Are similarity- or phylogeny-based methods more appropriate for classifying internal transcribed spacer (ITS) metagenomic amplicons?

New Phytologist

Volumn 192, Issue 3, 2011, Pages 775-782

  Porter, Teresita M ^a   Brian Golding, G ^a  

^a MCMASTER UNIVERSITY   (Canada)

Author keywords

BLAST; Environmental sampling; Internal transcribed spacer (ITS) region; MEGAN; Metagenomics; Next generation sequencing; Statistical Assignment Program (SAP)

Indexed keywords

RIBOSOMAL SPACER DNA;

CLASSIFICATION; COMPUTER SIMULATION; DATA SET; FRAGMENTATION; FUNGUS; GENERATION TIME; GENETIC ANALYSIS; GENOMICS; PHYLOGENETICS; PHYLOGENY; TAXONOMY; TRADE-OFF;

ARTICLE; CLASSIFICATION; COMPUTER SIMULATION; FUNGUS; GENETIC DATABASE; GENETICS; METAGENOMICS; METHODOLOGY; NUCLEOTIDE SEQUENCE; PHYLOGENY;

BASE SEQUENCE; COMPUTER SIMULATION; DATABASES, GENETIC; DNA, RIBOSOMAL SPACER; FUNGI; METAGENOMICS; PHYLOGENY;

FUNGI;

EID: 80054832176     PISSN: 0028646X     EISSN: 14698137     Source Type: Journal    
DOI: 10.1111/j.1469-8137.2011.03838.x     Document Type: Article

References (56)

