Taxonomic reference libraries for environmental barcoding: a best practice example from diatom research.

DNA barcoding uses a short fragment of a DNA sequence to identify a taxon. After obtaining the target sequence it is compared to reference sequences stored in a database to assign an organism name to it. The quality of data in the reference database is the key to the success of the analysis. In the...

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Autores principales:	Jonas Zimmermann, Nelida Abarca, Neela Enke, Oliver Skibbe, Wolf-Henning Kusber, Regine Jahn
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2014
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/41a065c465cf4384abc2a7723777a7cb
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spelling	oai:doaj.org-article:41a065c465cf4384abc2a7723777a7cb2021-11-25T05:58:48ZTaxonomic reference libraries for environmental barcoding: a best practice example from diatom research.1932-620310.1371/journal.pone.0108793https://doaj.org/article/41a065c465cf4384abc2a7723777a7cb2014-01-01T00:00:00Zhttps://doi.org/10.1371/journal.pone.0108793https://doaj.org/toc/1932-6203DNA barcoding uses a short fragment of a DNA sequence to identify a taxon. After obtaining the target sequence it is compared to reference sequences stored in a database to assign an organism name to it. The quality of data in the reference database is the key to the success of the analysis. In the here presented study, multiple types of data have been combined and critically examined in order to create best practice guidelines for taxonomic reference libraries for environmental barcoding. 70 unialgal diatom strains from Berlin waters have been established and cultured to obtain morphological and molecular data. The strains were sequenced for 18S V4 rDNA (the pre-Barcode for protists) as well as rbcL data, and identified by microscopy. LM and for some strains also SEM pictures were taken and physical vouchers deposited at the BGBM. 37 freshwater taxa from 15 naviculoid diatom genera were identified. Four taxa from the genera Amphora, Mayamaea, Planothidium and Stauroneis are described here as new. Names, molecular, morphological and habitat data as well as additional images of living cells are also available electronically in the AlgaTerra Information System. All reference sequences (or reference barcodes) presented here are linked to voucher specimens in order to provide a complete chain of evidence back to the formal taxonomic literature.Jonas ZimmermannNelida AbarcaNeela EnkeOliver SkibbeWolf-Henning KusberRegine JahnPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 9, Iss 9, p e108793 (2014)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Jonas Zimmermann Nelida Abarca Neela Enke Oliver Skibbe Wolf-Henning Kusber Regine Jahn Taxonomic reference libraries for environmental barcoding: a best practice example from diatom research.
description	DNA barcoding uses a short fragment of a DNA sequence to identify a taxon. After obtaining the target sequence it is compared to reference sequences stored in a database to assign an organism name to it. The quality of data in the reference database is the key to the success of the analysis. In the here presented study, multiple types of data have been combined and critically examined in order to create best practice guidelines for taxonomic reference libraries for environmental barcoding. 70 unialgal diatom strains from Berlin waters have been established and cultured to obtain morphological and molecular data. The strains were sequenced for 18S V4 rDNA (the pre-Barcode for protists) as well as rbcL data, and identified by microscopy. LM and for some strains also SEM pictures were taken and physical vouchers deposited at the BGBM. 37 freshwater taxa from 15 naviculoid diatom genera were identified. Four taxa from the genera Amphora, Mayamaea, Planothidium and Stauroneis are described here as new. Names, molecular, morphological and habitat data as well as additional images of living cells are also available electronically in the AlgaTerra Information System. All reference sequences (or reference barcodes) presented here are linked to voucher specimens in order to provide a complete chain of evidence back to the formal taxonomic literature.
format	article
author	Jonas Zimmermann Nelida Abarca Neela Enke Oliver Skibbe Wolf-Henning Kusber Regine Jahn
author_facet	Jonas Zimmermann Nelida Abarca Neela Enke Oliver Skibbe Wolf-Henning Kusber Regine Jahn
author_sort	Jonas Zimmermann
title	Taxonomic reference libraries for environmental barcoding: a best practice example from diatom research.
title_short	Taxonomic reference libraries for environmental barcoding: a best practice example from diatom research.
title_full	Taxonomic reference libraries for environmental barcoding: a best practice example from diatom research.
title_fullStr	Taxonomic reference libraries for environmental barcoding: a best practice example from diatom research.
title_full_unstemmed	Taxonomic reference libraries for environmental barcoding: a best practice example from diatom research.
title_sort	taxonomic reference libraries for environmental barcoding: a best practice example from diatom research.
publisher	Public Library of Science (PLoS)
publishDate	2014
url	https://doaj.org/article/41a065c465cf4384abc2a7723777a7cb
work_keys_str_mv	AT jonaszimmermann taxonomicreferencelibrariesforenvironmentalbarcodingabestpracticeexamplefromdiatomresearch AT nelidaabarca taxonomicreferencelibrariesforenvironmentalbarcodingabestpracticeexamplefromdiatomresearch AT neelaenke taxonomicreferencelibrariesforenvironmentalbarcodingabestpracticeexamplefromdiatomresearch AT oliverskibbe taxonomicreferencelibrariesforenvironmentalbarcodingabestpracticeexamplefromdiatomresearch AT wolfhenningkusber taxonomicreferencelibrariesforenvironmentalbarcodingabestpracticeexamplefromdiatomresearch AT reginejahn taxonomicreferencelibrariesforenvironmentalbarcodingabestpracticeexamplefromdiatomresearch
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Taxonomic reference libraries for environmental barcoding: a best practice example from diatom research.

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