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

Overview of attention for article published in FEMS Microbiology Ecology, February 2016
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About this Attention Score

  • In the top 25% of all research outputs scored by Altmetric
  • High Attention Score compared to outputs of the same age (84th percentile)
  • High Attention Score compared to outputs of the same age and source (84th percentile)

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Title
Determining threshold values for barcoding fungi: lessons from Cortinarius (Basidiomycota), a highly diverse and widespread ectomycorrhizal genus
Published in
FEMS Microbiology Ecology, February 2016
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.

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Mendeley readers

Mendeley readers

The data shown below were compiled from readership statistics for 92 Mendeley readers of this research output. Click here to see the associated Mendeley record.

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%
Attention Score in Context

Attention Score in Context

This research output has an Altmetric Attention Score of 12. This is our high-level measure of the quality and quantity of online attention that it has received. This Attention Score, as well as the ranking and number of research outputs shown below, was calculated when the research output was last mentioned on 07 November 2022.
All research outputs
#3,155,961
of 25,519,924 outputs
Outputs from FEMS Microbiology Ecology
#358
of 2,716 outputs
Outputs of similar age
#47,282
of 312,557 outputs
Outputs of similar age from FEMS Microbiology Ecology
#10
of 58 outputs
Altmetric has tracked 25,519,924 research outputs across all sources so far. Compared to these this one has done well and is in the 87th percentile: it's in the top 25% of all research outputs ever tracked by Altmetric.
So far Altmetric has tracked 2,716 research outputs from this source. They typically receive a little more attention than average, with a mean Attention Score of 6.1. This one has done well, scoring higher than 86% of its peers.
Older research outputs will score higher simply because they've had more time to accumulate mentions. To account for age we can compare this Altmetric Attention Score to the 312,557 tracked outputs that were published within six weeks on either side of this one in any source. This one has done well, scoring higher than 84% of its contemporaries.
We're also able to compare this research output to 58 others from the same source and published within six weeks on either side of this one. This one has done well, scoring higher than 84% of its contemporaries.