ITS1 versus ITS2 as DNA metabarcodes for fungi

Molecular Ecology Resources

Volumn 13, Issue 2, 2013, Pages 218-224

  Blaalid, R ^a   Kumar, S ^a   Nilsson, R H ^b   Abarenkov, K ^c   Kirk, P M ^d   Kauserud, H ^a  

^a UNIVERSITY OF OSLO   (Norway)

^b UNIVERSITY OF GOTHENBURG   (Sweden)

^c UNIVERSITY OF TARTU   (Estonia)

^d ROYAL BOTANIC GARDENS   (United Kingdom)

Author keywords

Amplicon sequencing; Community ecology; DNA barcoding; Fungi; Internal transcribed spacer (ITS); Pyrosequencing

Indexed keywords

FUNGAL DNA; RIBOSOMAL SPACER DNA;

ANGIOSPERM; ARTICLE; CLASSIFICATION; DNA SEQUENCE; FUNGUS; GENETIC MARKER; GENETICS; ISOLATION AND PURIFICATION; MICROBIOLOGY; PHYLOGENY;

ANGIOSPERMS; DNA, FUNGAL; DNA, RIBOSOMAL SPACER; FUNGI; GENETIC MARKERS; PHYLOGENY; SEQUENCE ANALYSIS, DNA;

FUNGI;

EID: 84873991067     PISSN: 1755098X     EISSN: 17550998     Source Type: Journal    
DOI: 10.1111/1755-0998.12065     Document Type: Article

References (45)

