Student or educator? Sign up with your school email and get 6 months of Pro free.
CoChat
Sign Up
Cited by 2,098

The DOI matches its Crossref record.

New primers to amplify the fungal ITS2 region - evaluation by 454-sequencing of artificial and natural communities

Open access
Ihrmark, Katarina, Bödeker, Inga T.M., Cruz-Martinez, Karelyn, Friberg, Hanna, Kubartova, Ariana, Schenck, Jessica, Strid, Ylva, Stenlid, Jan, Brandström-Durling, Mikael, Clemmensen, Karina E., Lindahl, Björn D.·2012·FEMS Microbiology Ecology
DOI 10.1111/j.1574-6941.2012.01437.x
Open this paper in CoChat — free account

Abstract

With recent methodological advances, molecular markers are increasingly used for semi-quantitative analyses of fungal communities. The aim to preserve quantitative relationships between genotypes through PCR places new demands on primers to accurately match target sites and provide short amplicons. The internal transcribed spacer (ITS) region of the ribosome encoding genes is a commonly used marker for many fungal groups. Here, we describe three new primers - fITS7, gITS7 and fITS9, which may be used to amplify the fungal ITS2 region by targeting sites in the 5.8S encoding gene. We evaluated the primers and compared their performance with the commonly used ITS1f primer by 454-sequencing of both artificially assembled templates and field samples. When the entire ITS region was amplified using the ITS1f/ITS4 primer combination, we found strong bias against species with longer amplicons. This problem could be overcome by using the new primers, which produce shorter amplicons and better preserve the quantitative composition of the template. In addition, the new primers yielded more diverse amplicon communities than the ITS1f primer.

Overview

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

A few free checks a day · papers already verified open instantly · results are public

Integrity signals

Registry

Crossref · 10.1111/j.1574-6941.2012.01437.x

Cites

Statistics

Verification

Claims the paper makes

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

A few free checks a day · papers already verified open instantly · results are public

Self-check

Percentages, sums and reported differences re-computed from the paper’s own numbers.

The self-check needs the paper’s full text.

Citations

Cites

No references could be resolved yet.

