Comparison and validation of some ITS primer pairs useful for fungal metabarcoding studies.

Current metabarcoding studies aiming to characterize microbial communities generally rely on the amplification and sequencing of relatively short DNA regions. For fungi, the internal transcribed spacer (ITS) region in the ribosomal RNA (rRNA) operon has been accepted as the formal fungal barcode. De...

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Autores principales:	Michiel Op De Beeck, Bart Lievens, Pieter Busschaert, Stéphan Declerck, Jaco Vangronsveld, Jan V Colpaert
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2014
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/538a1695feb346d6b54ba2614f192195
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spelling	oai:doaj.org-article:538a1695feb346d6b54ba2614f1921952021-11-18T08:15:27ZComparison and validation of some ITS primer pairs useful for fungal metabarcoding studies.1932-620310.1371/journal.pone.0097629https://doaj.org/article/538a1695feb346d6b54ba2614f1921952014-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/24933453/?tool=EBIhttps://doaj.org/toc/1932-6203Current metabarcoding studies aiming to characterize microbial communities generally rely on the amplification and sequencing of relatively short DNA regions. For fungi, the internal transcribed spacer (ITS) region in the ribosomal RNA (rRNA) operon has been accepted as the formal fungal barcode. Despite an increasing number of fungal metabarcoding studies, the amplification efficiency of primers is generally not tested prior to their application in metabarcoding studies. Some of the challenges that metabarcoding primers should overcome efficiently are the amplification of target DNA strands in samples rich in non-target DNA and environmental pollutants, such as humic acids, that may have been co-extracted with DNA. In the current study, three selected primer pairs were tested for their suitability as fungal metabarcoding primers. The selected primer pairs include two primer pairs that have been frequently used in fungal metabarcoding studies (ITS1F/ITS2 and ITS3/ITS4) and a primer pair (ITS86F/ITS4) that has been shown to efficiently amplify the ITS2 region of a broad range of fungal taxa in environmental soil samples. The selected primer pairs were evaluated in a 454 amplicon pyrosequencing experiment, real-time PCR (qPCR) experiments and in silico analyses. Results indicate that experimental evaluation of primers provides valuable information that could aid in the selection of suitable primers for fungal metabarcoding studies. Furthermore, we show that the ITS86F/ITS4 primer pair outperforms other primer pairs tested in terms of in silico primer efficiency, PCR efficiency, coverage, number of reads and number of species-level operational taxonomic units (OTUs) obtained. These traits push the ITS86F/ITS4 primer pair forward as highly suitable for studying fungal diversity and community structures using DNA metabarcoding.Michiel Op De BeeckBart LievensPieter BusschaertStéphan DeclerckJaco VangronsveldJan V ColpaertPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 9, Iss 6, p e97629 (2014)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Michiel Op De Beeck Bart Lievens Pieter Busschaert Stéphan Declerck Jaco Vangronsveld Jan V Colpaert Comparison and validation of some ITS primer pairs useful for fungal metabarcoding studies.
description	Current metabarcoding studies aiming to characterize microbial communities generally rely on the amplification and sequencing of relatively short DNA regions. For fungi, the internal transcribed spacer (ITS) region in the ribosomal RNA (rRNA) operon has been accepted as the formal fungal barcode. Despite an increasing number of fungal metabarcoding studies, the amplification efficiency of primers is generally not tested prior to their application in metabarcoding studies. Some of the challenges that metabarcoding primers should overcome efficiently are the amplification of target DNA strands in samples rich in non-target DNA and environmental pollutants, such as humic acids, that may have been co-extracted with DNA. In the current study, three selected primer pairs were tested for their suitability as fungal metabarcoding primers. The selected primer pairs include two primer pairs that have been frequently used in fungal metabarcoding studies (ITS1F/ITS2 and ITS3/ITS4) and a primer pair (ITS86F/ITS4) that has been shown to efficiently amplify the ITS2 region of a broad range of fungal taxa in environmental soil samples. The selected primer pairs were evaluated in a 454 amplicon pyrosequencing experiment, real-time PCR (qPCR) experiments and in silico analyses. Results indicate that experimental evaluation of primers provides valuable information that could aid in the selection of suitable primers for fungal metabarcoding studies. Furthermore, we show that the ITS86F/ITS4 primer pair outperforms other primer pairs tested in terms of in silico primer efficiency, PCR efficiency, coverage, number of reads and number of species-level operational taxonomic units (OTUs) obtained. These traits push the ITS86F/ITS4 primer pair forward as highly suitable for studying fungal diversity and community structures using DNA metabarcoding.
format	article
author	Michiel Op De Beeck Bart Lievens Pieter Busschaert Stéphan Declerck Jaco Vangronsveld Jan V Colpaert
author_facet	Michiel Op De Beeck Bart Lievens Pieter Busschaert Stéphan Declerck Jaco Vangronsveld Jan V Colpaert
author_sort	Michiel Op De Beeck
title	Comparison and validation of some ITS primer pairs useful for fungal metabarcoding studies.
title_short	Comparison and validation of some ITS primer pairs useful for fungal metabarcoding studies.
title_full	Comparison and validation of some ITS primer pairs useful for fungal metabarcoding studies.
title_fullStr	Comparison and validation of some ITS primer pairs useful for fungal metabarcoding studies.
title_full_unstemmed	Comparison and validation of some ITS primer pairs useful for fungal metabarcoding studies.
title_sort	comparison and validation of some its primer pairs useful for fungal metabarcoding studies.
publisher	Public Library of Science (PLoS)
publishDate	2014
url	https://doaj.org/article/538a1695feb346d6b54ba2614f192195
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Comparison and validation of some ITS primer pairs useful for fungal metabarcoding studies.

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