1. Abarenkov K, Nilsson RH, Larsson K-H, Alexander IJ, Eberhardt U, Erland S, Hoiland K, Kjoller R, Larsson E, Pennanen T et al. 2010. The UNITE database for molecular identification for fungi - recent updates and future perspectives. New Phytologist 186: 281-285.
2. Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ. 1997. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Research 25: 3389-3402.
3. Alvarez I, Wendel JF. 2003. Ribosomal ITS sequences and plant phylogenetic inference. Molecular Phylogenetics and Evolution 29: 417-434.
4. Amend AS, Seifert KA, Samson R, Bruns TD. 2010. Indoor fungal composition is geographically patterned and more diverse in temperate zones than in the tropics. Proceedings of the National Academy of Sciences, USA 107: 13748-13753.
5. Arnold AE, Henk DA, Eells RL, Lutzoni F, Vilgalys R. 2007. Diversity and phylogenetic affinities of foliar fungal endophytes in loblolly pine inferred by culturing and environmental PCR. Mycologia 99: 185-206.
6. Baldwin BG, Sanderson MJ, Porter JM, Wojciechowski MF. 1995. The ITS region of nuclear ribosomal DNA: a valuable source of evidence on angiosperm phylogeny. Annals of the Missouri Botanical Garden 82: 247-277.
7. Bartram AK, Lynch MDJ, Stearns JC, Moreno-Hagelsieb G, Neufeld JD. 2011. Generation of multimillion-sequence 16S rRNA gene libraries from complex microbial communities by assembling paired-end Illumina reads. Applied and Environmental Microbiology 77: 3846-3852.
8. Begerow D, Nilsson H, Unterseher M, Maier W. 2010. Current state and perspectives of fungal DNA barcoding and rapid identification procedures. Applied Microbiology and Biotechnology 87: 99-108.
9. Bellemain E, Carlsen T, Brochmann C, Coissac E, Taberlet P, Kauserud H. 2010. ITS as an environmental DNA barcode for fungi: an in silico approach reveals potential PCR biases. BMC Microbiology 10: 189.
10. Bidartondo M, Bruns T, Blackwell M, Edwards I, Taylor A, Horton T, Zhang N, Koljalg U, May G, Kuyper T et al. 2008. Preserving accuracy in GenBank. Science 319: 1616.
11. Brock PM, Doring H, Bidartondo MI. 2009. How to know unknown fungi: the role of a herbarium. New Phytologist 181: 719-724.
12. Bruns TD, White TJ, Taylor JW. 1991. Fungal molecular systematics. Annual Review of Ecology and Systematics 22: 525-564.
13. Buee M, Reich M, Murat C, Morin E, Nilsson RH, Uroz S, Martin F. 2009. 454 pyrosequencing analyses of forest soils reveal an unexpectedly high fungal diversity. New Phytologist 184: 449-456.
14. Caporaso JG, Lauber CL, Walters WA, Berg-Lyons D, Lozupone CA, Tumbaugh PJ, Fierer N, Knight R. 2010. Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample. Proceedings of the National Academy of Sciences, USA 108: 4516-4522.
15. Feibelman T, Bayman P, Cibula WG. 1994. Length variation in the internal transcribed spacer of ribosomal DNA in chanterelles. Mycological Research 98: 614-618.
16. 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.
17. Geml J, Laursen GA, Herriott IC, McFarland JM, Booth MG, Lennon N, Nusbaum HC, Taylor DL. 2010. Phylogenetic and ecological analyses of soil and sporocarp DNA sequences reveal high diversity and strong habitat partitioning in the boreal ectomycorrhizal genus Russula (Russulales; Basidiomycota). New Phytologist 187: 494-507.
18. Geml J, Laursen GA, Timling I, McFarland JM, Booth MG, Lennon N, Nusbaum C, Taylor DL. 2009. Molecular phylogenetic biodiversity assessment of arctic and boreal ectomycorrhizal Lactarius Pers. (Russulales; Basidiomycota) in Alaska, based on soil and sporocarp DNA. Molecular Ecology 18: 2213-2227.
19. Hawksworth DL. 2001. The magnitude of fungal diversity: the 1.5million species estimate revisited. Mycological Research 105: 1422-1432.
20. Hibbett DS, Ohman A, Glotzer D, Nuhn M, Kirk P, Nilsson RH. 2011. Progress in molecular and morphological taxon discovery in Fungi and options for formal classification of environmental sequences. Fungal Biology Reviews 25: 38-47.
21. Hugenholtz P, Huber T. 2003. Chimeric 16S rDNA sequences of diverse origin are accumulating in the public databases. International Journal of Systematic and Evolutionary Microbiology 53: 289-293.
22. Hugenholtz P, Pace NR. 1996. Identifying microbial diversity in the natural environment: a molecular phylogenetic approach. Trends in Biotechnology 14: 190-197.
23. Huson DH, Auch AF, Qi J, Schuster SC. 2007. MEGAN analysis of metagenomic data. Genome Research 17: 377-386.
24. Jumpponen A. 2007. 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.
25. Jumpponen A, Jones KL. 2009. Massively parallel 454 sequencing indicates hyperdiverse fungal communities in temperate Quercus macrocarpa phyllosphere. New Phytologist 184: 438-448.
26. Jumpponen A, Jones KL, Blair J. 2010a. Vertical distribution of fungal communities in tallgrass prairie soil. Mycologia 102: 1027-1041.
27. Jumpponen A, Jones KL, Mattox JD, Yaege C. 2010b. Massively parallel 454-sequencing of fungal communities in Quercus spp. ectomycorrhizas indicates seasonal dynamics in urban and rural sites. Molecular Ecology 19: 41-53.
28. Koetschan C, Forster F, Keller A, Schleicher T, Ruderisch B, Schwarz R, Muller T, Wolf M, Schultz J. 2010. The ITS2 database III - sequences and structures for phylogeny. Nucleic Acids Research 38: D275-D279.
29. Koski LB, Golding GB. 2001. The closest BLAST hit is often not the nearest neighbor. Journal of Molecular Evolution 52: 540-542.
