Title |
Determining threshold values for barcoding fungi: lessons from Cortinarius (Basidiomycota), a highly diverse and widespread ectomycorrhizal genus
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Published in |
FEMS Microbiology Ecology, February 2016
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DOI | 10.1093/femsec/fiw045 |
Pubmed ID | |
Authors |
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 |
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 97.0-99.5% sequence similarity using clustering optimization and UNITE SH, and from 1-2% sequence dissimilarity with CROP. Errors for the optimal cut-off ranged from 0-70%, 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. |
X Demographics
Geographical breakdown
Country | Count | As % |
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France | 4 | 20% |
Japan | 2 | 10% |
Belgium | 1 | 5% |
Norway | 1 | 5% |
Netherlands | 1 | 5% |
Canada | 1 | 5% |
Estonia | 1 | 5% |
Unknown | 9 | 45% |
Demographic breakdown
Type | Count | As % |
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Scientists | 11 | 55% |
Members of the public | 9 | 45% |
Mendeley readers
Geographical breakdown
Country | Count | As % |
---|---|---|
Unknown | 92 | 100% |
Demographic breakdown
Readers by professional status | Count | As % |
---|---|---|
Student > Ph. D. Student | 19 | 21% |
Student > Master | 16 | 17% |
Researcher | 15 | 16% |
Student > Bachelor | 8 | 9% |
Student > Doctoral Student | 3 | 3% |
Other | 11 | 12% |
Unknown | 20 | 22% |
Readers by discipline | Count | As % |
---|---|---|
Agricultural and Biological Sciences | 38 | 41% |
Environmental Science | 12 | 13% |
Biochemistry, Genetics and Molecular Biology | 10 | 11% |
Immunology and Microbiology | 2 | 2% |
Pharmacology, Toxicology and Pharmaceutical Science | 1 | 1% |
Other | 3 | 3% |
Unknown | 26 | 28% |