1. Abarenkov K, Nilsson RH, Larsson KH et al. (2010a) The UNITE database for molecular identification of fungi-recent updates and future perspectives. New Phytologist, 186, 281-285.
2. Abarenkov K, Tedersoo L, Nilsson RH et al. (2010b) PlutoF-a Web based workbench for ecological and taxonomical research, with an online implementation for fungal ITS sequences. Evolutionary Bioinformatics, 6, 189-196.
3. Altschul SF, Madden TL, Schäffer AA et al. (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Research, 25, 3389-3402.
4. Arfi Y, Buée M, Marchand C, Record E (2011) Multiple markers pyrosequencing reveals highly diverse and host-specific fungal communities on the mangrove trees Avicennia marina and Rhizophora stylosa. FEMS Microbiology Ecology, 79, 433-444.
5. Balajee SA, Borman AM, Brandt ME et al. (2009) Sequence-based identification of Aspergillus, Fusarium, and Mucorales species in the clinical mycology laboratory: where are we and where should we go from here? Journal of Clinical Microbiology, 47, 877-884.
6. Bellemain E, Carlsen T, Brochmann C et al. (2010) ITS as an environmental DNA barcode for fungi: an in silico approach reveals potential PCR biases. BMC Microbiology, 10, 189.
7. Berry D, Ben K, Wagner M, Loy A (2011) Barcoded primers used in multiplex amplicon pyrosequencing bias amplification. Applied and Environmental Microbiology, 77, 7846-7849.
8. Bjorbækmo MFM, Carlsen T, Brysting AK et al. (2010) High diversity of root associated fungi in both arctic and alpine Dryas octopetala. BMC Plant Biology, 10, 244.
9. Blaalid R, Carlsen T, Kumar S et al. (2012) Changes in the root-associated fungal communities along a primary succession gradient analysed by 454 pyrosequencing. Molecular Ecology, 21, 1897-1908.
10. Buèe M, Reich M, Murat C et al. (2009) 454 Pyrosequencing analyses of forest soils reveal an unexpectedly high fungal diversity. New Phytologist, 184, 449-456.
11. Carlsen T, Aas AB, Lindner D et al. (2012) Don't make a mista(g)ke: Is tag switching an overlooked source of error in amplicon pyrosequencing studies? Fungal Ecology, 5, 747-749.
12. Davey ML, Heegaard E, Halvorsen R et al. (2012) Seasonal trends in the biomass and structure of bryophyte-associated fungal communities explored by 454-pyrosequencing. New Phytologist, 195, 844-856.
13. Edgar RC (2010) Search and clustering orders of magnitude faster than BLAST. Bioinformatics, 26, 2460-2461.
14. Gardes M, Bruns TD (1993) ITS primers with enhanced specificity for basidiomycetes application to the identification of mycorrhizae and rusts. Molecular Ecology, 2, 113-118.
15. Gazis R, Rhener S, Chaverri P (2011) Species delimitation in fungal endophyte diversity studies and its implications in ecological and biogeographic inferences. Molecular Ecology, 30, 3001-3013.
16. Gillevet P, Sikaroodia M, Keshavarzianc A, Mutluc EA (2010) Quantitative Assessment of the Human Gut Microbiome Using Multitag Pyrosequencing. Chemistry & Biodiversity, 7, 1065-1075.
17. Jumpponen A (2004) Soil fungal communities underneath willow canopies on a primary successional glacier forefront: rDNA sequence results can be affected by primer selection and chimeric data. Microbial Ecology, 53, 233-246.
18. Jumpponen A, Jones KL (2009) Massively parallel 454 sequencing indicates hyperdiverse fungal communities in temperate Quercus macrocarpa phylloshere. New Phytologist, 184, 438-448.
19. Karsch-Mizrachi I, Nakamura Y, Cochrane G et al. (2012) The International Nucleotide Database Collaboration. Nucleic Acids Research, 40, 33-37.
20. Kauserud H, Kumar S, Brysting AK et al. (2012) High consistency between replicate 454 pyrosequencing analyses of ectomycorrhizal plant root samples. Mycorrhiza, 22, 309-315.
21. Kodama Y, Shumway M et al. (2012) The sequence read archive: explosive growth of sequence data. Nucleic Acids Research, 40, 54-56.
22. Kumar S, Skjærveland Å, Orr R et al. (2009) AIR: A batch-oriented web program package for construction of supermatrices ready for phylogenomic analyses. BMC Bioinformatics, 10, 357.
23. Kumar S, Carlsen T, Mevik B et al. (2011) CLOTU: an online pipeline for processing and clustering of 454 amplicon reads into OTUs followed by taxonomic annotation. BMC Bioinformatics, 12, 182.
24. Larsson KH, Larsson E, Kõljalg U (2004) High phylogenetic diversity among corticioid homobasidiomycetes. Mycological Research, 108, 983-1002.
25. Li W, Godzik A (2006) CD-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences. Bioinformatics, 22, 1658-1659.
26. Margulies M, Egholm M, Altman WE et al. (2005) Genome sequencing in microfabricated high-density picolitre reactors. Nature, 437, 376-380.
27. Mello A, Napoli C, Morin CME et al. (2011) ITS-1 versus ITS-2 pyrosequencing: a comparison of fungal populations in truffle grounds. Mycologia, 103, 1184-1193.
28. Miller SL, Larsson E, Larsson KH et al. (2006) Perspectives in the new Russulales. Mycologia, 98, 960-970.
29. Morris HM, Smith ME, Rizzo DM et al. (2008) Contrasting ectomycorrhizal fungal communities on the roots of co-occurring oaks (Quercus spp.) in a California woodland. New Phytologist, 178, 167-176.
30. Mullineux T, Hausner G (2009) Evolution of rDNA ITS1 and ITS2 sequences and RNA secondary structures within members of the fungal genera Grosmannia and Leptographium. Fungal Genetics and Biology, 46, 855-867.
31. Nilsson RH, Kristiansson E, Ryberg M et al. (2008) Intraspecific ITS variability in the kingdom Fungi as expressed in the international sequence databases and its implications for molecular species identification. Evolutionary Bioinformatics, 4, 193-201.
32. Nilsson RH, Ryberg M, Abarenkov K, Sjökvist E, Kristiansson E (2009) The ITS region as a target for characterization of fungal communities using emerging sequencing technologies. FEMS Microbiology Letters, 296, 97-101.
33. Nilsson RH, Veldre V, Hartmann M et al. (2010) An open source package for automated extraction of ITS1 and ITS2 from fungal ITS sequences for use in high-troughput community assays and molecular ecology. Fungal Ecology, 3, 284-287.
34. O′Brien HE, Parrent JL, Jackson JA et al. (2005) Fungal Community analysis by large-scale sequencing of environmental samples. Applied and Environmental Microbiology, 71, 5544-5550.
35. Pommier T, Cranbäck B, Lundberg P et al. (2009) RAMI: a tool for identification and characterization of phylogenetic clusters in microbial communities. Bioinformatics, 25, 736-742.
36. Quince C, Lanzén A, Curtis TP et al. (2009) Accurate determination of microbial diversity from 454 pyrosequencing data. Nature Methods, 6, 639.
37. Ryberg M, Kristiansson E, Sjökvist E, Nilsson RH (2008) An outlook on the fungal internal transcribed spacer sequences in GenBank and the introduction of a web-based tool for the exploration of fungal diversity. New Phytologist, 181, 471-477.
38. Schoch CL, Seifert K, Huhndorf S et al. (2012) Nuclear ribosomal internal transcribed spacer (ITS) region as a universal DNA barcode marker for Fungi. Proceedings of the National Academy of Sciences of the United States of America, 109, 6241-6246.
39. Stackebrandt E, Goebel BM (1994) Taxonomic Note: A Place for DNA-DNA Re-association and 16s rRNA Sequence Analysis in the Present Species Definition in Bacteriology. International Journal of Systematic Bacteriology, 44, 846-849.
40. Taberlet P, Coissac E, Hajibabaei M, Rieseberg LH (2012) Environmental DNA. Molecular Ecology, 21, 1789-1793.
41. Tedersoo L, Nilsson RH, Abarenkov K et al. (2010) 454 Pyrosequencing and Sanger sequencing of tropical mycorrhiza fungi provide similar results but reveal substantial methodological biases. New Phytologist, 188, 291-301.
42. Walker JF, Miller OK Jr, Horton JL (2008) Seasonal dynamics of ectomycorrhizal fungus assemblages on oak seedlings in the southeastern Appalachian Mountains. Mycorrhiza, 18, 123-132.
43. Wallander H, Johansson E, Brandström M, Lindahl B (2010) Production of ectomycorrhizal mycelium peaks during canopy closure in Norway spruce forests. New Phytologist, 187, 1124-1134.
44. White TJ, Bruns T, Taylor J (1990) Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics. In: PCR Protocols: A Guide to Methods and Applications, pp. 315-322. Academic Press, Orlando, Florida.
45. Zinger L, Gobet A, Pommier T (2009) Two decades of describing the unseen majority of aquatic microbial diversity. Molecular Ecology, 21, 1878-1896.