Determining threshold values for barcoding fungi: lessons from Cortinarius (Basidiomycota), a highly diverse and widespread ectomycorrhizal genus

Sigisfredo Garnica; Max Emil Schön; Kessy Abarenkov; Kai Riess; Kare Liimatainen; Tuula Niskanen; Bálint Dima; Karl Soop; Tobias Guldberg Frøslev; Thomas Stjernegaard Jeppesen; Ursula Peintner; Regina Kuhnert-Finkernagel; Tor Erik Brandrud; Günter Saar; Bernhard Oertel; Joseph F. Ammirati

doi:10.1093/femsec/fiw045

Determining threshold values for barcoding fungi: lessons from Cortinarius (Basidiomycota), a highly diverse and widespread ectomycorrhizal genus

Sigisfredo Garnica, Max Emil Schön, Kessy Abarenkov, Kai Riess, Kare Liimatainen, Tuula Niskanen, Bálint Dima, Karl Soop, Tobias Guldberg Frøslev, Thomas Stjernegaard Jeppesen, Ursula Peintner, Regina Kuhnert-Finkernagel, Tor Erik Brandrud, Günter Saar, Bernhard Oertel, Joseph F. Ammirati

60 Citations (Scopus)

Abstract

Different distance-based threshold selection approaches were used to assess and compare use of the internal transcribed spacer (ITS) region to distinguish among 901 Cortinarius species represented by > 3000 collections. Sources of error associated with genetic markers and selection approaches were explored and evaluated using MOTUs from genus and lineage based-alignments. Our study indicates that 1%-2% more species can be distinguished by using the full-length ITS barcode as compared to either the ITS1 or ITS2 regions alone. Optimal threshold values for different picking approaches and genetic marker lengths inferred from a subset of species containing major lineages ranged from 97.0% to 99.5% sequence similarity using clustering optimization and UNITE SH, and from 1% to 2% sequence dissimilarity with CROP. Errors for the optimal cutoff ranged from 0% to 70%, and these can be reduced to a maximum of 22% when excluding species lacking a barcode gap. A threshold value of 99% is suitable for distinguishing species in the majority of lineages in the genus using the entire ITS region but only 90% of the species could be identified using just the ITS1 or ITS2 region. Prior identification of species, lacking barcode gaps and their subsequent separate analyses, maximized the accuracy of threshold approaches.

Original language	English
Article number	fiw045
Journal	FEMS Microbiology Ecology
Volume	92
Issue number	4
Number of pages	16
ISSN	0168-6496
DOIs	https://doi.org/10.1093/femsec/fiw045
Publication status	Published - Apr 2016

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Garnica, S., Schön, M. E., Abarenkov, K., Riess, K., Liimatainen, K., Niskanen, T., Dima, B., Soop, K., Frøslev, T. G., Jeppesen, T. S., Peintner, U., Kuhnert-Finkernagel, R., Brandrud, T. E., Saar, G., Oertel, B., & Ammirati, J. F. (2016). Determining threshold values for barcoding fungi: lessons from Cortinarius (Basidiomycota), a highly diverse and widespread ectomycorrhizal genus. FEMS Microbiology Ecology, 92(4), [fiw045]. https://doi.org/10.1093/femsec/fiw045

Garnica, S, Schön, ME, Abarenkov, K, Riess, K, Liimatainen, K, Niskanen, T, Dima, B, Soop, K, Frøslev, TG, Jeppesen, TS, Peintner, U, Kuhnert-Finkernagel, R, Brandrud, TE, Saar, G, Oertel, B & Ammirati, JF 2016, 'Determining threshold values for barcoding fungi: lessons from Cortinarius (Basidiomycota), a highly diverse and widespread ectomycorrhizal genus', FEMS Microbiology Ecology, vol. 92, no. 4, fiw045. https://doi.org/10.1093/femsec/fiw045

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abstract = "Different distance-based threshold selection approaches were used to assess and compare use of the internal transcribed spacer (ITS) region to distinguish among 901 Cortinarius species represented by > 3000 collections. Sources of error associated with genetic markers and selection approaches were explored and evaluated using MOTUs from genus and lineage based-alignments. Our study indicates that 1%-2% more species can be distinguished by using the full-length ITS barcode as compared to either the ITS1 or ITS2 regions alone. Optimal threshold values for different picking approaches and genetic marker lengths inferred from a subset of species containing major lineages ranged from 97.0% to 99.5% sequence similarity using clustering optimization and UNITE SH, and from 1% to 2% sequence dissimilarity with CROP. Errors for the optimal cutoff ranged from 0% to 70%, and these can be reduced to a maximum of 22% when excluding species lacking a barcode gap. A threshold value of 99% is suitable for distinguishing species in the majority of lineages in the genus using the entire ITS region but only 90% of the species could be identified using just the ITS1 or ITS2 region. Prior identification of species, lacking barcode gaps and their subsequent separate analyses, maximized the accuracy of threshold approaches.",

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AU - Jeppesen, Thomas Stjernegaard

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AU - Kuhnert-Finkernagel, Regina

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AB - Different distance-based threshold selection approaches were used to assess and compare use of the internal transcribed spacer (ITS) region to distinguish among 901 Cortinarius species represented by > 3000 collections. Sources of error associated with genetic markers and selection approaches were explored and evaluated using MOTUs from genus and lineage based-alignments. Our study indicates that 1%-2% more species can be distinguished by using the full-length ITS barcode as compared to either the ITS1 or ITS2 regions alone. Optimal threshold values for different picking approaches and genetic marker lengths inferred from a subset of species containing major lineages ranged from 97.0% to 99.5% sequence similarity using clustering optimization and UNITE SH, and from 1% to 2% sequence dissimilarity with CROP. Errors for the optimal cutoff ranged from 0% to 70%, and these can be reduced to a maximum of 22% when excluding species lacking a barcode gap. A threshold value of 99% is suitable for distinguishing species in the majority of lineages in the genus using the entire ITS region but only 90% of the species could be identified using just the ITS1 or ITS2 region. Prior identification of species, lacking barcode gaps and their subsequent separate analyses, maximized the accuracy of threshold approaches.

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Determining threshold values for barcoding fungi: lessons from Cortinarius (Basidiomycota), a highly diverse and widespread ectomycorrhizal genus

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