Research works printed but not linked: 27

  1. Abarenkov, 2010, PlutoF-a web based workbench for ecological and taxonomic research, with an online implementation for fungal ITS sequences, Evol Bioinform, 6, 189, 10.4137/EBO.S6271 · DOI · Paper page
  2. Alon, 2011, Barcoding bias in high-throughput multiplex sequencing of miRNA, Genome Res, 21, 1506, 10.1101/gr.121715.111 · DOI
  3. Amend, 2010, Quantifying microbial communities with 454 pyrosequencing: does read abundance count?, Mol Ecol, 19, 5555, 10.1111/j.1365-294X.2010.04898.x · DOI
  4. Begerow, 2010, Current state and perspectives of fungal DNA barcoding and rapid identification procedures, Appl Microbiol Biotechnol, 87, 99, 10.1007/s00253-010-2585-4 · DOI
  5. Bellemain, 2010, ITS as an environmental DNA barcode for fungi: an in silico approach reveals potential PCR biases, BMC Microbiol, 10, 189, 10.1186/1471-2180-10-189 · DOI · Paper page
  6. Bio-Rad Laboratories Inc, 2006, Real-Time PCR Applications Guide
  7. Engelbrektson, 2010, Experimental factors affecting PCR-based estimates of microbial species richness and evenness, ISME J, 4, 642, 10.1038/ismej.2009.153 · DOI · Paper page
  8. Frank, 2009, BARCRAWL and BARTAB: software for design and implementation of barcoded primers for highly multiplexed DNA sequencing, BMC Bioinformatics, 10, 362, 10.1186/1471-2105-10-362 · DOI
  9. Gardes, 1993, ITS primers with enhanced specificity for basidiomycetes - application to the identification of mycorrhizae and rusts, Mol Ecol, 2, 113, 10.1111/j.1365-294X.1993.tb00005.x · DOI · Paper page
  10. Hibbett, 2009, Fungal ecology catches fire, New Phytol, 184, 279, 10.1111/j.1469-8137.2009.03042.x · DOI
  11. Hibbett, 2011, Progress in molecular and morphological taxon discovery in Fungi and options for formal classification of environmental sequences, Fungal Biol Rev, 25, 38, 10.1016/j.fbr.2011.01.001 · DOI
  12. Horton, 2001, The molecular revolution in ectomycorrhizal ecology: peeking into the black-box, Mol Ecol, 10, 1855, 10.1046/j.0962-1083.2001.01333.x · DOI
  13. Huber, 2009, Effect of PCR amplicon size on assessments of clone library microbial diversity and community structure, Environ Microbiol, 11, 1292, 10.1111/j.1462-2920.2008.01857.x · DOI
  14. Kanagawa, 2003, Bias and artifacts in multitemplate polymerase chain reactions (PCR), J Biosci Bioeng, 96, 317, 10.1016/S1389-1723(03)90130-7 · DOI · Paper page
  15. Lane, 1985, Rapid-determination of 16S ribosomal-RNA sequences for phylogenetic analyses, P Natl Acad Sci USA, 82, 6955, 10.1073/pnas.82.20.6955 · DOI
  16. 454 Life Sciences Corp., 2011, 454 Sequencing System - Guidelines for Amplicon Experimental Design
  17. Margulies, 2005, Genome sequencing in microfabricated high-density picolitre reactors, Nature, 437, 376, 10.1038/nature03959 · DOI · Paper page
  18. Martin, 2005, Fungal-specific PCR primers developed for analysis of the ITS region of environmental DNA extracts, BMC Microbiol, 5, 28, 10.1186/1471-2180-5-28 · DOI · Paper page
  19. Moncalvo, 2006, The cantharelloid clade: dealing with incongruent gene trees and phylogenetic reconstruction methods, Mycologia, 98, 937, 10.1080/15572536.2006.11832623 · DOI
  20. Nilsson, 2010, An open source chimera checker for the fungal ITS region, Mol Ecol Resour, 10, 1076, 10.1111/j.1755-0998.2010.02850.x · DOI
  21. Polz, 1998, Bias in template-to-product ratios in multitemplate PCR, Appl Environ Microbiol, 64, 3724, 10.1128/AEM.64.10.3724-3730.1998 · DOI · Paper page
  22. Quince, 2011, Removing noise from pyrosequenced amplicons, BMC Bioinformatics, 12, 38, 10.1186/1471-2105-12-38 · DOI · Paper page
  23. Rosling, 2011, Archaeorhizomycetes: unearthing an ancient class of ubiquitous soil fungi, Science, 333, 876, 10.1126/science.1206958 · DOI · Paper page
  24. Schoch, 2012, Nuclear ribosomal internal transcribed spacer (ITS) region as a universal DNA barcode marker for Fungi, P Natl Acad Sci USA, 109, 6241, 10.1073/pnas.1117018109 · DOI
  25. Urich, 2008, Simultaneous assessment of soil microbial community structure and function through analysis of the meta-transcriptome, PLoS ONE, 3, e2527, 10.1371/journal.pone.0002527 · DOI
  26. Tuinen, 1998, Characterization of root colonization profiles by a microcosm community of arbuscular mycorrhizal fungi using 25S rDNA-targeted nested PCR, Mol Ecol, 7, 879, 10.1046/j.1365-294x.1998.00410.x · DOI
  27. White, 1990, PCR Protocols: A Guide to Methods and Applications, 315, 10.1016/B978-0-12-372180-8.50042-1 · DOI · Paper page

Cited by

Metadata

Authors
Ihrmark, K., Bödeker, I. T. M., Cruz-Martinez, K., Friberg, H., Kubartova, A., Schenck, J., Strid, Y., Stenlid, J., Brandström-Durling, M., Clemmensen, K. E., & Lindahl, B. D.
Venue
FEMS Microbiology Ecology
Publisher
Oxford University Press (OUP)
Published
2012-07-27
Volume
82
Issue
3
Pages
666-677
ISSN
0168-6496 (ISSN-L)
DOI
10.1111/j.1574-6941.2012.01437.x
OpenAlex
W2051201019
Cited by
2,098
References
0
FWCI
38.94
Type
journal article
Language
en
Open access
bronze

About these checks

Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.

Statistics and arithmetic are recomputed, not judged.

Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.

What counts as a claim ›How we measure confidence ›How we check this ›

Are you an author, or do you see a problem with this page? Request a review

Data sources

Bibliographic data: Semantic Scholar, OpenAlex, Crossref.

Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).

Semantic Scholar’s data is described in: Kinney, R., et al. (2023). The Semantic Scholar Open Data Platform. arXiv:2301.10140.