Internal transcribed spacer primer evaluation for vascular plant metabarcoding

The unprecedented ongoing biodiversity decline necessitates scalable means of monitoring in order to fully understand the underlying causes. DNA metabarcoding has the potential to provide a powerful tool for accurate and rapid biodiversity monitoring. Unfortunately, in many cases, a lack of universa...

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Autores principales:	Andreas Kolter, Birgit Gemeinholzer
Formato:	article
Lenguaje:	EN
Publicado:	Pensoft Publishers 2021
Materias:	Ecology QH540-549.5
Acceso en línea:	https://doaj.org/article/625053c74c6047fcad468e2ff18376be
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spelling	oai:doaj.org-article:625053c74c6047fcad468e2ff18376be2021-12-02T18:09:46ZInternal transcribed spacer primer evaluation for vascular plant metabarcoding10.3897/mbmg.5.681552534-9708https://doaj.org/article/625053c74c6047fcad468e2ff18376be2021-09-01T00:00:00Zhttps://mbmg.pensoft.net/article/68155/download/pdf/https://mbmg.pensoft.net/article/68155/download/xml/https://mbmg.pensoft.net/article/68155/https://doaj.org/toc/2534-9708The unprecedented ongoing biodiversity decline necessitates scalable means of monitoring in order to fully understand the underlying causes. DNA metabarcoding has the potential to provide a powerful tool for accurate and rapid biodiversity monitoring. Unfortunately, in many cases, a lack of universal standards undermines the widespread application of metabarcoding. One of the most important considerations in metabarcoding of plants, aside from selecting a potent barcode marker, is primer choice. Our study evaluates published ITS primers in silico and in vitro, through mock communities and presents newly designed primers. We were able to show that a large proportion of previously available ITS primers have unfavourable attributes. Our combined results support the recommendation of the introduced primers ITS-3p62plF1 and ITS-4unR1 as the best current universal plant specific ITS2 primer combination. We also found that PCR optimisation, such as the addition of 5% DMSO, is essential to obtain meaningful results in ITS2 metabarcoding. Finally, we conclude that continuous quality assurance is indispensable for reliable metabarcoding results.Andreas KolterBirgit GemeinholzerPensoft PublishersarticleEcologyQH540-549.5ENMetabarcoding and Metagenomics, Vol 5, Iss , Pp 133-152 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Ecology QH540-549.5
spellingShingle	Ecology QH540-549.5 Andreas Kolter Birgit Gemeinholzer Internal transcribed spacer primer evaluation for vascular plant metabarcoding
description	The unprecedented ongoing biodiversity decline necessitates scalable means of monitoring in order to fully understand the underlying causes. DNA metabarcoding has the potential to provide a powerful tool for accurate and rapid biodiversity monitoring. Unfortunately, in many cases, a lack of universal standards undermines the widespread application of metabarcoding. One of the most important considerations in metabarcoding of plants, aside from selecting a potent barcode marker, is primer choice. Our study evaluates published ITS primers in silico and in vitro, through mock communities and presents newly designed primers. We were able to show that a large proportion of previously available ITS primers have unfavourable attributes. Our combined results support the recommendation of the introduced primers ITS-3p62plF1 and ITS-4unR1 as the best current universal plant specific ITS2 primer combination. We also found that PCR optimisation, such as the addition of 5% DMSO, is essential to obtain meaningful results in ITS2 metabarcoding. Finally, we conclude that continuous quality assurance is indispensable for reliable metabarcoding results.
format	article
author	Andreas Kolter Birgit Gemeinholzer
author_facet	Andreas Kolter Birgit Gemeinholzer
author_sort	Andreas Kolter
title	Internal transcribed spacer primer evaluation for vascular plant metabarcoding
title_short	Internal transcribed spacer primer evaluation for vascular plant metabarcoding
title_full	Internal transcribed spacer primer evaluation for vascular plant metabarcoding
title_fullStr	Internal transcribed spacer primer evaluation for vascular plant metabarcoding
title_full_unstemmed	Internal transcribed spacer primer evaluation for vascular plant metabarcoding
title_sort	internal transcribed spacer primer evaluation for vascular plant metabarcoding
publisher	Pensoft Publishers
publishDate	2021
url	https://doaj.org/article/625053c74c6047fcad468e2ff18376be
work_keys_str_mv	AT andreaskolter internaltranscribedspacerprimerevaluationforvascularplantmetabarcoding AT birgitgemeinholzer internaltranscribedspacerprimerevaluationforvascularplantmetabarcoding
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Internal transcribed spacer primer evaluation for vascular plant metabarcoding

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