Comparison of ITS1 and ITS2 rDNA in 454 sequencing of hyperdiverse fungal communities

Fungal Ecology

Volumn 6, Issue 1, 2013, Pages 102-109

  Bazzicalupo, Anna L ^a   Bálint, Miklós ^a,b   Schmitt, Imke ^a,c  

^a SENCKENBERG DEUTSCHES ENTOMOLOGISCHES INSTITUT   (Germany)

^b BABE BOLYAI UNIVERSITY   (Romania)

^c GOETHE UNIVERSITY   (Germany)

Author keywords

Community ecology; Diversity; Endophytes; Environmental barcoding; Internal transcribed spacer; Metabarcoding; Next generation sequencing; Operational taxonomic units; Richness

Indexed keywords

FUNGI;

EID: 84871736911     PISSN: 17545048     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.funeco.2012.09.003     Document Type: Article

References (50)

1. Acinas S.G., Sarma-Rupavtarm R., Klepac-Ceraj V., Polz M.F. PCR-induced sequence artifacts and bias: insights from comparison of two 16S rRNA clone libraries constructed from the same sample. Applied and Environmental Microbiology 2005, 71:8966-8969.
2. Altschul S.F., Madden T.L., Schäffer A.A., Zhang J., Zhang Z., Miller W., Lipman D.J. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Research 1997, 25:3389-3402.
3. Amend A.S., Seifert K.A., Bruns T.D. Quantifying microbial communities with 454 pyrosequencing: does read abundance count?. Molecular Ecology 2010, 19:5555-5565.
4. Balzer S., Malde K., Jonassen I. Systematic exploration of error sources in pyrosequencing flowgram data. Bioinformatics 2011, 27:i304-i309.
5. Bellemain E., Carlsen T., Brochmann C., Coissac E., Taberlet P., Kauserud H. ITS as an environmental DNA barcode for fungi: an in silico approach reveals potential PCR biases. BMC Microbiology 2010, 10:189.
6. Benson D.A., Karsch-Mizrachi I., Lipman D.J., Ostell J., Wheeler D.L. GenBank. Nucleic Acids Research 2008, 36:D25-D30.
7. Bik H.M., Porazinska D.L., Creer S., Caporaso J.G., Knight R., Thomas W.K. Sequencing our way towards understanding global eukaryotic biodiversity. Trends in Ecology & Evolution 2012, 27:233-243.
8. Bulmer M.G. On fitting the Poisson lognormal distribution to species-abundance data. Biometrics 1974, 30:101-110.
9. Coleman A.W. Is there a molecular key to the level of 'biological species' in eukaryotes? A DNA guide. Molecular Phylogenetics and Evolution 2009, 50:197-203.
10. Conover W.J. Practical Nonparametric Statistics 1999, Wiley.
11. Degnan P.H., Ochman H. Illumina-based analysis of microbial community diversity. The ISME Journal 2011, 6:183-194.
12. Delmont T.O., Robe P., Cecillon S., Clark I.M., Constancias F., Simonet P., Hirsch P.R., Vogel T.M. Accessing the soil metagenome for studies of microbial diversity. Applied and Environmental Microbiology 2011, 77:1315-1324.
13. Feliner G.N., Rosselló J.A. Better the devil you know? Guidelines for insightful utilization of nrDNA ITS in species-level evolutionary studies in plants. Molecular Phylogenetics and Evolution 2007, 44:911-919.
14. Fonseca V.G., Nichols B., Lallias D., Quince C., Carvalho G.R., Power D.M., Creer S. Sample richness and genetic diversity as drivers of chimera formation in nSSU metagenetic analyses. Nucleic Acids Research 2012, 40:e66.
15. Gardes M., Bruns T.D. ITS primers with enhanced specificity for basidiomycetes - application to the identification of mycorrhizae and rusts. Molecular Ecology 1993, 2:113-118.
