487
url http://dx.doi.org/10.3897/mbmg.3.35060
http://hdl.handle.net/11449/205143
identifier_str_mv Metabarcoding and Metagenomics, v. 3, p. 69-76.
2534-9708
10.3897/mbmg.3.35060
2-s2.0-85082304487
dc.language.iso.fl_str_mv eng
language eng
dc.relation.none.fl_str_mv Metabarcoding and Metagenomics
dc.rights.driver.fl_str_mv info:eu-repo/semantics/openAccess
eu_rights_str_mv openAccess
dc.format.none.fl_str_mv 69-76
dc.source.none.fl_str_mv Scopus
reponame:Repositório Institucional da UNESP
instname:Universidade Estadual Paulista (UNESP)
instacron:UNESP
instname_str Universidade Estadual Paulista (UNESP)
instacron_str UNESP
institution UNESP
reponame_str Repositório Institucional da UNESP
collection Repositório Institucional da UNESP
repository.name.fl_str_mv Repositório Institucional da UNESP - Universidade Estadual Paulista (UNESP)
repository.mail.fl_str_mv
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