ITS1 versus ITS2 as DNA metabarcodes for fungi.

作者: R. Blaalid , S. Kumar , R. H. Nilsson , K. Abarenkov , P. M. Kirk

DOI: 10.1111/1755-0998.12065

关键词: Computational biologyFungal geneticsPyrosequencingGeneticsInternal transcribed spacerDNA barcodingRibosomal RNAGenetic markerBiologyOperational taxonomic unitSequence analysis

摘要: … Clustering analyses of the 134 692 ITS1 and ITS2 pyrosequences using a 97% similarity cut-… and ITS2 to a large extent yield similar results when used as DNA metabarcodes for fungi. …

参考文章(45)
R. Henrik Nilsson, Erik Kristiansson, Martin Ryberg, Nils Hallenberg, Karl-Henrik Larsson, Intraspecific ITS Variability in the Kingdom Fungi as Expressed in the International Sequence Databases and Its Implications for Molecular Species Identification Evolutionary Bioinformatics. ,vol. 2008, pp. 193- 201 ,(2008) , 10.4137/EBO.S653
LUCIE ZINGER, ANGÉLIQUE GOBET, THOMAS POMMIER, Two decades of describing the unseen majority of aquatic microbial diversity. Molecular Ecology. ,vol. 21, pp. 1878- 1896 ,(2012) , 10.1111/J.1365-294X.2011.05362.X
Kessy Abarenkov, Leho Tedersoo, R. Henrik Nilsson, Kai Vellak, Irja Saar, Vilmar Veldre, Erast Parmasto, Marko Prous, Anne Aan, Margus Ots, Olavi Kurina, Ivika Ostonen, Janno Jõgeva, Siim Halapuu, Kadri Põldmaa, Märt Toots, Jaak Truu, Karl-Henrik Larsson, Urmas Kõljalg, PlutoF—a Web Based Workbench for Ecological and Taxonomic Research, with an Online Implementation for Fungal ITS Sequences Evolutionary Bioinformatics. ,vol. 6, pp. 189- 196 ,(2010) , 10.4137/EBO.S6271
Christopher Quince, Anders Lanzén, Thomas P Curtis, Russell J Davenport, Neil Hall, Ian M Head, L Fiona Read, William T Sloan, Accurate determination of microbial diversity from 454 pyrosequencing data Nature Methods. ,vol. 6, pp. 639- 641 ,(2009) , 10.1038/NMETH.1361
Rolf Henrik Nilsson, Martin Ryberg, Kessy Abarenkov, Elisabet Sjökvist, Erik Kristiansson, The ITS region as a target for characterization of fungal communities using emerging sequencing technologies Fems Microbiology Letters. ,vol. 296, pp. 97- 101 ,(2009) , 10.1111/J.1574-6968.2009.01618.X
David Berry, Karim Ben Mahfoudh, Michael Wagner, Alexander Loy, Barcoded Primers Used in Multiplex Amplicon Pyrosequencing Bias Amplification Applied and Environmental Microbiology. ,vol. 77, pp. 7846- 7849 ,(2011) , 10.1128/AEM.05220-11
Kessy Abarenkov, R. Henrik Nilsson, Karl-Henrik Larsson, Ian J. Alexander, Ursula Eberhardt, Susanne Erland, Klaus Høiland, Rasmus Kjøller, Ellen Larsson, Taina Pennanen, Robin Sen, Andy F. S. Taylor, Leho Tedersoo, Björn M. Ursing, Trude Vrålstad, Kare Liimatainen, Ursula Peintner, Urmas Kõljalg, The UNITE database for molecular identification of fungi - recent updates and future perspectives New Phytologist. ,vol. 186, pp. 281- 285 ,(2010) , 10.1111/J.1469-8137.2009.03160.X