16. Grøtan V., Engen S. poilog: Poisson lognormal and bivariate Poisson lognormal distribution 2008, (accessed 10.12.11.). http://cran.r-project.org/web/packages/poilog.
17. Hebert P.D.N., Cywinska A., Ball S.L., Waard J.R. Biological identifications through DNA barcodes. Proceedings of the Royal Society B: Biological Sciences 2003, 270:313-321.
18. Huse S.M., Huber J.A., Morrison H.G., Sogin M.L., Welch D. Accuracy and quality of massively parallel DNA pyrosequencing. Genome Biology 2007, 8:R143.
19. Huson D.H., Mitra S., Ruscheweyh H.-J., Weber N., Schuster S.C. Integrative analysis of environmental sequences using MEGAN4. Genome Research 2011, 21:1552-1560.
20. 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. New primers to amplify the fungal ITS2 region - evaluation by 454-sequencing of artificial and natural communities. FEMS Microbiology Ecology 2012, 10.1111/j.1574-6941.2012.01437.x.
21. Jumpponen A., Jones K.L. Massively parallel 454 sequencing indicates hyperdiverse fungal communities in temperate Quercus macrocarpa phyllosphere. New Phytologist 2009, 184:438-448.
22. Keijser B.J.F., Zaura E., Huse S.M., van der Vossen J.M.B.M., Schuren F.H.J., Montijn R.C., ten Cate J.M., Crielaard W. Pyrosequencing analysis of the oral microflora of healthy adults. Journal of Dental Research 2008, 87:1016-1020.
23. Keller S.R., Olson M.S., Silim S., Schroeder W., Tiffin P. Genomic diversity, population structure, and migration following rapid range expansion in the Balsam poplar, Populus balsamifera. Molecular Ecology 2010, 19:1212-1226.
24. Keller A., Schleicher T., Schultz J., Müller T., Dandekar T., Wolf M. 5.8S-28S rRNA interaction and HMM-based ITS2 annotation. Gene 2009, 430:50-57.
25. Martin K.J., Rygiewicz P.T. Fungal-specific PCR primers developed for analysis of the ITS region of environmental DNA extracts. BMC Microbiology 2005, 5:28.
26. Mello A., Napoli C., Murat C., Morin E., Marceddu G., Bonfante P. ITS-1 versus ITS-2 pyrosequencing: a comparison of fungal populations in truffle grounds. Mycologia 2011, 103:1184-1193.
27. Nilsson R.H., Ryberg M., Abarenkov K., Sjökvist E., Kristiansson E. The ITS region as a target for characterization of fungal communities using emerging sequencing technologies. FEMS Microbiology Letters 2009, 296:97-101.
28. Nilsson R.H., Veldre V., Hartmann M., Unterseher M., Amend A., Bergsten J., Kristiansson E., Ryberg M., Jumpponen A., Abarenkov K. 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 Ecology 2010, 3:284-287.
29. Oksanen J., Blanchet F.G., Kindt R., Legendre P., Minchin P.R., O'Hara R.B., Simpson G.L., Solymos P., Stevens M.H.H., Wagner H. vegan: community ecology package 2011, Community Ecology Package, vegan, (accessed 10.12.11.). http://cran.r-project.org/web/packages/poilog.
30. Phillips C.D., Phelan G., Dowd S.E., McDonough M.M., Ferguson A.W., Delton Hanson J., Siles L., Ordóñez-garza N., San Francisco M., Baker R.J. Microbiome analysis among bats describes influences of host phylogeny, life history, physiology and geography. Molecular Ecology 2012, 21:2617-2627.
31. Porter T.M., Golding B. Are similarity- or phylogeny-based methods more appropriate for classifying internal transcribed spacer (ITS) metagenomic amplicons?. New Phytologist 2011, 192:775-782.
32. Quince C., Lanzen A., Davenport R., Turnbaugh P. Removing noise from pyrosequenced amplicons. BMC Bioinformatics 2011, 12:38.
