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dc.contributor.author
Zhan, Aibin
dc.contributor.author
Hulák, Martin
dc.contributor.author
Sylvester, Francisco
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dc.contributor.author
Huang, Xiaoting
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Adebayo, Abisola A.
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Abbott, Cathryn L.
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Adamowicz, Sarah J.
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Heath, Daniel D.
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Cristescu, Melania E.
dc.contributor.author
Macisaac, Hugh
dc.date.available
2015-11-05T18:05:40Z
dc.date.issued
2013-06
dc.identifier.citation
Zhan, Aibin; Hulák, Martin; Sylvester, Francisco; Huang, Xiaoting; Adebayo, Abisola A.; et al.; High sensitivity of 454 pyrosequencing for detection of rare species in aquatic communities; Wiley; Methods in Ecology and Evolution; 4; 6; 6-2013; 558-565
dc.identifier.issn
2041-210X
dc.identifier.uri
http://hdl.handle.net/11336/2674
dc.description.abstract
1. Concerns regarding the rapid loss of endemic biodiversity, and introduction and spread of non-indigenous species, have focused attention on the need and ability to detect species present in communities at low abundance. However, detection of rare species poses immense technical challenges, especially for morphologically cryptic species, microscopic taxa and those beneath the water surface in aquatic ecosystems.
2. Next-generation sequencing technology provides a robust tool to assess biodiversity, especially for detection of rare species. Here, we assess the sensitivity of 454 pyrosequencing for detection of rare species using known indicator species spiked into existing complex plankton samples. In addition, we develop universal small subunit ribosomal DNA primers for amplification of a wide range of taxa for detailed description of biodiversity in complex communities.
3. A universality test of newly designed primers for the hypervariable V4 region of the nuclear small subunit ribosomal DNA (V4-nSSU) using a plankton sample collected from Hamilton Harbor showed that 454 pyrosequencing based on this universal primer pair can recover a wide range of taxa, including animals, plants (algae), fungi, blue-green algae and protists.
4. A sensitivity test showed that 454 pyrosequencing based on newly designed universal V4-nSSU primers was extremely sensitive for detection of very rare species. Pyrosequencing was able to recover spiked indicator species with biomass percentage as low as approximately 2 3 9 105 % when 24 artificially assembled samples were tagged and sequenced in one PicoTiter plate (i.e. sequencing depth of an equivalent of 1/24 PicoTiter plate). In addition, spiked rare species were sometimes recovered as singletons (i.e. Operational Taxonomic Units represented by a single sequence), suggesting that at least some singletons are informative for recovering unique lineages in ‘rare biospheres’.
5. The method established here allows biologists to better investigate the composition of aquatic communities, especially for detection of rare taxa. Despite a small-scale pyrosequencing effort, we demonstrate the extreme sensitivity of pyrosequencing using rare species spiked into plankton samples. We propose that the method is a powerful tool for detection of rare native and/or alien species.
dc.format
application/pdf
dc.language.iso
eng
dc.publisher
Wiley
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dc.rights
info:eu-repo/semantics/openAccess
dc.rights.uri
https://creativecommons.org/licenses/by-nc-sa/2.5/ar/
dc.subject
ALIEN INVASIVE SPECIES
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BIODIVERSITY
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ENDANGERED SPECIES
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NEXT-GENERATION SEQUENCING (NGS)
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NON-INDIGENOUS SPECIES
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NSSU RDNA
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PLANKTON
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UNIVERSAL PRIMERS
dc.subject.classification
Conservación de la Biodiversidad
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dc.subject.classification
Ciencias Biológicas
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dc.subject.classification
CIENCIAS NATURALES Y EXACTAS
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dc.subject.classification
Ecología
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dc.subject.classification
Ciencias Biológicas
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dc.subject.classification
CIENCIAS NATURALES Y EXACTAS
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dc.title
High sensitivity of 454 pyrosequencing for detection of rare species in aquatic communities
dc.type
info:eu-repo/semantics/article
dc.type
info:ar-repo/semantics/artículo
dc.type
info:eu-repo/semantics/publishedVersion
dc.date.updated
2016-03-30 10:35:44.97925-03
dc.journal.volume
4
dc.journal.number
6
dc.journal.pagination
558-565
dc.journal.pais
Estados Unidos
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dc.journal.ciudad
Hoboken
dc.conicet.avisoEditorial
This is the peer reviewed version of the following article: Zhan, Aibin; Hulák, Martin; Sylvester, Francisco; Huang, Xiaoting; Adebayo, Abisola A.; et al.; High sensitivity of 454 pyrosequencing for detection of rare species in aquatic communities; Wiley; Methods in Ecology and Evolution; 4; 6; 6-2013; 558-565, which has been published in final form at http://dx.doi.org/DOI:10.1111/2041-210X.12037. This article may be used for non-commercial purposes in accordance with Wiley Terms and Conditions for Self-Archiving. © 2013 British Ecological Society
dc.description.fil
Fil: Zhan, Aibin. University of Windsor. Great Lakes Institute for Enviromental Research; Canadá
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Fil: Hulák, Martin. University of Windsor. Great Lakes Institute for Enviromental Research; Canadá
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Fil: Sylvester, Francisco. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Ecología, Genética y Evolución de Buenos Aires; Argentina. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Departamento de Ecología, Genética y Evolución; Argentina
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Fil: Huang, Xiaoting. Ocean University of China. College of Marine Life Sciences. Ministry of Education. Key Laboratory of Marine Genetics and Breeding; China
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Fil: Adebayo, Abisola A.. University of Windsor. Great Lakes Institute for Enviromental Research; Canadá
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Fil: Abbott, Cathryn L.. Fisheries and Oceans Canada. Pacific Biological Station; Canadá
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Fil: Adamowicz, Sarah J.. University of Guelph. Department of Integrative Biology; Canadá. University Of Guelph. Biodiversity Institute Of Ontario; Canadá
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Fil: Heath, Daniel D.. University of Windsor. Great Lakes Institute for Enviromental Research; Canadá
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Fil: Cristescu, Melania E.. University of Windsor. Great Lakes Institute for Enviromental Research; Canadá. McGill University. Department of Biology; Canadá
dc.description.fil
Fil: Macisaac, Hugh. University of Windsor. Great Lakes Institute for Enviromental Research; Canadá
dc.journal.title
Methods in Ecology and Evolution
dc.relation.alternativeid
info:eu-repo/semantics/altIdentifier/doi/http://dx.doi.org/DOI:10.1111/2041-210X.12037
dc.relation.alternativeid
info:eu-repo/semantics/altIdentifier/url/http://onlinelibrary.wiley.com/doi/10.1111/2041-210X.12037/abstract
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