Fungal identification using a Bayesian classifier and the Warcup training set of internal transcribed spacer sequences

Mycologia

Volumn 108, Issue 1, 2016, Pages 1-5

  Deshpande, Vinita ^a   Wang, Qiong ^b   Greenfield, Paul ^c   Charleston, Michael ^a,d   Porras Alfaro, Andrea ^e   Kuske, Cheryl R ^f   Cole, James R ^b   Midgley, David J ^c   Tran Dinh, Nai ^c  

^a UNIVERSITY OF SYDNEY   (Australia)

^b MICHIGAN STATE UNIVERSITY   (United States)

^c CSIRO   (Australia)

^d UNIVERSITY OF TASMANIA   (Australia)

^e WESTERN ILLINOIS UNIVERSITY   (United States)

^f LOS ALAMOS NATIONAL LABORATORY   (United States)

Author keywords

Ecogenome; Fungal classification; Fungi; Identification; ITS

Indexed keywords

BAYESIAN ANALYSIS; CLASSIFICATION; DNA; FUNGUS; GENETIC ANALYSIS; GENETIC MARKER; GENOME; NOMENCLATURE; TAXONOMY;

FUNGI;

FUNGAL DNA; RIBOSOMAL SPACER DNA;

BAYES THEOREM; CHEMISTRY; CLASSIFICATION; DNA SEQUENCE; FUNGUS; GENETICS; INFORMATION PROCESSING; REPRODUCIBILITY;

BAYES THEOREM; DATASETS AS TOPIC; DNA, FUNGAL; DNA, RIBOSOMAL SPACER; FUNGI; REPRODUCIBILITY OF RESULTS; SEQUENCE ANALYSIS, DNA;

EID: 84962270380     PISSN: 00275514     EISSN: 15572536     Source Type: Journal    
DOI: 10.3852/14-293     Document Type: Article

References (10)

1. Abarenkov K, Henrik Nilsson R, Larsson K-H, Alexander IJ, Eberhardt U, Erland S, Høiland K, Kjøller R, Larsson E, Pennanen T, Sen R, Taylor AFS, Tedersoo L, Ursing BM, Vrålstad T, Liimatainen K, Peintner U, Kõljalg U. 2010. The UNITE database for molecular identification of fungi-recent updates and future perspectives. New Phytol 186:281-285, doi:10.1111/j.1469-8137.2009. 03160.x
2. Blackwell M. 2011. The fungi: 1, 2, 3 ... 5.1 million species? Am J Bot 98:426-38, doi:10.3732/ajb.1000298
3. Edgar RC. 2010. Search and clustering hundreds of times faster than BLAST. Bioinformatics 1-3, doi:10.1093/bioinformatics/btq461
4. Koljalg U, Nilsson RH, Abarenkov K, Tedersoo L, Taylor AFS, Bahram M, Bates ST, Bruns, Thomas D, Bengtssonpalme J, Callaghan TM, Douglas B, Drenkhan T, Eberhardt U, Duenas M, Grebenc T, Griffith GW, Hartmann M, Kirk PM, Kohout P, Larsson E, Lindahl BD, Lucking R, Martin MP, Matheny PB, Nguyen NH, Niskanen T, Oja J, Peay KG, Peintner U, et al. 2013. Toward a unified paradigm for sequence-based identification of fungi. Mol Ecol 22:5271-5277, doi:10.1111/mec.12481
5. Liu K-L, Porras-Alfaro A, Kuske CR, Eichorst SA, Xie G. 2012. Accurate, rapid taxonomic classification of fungal largesubunit rRNA genes. Appl Environ Microbiol 78:1523-33, doi:10.1128/AEM.06826-11
6. Nilsson RH, Veldre V, Hartmann M, Unterseher M, Amend A, Bergsten J, Kristiansson E, Ryberg M, Jumpponen A, Abarenkov K. 2010. An open source software package for automated extraction of ITS1 and ITS2 from fungal ITS sequences for use in high-throughput community assays and molecular ecology. Fungal Ecol 3:284-287, doi:10.1016/j.funeco.2010.05.002
7. Porras-Alfaro A, Liu K-L, Kuske CR, Xie G. 2014. From genus to phylum: large-subunit and internal transcribed spacer rRNA operon regions show similar classification accuracies influenced by database composition. Appl Environ Microbiol 80:829-40, doi:10.1128/AEM.02894-13
8. Quast C, Pruesse E, Yilmaz P, Gerken J, Schweer T, Yarza P, Peplies J, Glöckner FO. 2013. The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucleic Acids Res 41:D590-596, doi:10.1093/nar/gks1219
9. Tedersoo L, Bahram M, Polme S, Koljalg U, Yorou NS, Wijesundera R, Ruiz LV, Vasco-Palacios AM, Thu PQ, Suija A, Smith ME, Sharp C, Saluveer E, Saitta A, Rosas M, Riit T, Ratkowsky D, Pritsch K, Poldmaa K, Piepenbring M, Phosri C, Peterson M, Parts K, Partel K, Otsing E, Nouhra E, Njouonkou AL, Nilsson RH, Morgado LN, et al. 2014. Global diversity and geography of soil fungi. Science (80-)346:1256688-1256688, doi:10.1126/science.1256688
10. Wang Q, Garrity GM, Tiedje JM, Cole JR. 2007. Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Appl Environ Microbiol 73:5261-5267, doi:10.1128/AEM.00062-07