33. R Development Core Team R: a language and environment for statistical computing 2011, Vienna, Austria, (accessed 10.12.11.). http://cran.r-project.org/.
34. Russell D.J., Way S.F., Benson A.K., Sayood K. A grammar-based distance metric enables fast and accurate clustering of large sets of 16S sequences. BMC Bioinformatics 2010, 11:601.
35. Schloss P.D., Westcott S.L., Ryabin T., Hall J.R., Hartmann M., Hollister E.B., Lesniewski R.A., Oakley B.B., Parks D.H., Robinson C.J., Sahl J.W., Stres B., Thallinger G.G., Van Horn D.J., Weber C.F. Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities. Applied and Environmental Microbiology 2009, 75:7537-7541.
36. Schoch C.L., Seifert K.A., Huhndorf S., Robert V., Spouge J.L., et al. 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 2012, 109:6241-6246.
37. Selig C., Wolf M., Müller T., Dandekar T., Schultz J. The ITS2 Database II: homology modelling RNA structure for molecular systematics. Nucleic Acids Research 2008, 36:D377-D380.
38. Tabachnick B.G., Fidell L.S. Using Multivariate Statistics 2006, Allyn & Bacon.
39. Taberlet P., Coissac E., Hajibabaei M., Rieseberg L.H. Environmental DNA. Molecular Ecology 2012, 21:1789-1793.
40. Tedersoo L., Nilsson R.H., Abarenkov K., Jairus T., Sadam A., Saar I., Bahram M., Bechem E., Chuyong G., Kõljalg U. 454 Pyrosequencing and Sanger sequencing of tropical mycorrhizal fungi provide similar results but reveal substantial methodological biases. New Phytologist 2010, 188:291-301.
41. Toju H., Tanabe A.S., Yamamoto S., Sato H. High-coverage ITS primers for the DNA-based identification of Ascomycetes and Basidiomycetes in environmental samples. PLoS ONE 2012, 7:e40863.
42. Turnbaugh P.J., Hamady M., Yatsunenko T., Cantarel B.L., Duncan A., Ley R.E., Sogin M.L., Jones W.J., Roe B.A., Affourtit J.P., Egholm M., Henrissat B., Heath A.C., Knight R., Gordon J.I. A core gut microbiome in obese and lean twins. Nature 2009, 457:480-484.
43. Unterseher M., Jumpponen A., Öpik M., Tedersoo L., Moora M., Dormann C.F., Schnittler M. Species abundance distributions and richness estimations in fungal metagenomics - lessons learned from community ecology. Molecular Ecology 2011, 20:275-285.
44. Venables W.N., Ripley B.D. Modern Applied Statistics with S 2002, Springer, NY, USA.
45. Vestheim H., Jarman S. Blocking primers to enhance PCR amplification of rare sequences in mixed samples - a case study on prey DNA in Antarctic krill stomachs. Frontiers in Zoology 2008, 5:12.
46. Wang Y., Naumann U., Wright S.T., Warton D.I. mvabund- an R package for model-based analysis of multivariate abundance data. Methods in Ecology and Evolution 2012, 3:471-474.
47. Warton D.I. Many zeros does not mean zero inflation: comparing the goodness-of-fit of parametric models to multivariate abundance data. Environmetrics 2005, 16:275-289.
48. Warton D.I. Penalized normal likelihood and ridge regularization of correlation and covariance matrices. Journal of the American Statistical Association 2008, 103:340-349.
49. Weiß M., Sýkorová Z., Garnica S., Riess K., Martos F., Krause C., Oberwinkler F., Bauer R., Redecker D. Sebacinales everywhere: previously overlooked ubiquitous fungal endophytes. PLoS ONE 2011, 6:e16793.
50. White T., Bruns T., Lee S., Taylor J. PCR protocols a guide to methods and applications. PCR Protocols: a guide to methods and applications 1990, 315-322. Academic Press, San Diego. M. Innis, D. Gelfand, J. Shinsky, T. White (Eds.).