30. Kunin V, Engelbrektson A, Ochman H, Hugenholtz P. 2010. Wrinkles in the rare biosphere: pyrosequencing error can lead to artificial inflation of diversity estimates. Environmental Microbiology 12: 118-123.
31. Lara E, Moreira D, Lopez-Garcia P. 2010. The environmental clade LKM11 and Rozella from the deepest branching clade of fungi. Protist 161: 116-121.
32. Liu Z, DeSantis TZ, Andersen GL, Knight R. 2008. Accurate taxonomy assignments from 16S rRNA sequences produced by highly parallel pyrosequencers. Nucleic Acids Research 36: 11.
33. Liu Z, Lozupone C, Hamady M, Bushman FD, Knight R. 2007. Short pyrosequencing reads suffice for accurate microbial community analysis. Nucleic Acids Research 35: 10.
34. McLaughlin DJ, Hibbett DS, Lutzoni F, Spatafora JW, Vilglays R. 2009. The search for the fungal tree of life. Trends in Microbiology 17: 488-497.
35. Munch K, Boomsma W, Huelsenbeck JP, Willerslev E, Nielsen R. 2008. Statistical assignment of DNA sequences using Bayesian phylogenetics. Systematic Biology 57: 750-757.
36. Nagano Y, Nagahama T, Hatada Y, Nunoura T, Takami H, Miyazaki J, Takai K, Horikoshi K. 2010. Fungal diversity in deep-sea sediments - the presence of novel fungal groups. Fungal Ecology 3: 316-325.
37. Nagy LG, Petkovits T, Kovacs GM, Voigt K, Vagvolgyi C, Papp T. 2011. Where is the unseen fungal diversity hidden? A study of Mortierella reveals a large contribution of reference collections to the identification of fungal environmental sequences. New Phytologist. doi:.
38. Nilsson RH, Abarenkov K, Veldre V, Nylinder S, wit PD, Brosche S, Alfredsson JF, Ryberg M, Kristiansson E. 2010. An open source chimera checker for the fungal ITS region. Molecular Ecology Resources 10: 1076-1081.
39. Nilsson RH, Bok G, Ryberg M, Kristiansson E, Hallenberg N. 2009a. A software pipeline for processing and identification of fungal ITS sequences. Source Code for Biology and Medicine 4: 1.
40. Nilsson RH, Kristiansson E, Ryberg M, Larsson K-H. 2005. Approaching the taxonomic affiliation of unidentified sequences in public databases - an example from the mycorrhizal fungi. BMC Bioinformatics 6: 7.
41. Nilsson RH, Ryberg M, Abarenkov K, Sjokvist E, Kristiansson E. 2009b. The ITS region as a target for characterization of fungal communities using emerging sequencing technologies. FEMS Microbiology Letters 296: 97-101.
42. O'Brien HE, Parrent JL, Jackson JA, Moncalvo J-M, Vilgalys R. 2005. Fungal community analysis by large-scale sequencing of environmental samples. Applied and Environmental Microbiology 71: 5544-5550.
43. Opik M, Metsis M, Daniell TJ, Zobel M, Moora M. 2009. Large-scale parallel 454 sequencing reveals host ecological group specificity of arbuscular mycorrhizal fungi in a boreonemoral forest. New Phytologist 184: 424-437.
44. Porter TM, Schadt CW, Rizvi L, Martin AP, Schmidt SK, Scott-Denton L, Vilgalys R, Moncalvo J-M. 2008a. Widespread occurrence and phylogenetic placement of a soil clone group adds a prominent new branch to the fungal tree of life. Molecular Phylogenetics and Evolution 46: 635-644.
45. Porter TM, Skillman JE, Moncalvo J-M. 2008b. Fruiting body and soil rDNA sampling detects complementary assemblage of Agaricomycotina (Basidiomycota, Fungi) in a hemlock-dominated forest plot in southern Ontario. Molecular Ecology 17: 3037-3050.
46. Pringle A, Moncalvo J-M, Vilglays R. 2003. Revisiting the rDNA sequence diversity of a natural population of the arbuscular mycorrhizal fungus Acaulospora colossica. Mycorrhiza 13: 227-231.
47. Ryberg M, Kristiansson E, Sjokvist E, Nilsson RH. 2009. 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.
48. Schadt CW, Martin AP, Lipson DA, Schmidt SK. 2003. Seasonal dynamics of previously unknown fungal lineages in tundra soils. Science 301: 1359-1361.
49. Seifert KA. 2009. Progress towards DNA barcoding of fungi. Molecular Ecology Resources 9: 83-89.
50. Spatafora JW. 2005. Assembling the Fungal Tree of Life (AFTOL). Mycological Research 109: 755-756.
51. Stajich JE, Block D, Boulez K, Brenner SE, Chervitz SA, Dagdigian C, Fuellen G, Gilbert JGR, Korf I, Lapp H et al. 2002. The Bioperl toolkit: perl modules for the life sciences. Genome Research 12: 1611-1618.
52. Taylor DL, Houston S. 2011. A bioinformatics pipeline for sequence-based analyses of fungal biodiversity. In: Xu J-R, Bluhm BH, eds. Fungal genomics: methods and protocols. New York, NY, USA: Humana Press, 141-155.
53. Taylor JW, Jacobson DJ, Kroken S, Kasuga T, Geiser DM, Hibbett DS, Fisher MC. 2000. Phylogenetic species recognition and species concepts in fungi. Fungal Genetics and Biology 31: 21-32.
54. Tedersoo L, Nilsson RH, Abarenkov K, Jairus T, Sadam A, Saar I, Bahram M, Bechem E, CHuyong G, Koljalg U. 2010. 454 pyrosequencing and Sanger sequencing of tropical mycorrhizal fungi provide similar results but reveal substantial methodological biases. New Phytologist 188: 291-301.
55. Vandenkoornhuyse P, Baldauf SL, Leyval C, Straczek J, Young JPW. 2002. Extensive fungal diversity in plant roots. Science 295: 2051.
56. White TJ, Bruns T, Lee S, Taylor J. 1990. Amplification and direct sequencing of fungal ribsomal RNA genes for phylogenetics. In: Innis MA, Gelfand DH, Sninsky JJ, White TJ, eds. PCR protocols. San Diego, CA, USA: Academic Press, 315-322.