DNA metabarcoding of Neotropical ichthyoplankton: Enabling high accuracy with lower cost
Autor(a) principal: | |
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Data de Publicação: | 2019 |
Outros Autores: | , , , , , , , |
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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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 |
|
_version_ |
1808128391403012096 |