Does One Size Fit All? Variations in the DNA Barcode Gaps of Macrofungal Genera

The nuclear ribosomal internal transcribed spacer (nrITS) region has been widely used in fungal diversity studies. Environmental metabarcoding has increased the importance of the fungal DNA barcode in documenting fungal diversity and distribution. The DNA barcode gap is seen as the difference betwee...
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Autor*in:	Andrew W. Wilson [verfasserIn] Ursula Eberhardt [verfasserIn] Nhu Nguyen [verfasserIn] Chance R. Noffsinger [verfasserIn] Rachel A. Swenie [verfasserIn] Justin L. Loucks [verfasserIn] Brian A. Perry [verfasserIn] Mariana Herrera [verfasserIn] Todd W. Osmundson [verfasserIn] Sarah DeLong-Duhon [verfasserIn] Henry J. Beker [verfasserIn] Gregory M. Mueller [verfasserIn]

Format:	E-Artikel
Sprache:	Englisch

Erschienen:	2023

Schlagwörter:	DNA barcode pairwise distances nrITS ITS1 ITS2

Übergeordnetes Werk:	In: Journal of Fungi - MDPI AG, 2015, 9(2023), 8, p 788
Übergeordnetes Werk:	volume:9 ; year:2023 ; number:8, p 788

Links:	Link aufrufen Link aufrufen Link aufrufen Journal toc

DOI / URN:	10.3390/jof9080788

Katalog-ID:	DOAJ093595492

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callnumber-first	Q - Science
author	Andrew W. Wilson
spellingShingle	Andrew W. Wilson misc QH301-705.5 misc DNA barcode misc pairwise distances misc nrITS misc ITS1 misc ITS2 misc Biology (General) Does One Size Fit All? Variations in the DNA Barcode Gaps of Macrofungal Genera
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topic_title	QH301-705.5 Does One Size Fit All? Variations in the DNA Barcode Gaps of Macrofungal Genera DNA barcode pairwise distances nrITS ITS1 ITS2
topic	misc QH301-705.5 misc DNA barcode misc pairwise distances misc nrITS misc ITS1 misc ITS2 misc Biology (General)
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title	Does One Size Fit All? Variations in the DNA Barcode Gaps of Macrofungal Genera
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title_auth	Does One Size Fit All? Variations in the DNA Barcode Gaps of Macrofungal Genera
abstract	The nuclear ribosomal internal transcribed spacer (nrITS) region has been widely used in fungal diversity studies. Environmental metabarcoding has increased the importance of the fungal DNA barcode in documenting fungal diversity and distribution. The DNA barcode gap is seen as the difference between intra- and inter-specific pairwise distances in a DNA barcode. The current understanding of the barcode gap in macrofungi is limited, inhibiting the development of best practices in applying the nrITS region toward research on fungal diversity. This study examined the barcode gap using 5146 sequences representing 717 species of macrofungi from eleven genera, eight orders and two phyla in datasets assembled by taxonomic experts. Intra- and inter-specific pairwise distances were measured from sequence and phylogenetic data. The results demonstrate that barcode gaps are influenced by differences in intra- and inter-specific variance in pairwise distances. In terms of DNA barcode behavior, variance is greater in the ITS1 than ITS2, and variance is greater in both relative to the combined nrITS region. Due to the difference in variance, the barcode gaps in the ITS2 region are greater than in the ITS1. Additionally, the taxonomic approach of “splitting” taxa into numerous taxonomic units produces greater barcode gaps when compared to “lumping”. The results show variability in the barcode gaps between fungal taxa, demonstrating a need to understand the accuracy of DNA barcoding in quantifying species richness. For taxonomic studies, variability in nrITS sequence data supports the application of multiple molecular markers to corroborate the taxonomic and systematic delineation of species.
abstractGer	The nuclear ribosomal internal transcribed spacer (nrITS) region has been widely used in fungal diversity studies. Environmental metabarcoding has increased the importance of the fungal DNA barcode in documenting fungal diversity and distribution. The DNA barcode gap is seen as the difference between intra- and inter-specific pairwise distances in a DNA barcode. The current understanding of the barcode gap in macrofungi is limited, inhibiting the development of best practices in applying the nrITS region toward research on fungal diversity. This study examined the barcode gap using 5146 sequences representing 717 species of macrofungi from eleven genera, eight orders and two phyla in datasets assembled by taxonomic experts. Intra- and inter-specific pairwise distances were measured from sequence and phylogenetic data. The results demonstrate that barcode gaps are influenced by differences in intra- and inter-specific variance in pairwise distances. In terms of DNA barcode behavior, variance is greater in the ITS1 than ITS2, and variance is greater in both relative to the combined nrITS region. Due to the difference in variance, the barcode gaps in the ITS2 region are greater than in the ITS1. Additionally, the taxonomic approach of “splitting” taxa into numerous taxonomic units produces greater barcode gaps when compared to “lumping”. The results show variability in the barcode gaps between fungal taxa, demonstrating a need to understand the accuracy of DNA barcoding in quantifying species richness. For taxonomic studies, variability in nrITS sequence data supports the application of multiple molecular markers to corroborate the taxonomic and systematic delineation of species.
abstract_unstemmed	The nuclear ribosomal internal transcribed spacer (nrITS) region has been widely used in fungal diversity studies. Environmental metabarcoding has increased the importance of the fungal DNA barcode in documenting fungal diversity and distribution. The DNA barcode gap is seen as the difference between intra- and inter-specific pairwise distances in a DNA barcode. The current understanding of the barcode gap in macrofungi is limited, inhibiting the development of best practices in applying the nrITS region toward research on fungal diversity. This study examined the barcode gap using 5146 sequences representing 717 species of macrofungi from eleven genera, eight orders and two phyla in datasets assembled by taxonomic experts. Intra- and inter-specific pairwise distances were measured from sequence and phylogenetic data. The results demonstrate that barcode gaps are influenced by differences in intra- and inter-specific variance in pairwise distances. In terms of DNA barcode behavior, variance is greater in the ITS1 than ITS2, and variance is greater in both relative to the combined nrITS region. Due to the difference in variance, the barcode gaps in the ITS2 region are greater than in the ITS1. Additionally, the taxonomic approach of “splitting” taxa into numerous taxonomic units produces greater barcode gaps when compared to “lumping”. The results show variability in the barcode gaps between fungal taxa, demonstrating a need to understand the accuracy of DNA barcoding in quantifying species richness. For taxonomic studies, variability in nrITS sequence data supports the application of multiple molecular markers to corroborate the taxonomic and systematic delineation of species.
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title_short	Does One Size Fit All? Variations in the DNA Barcode Gaps of Macrofungal Genera
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Additionally, the taxonomic approach of “splitting” taxa into numerous taxonomic units produces greater barcode gaps when compared to “lumping”. The results show variability in the barcode gaps between fungal taxa, demonstrating a need to understand the accuracy of DNA barcoding in quantifying species richness. 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