Comparing COI and ITS as DNA barcode markers for mushrooms and allies (Agaricomycotina)

PLoS ONE

Volumn 6, Issue 9, 2011, Pages

  Dentinger, Bryn T M ^a,b,c   Didukh, Maryna Y ^a,b   Moncalvo, Jean Marc ^a,b  

^a UNIVERSITY OF TORONTO   (Canada)

^b DEPARTMENT OF NATURAL HISTORY   (Canada)

^c JODRELL LABORATORY   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

CYTOCHROME C OXIDASE; INTERNAL TRANSCRIBED SPACER; RIBOSOME DNA; SPACER DNA;

AGARICOMYCOTINA; ARTICLE; BASIDIOMYCETES; COI GENE; COMPARATIVE GENE MAPPING; CONTROLLED STUDY; DNA BARCODING; GENE LOCUS; GENE SEQUENCE; GENETIC SIMILARITY; GENETIC VARIABILITY; INTRON; ITS GENE; MITOCHONDRIAL GENE; MORPHOSPECIES; MUSHROOM; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENY; POLYMERASE CHAIN REACTION; PROMOTER REGION; SEQUENCE ALIGNMENT; UNINDEXED SEQUENCE; AGARICALES; BIOLOGICAL MODEL; CANADA; COMPARATIVE STUDY; DNA SEQUENCE; GENETIC MARKER; GENETIC PROCEDURES; GENETICS; INFORMATION PROCESSING; METABOLISM; METHODOLOGY; UNITED STATES;

BASIDIOMYCOTA;

AGARICALES; AUTOMATIC DATA PROCESSING; DNA BARCODING, TAXONOMIC; DNA, INTERGENIC; DNA, RIBOSOMAL; ELECTRON TRANSPORT COMPLEX IV; GENETIC MARKERS; GENETIC TECHNIQUES; INTRONS; MARYLAND; MODELS, GENETIC; ONTARIO; PHYLOGENY; POLYMERASE CHAIN REACTION; QUEBEC; SEQUENCE ANALYSIS, DNA;

EID: 80053068046     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0025081     Document Type: Article

References (48)

1. Hebert PDN, Cywinska A, Ball SL, deWaard JR, (2003) Biological identifications through DNA barcodes. Proc Natl Acad Sci U S A 270: 313-321.
2. Hajibabaei M, Singer GAC, Hebert PDN, Hickey DA, (2007) DNA barcoding: how it complements taxonomy, molecular phylogenetics and population genetics. Trends Genet 23: 167-172.
3. Kress WJ, Erickson D, (2008) DNA barcoding - a windfall for tropical biology? Biotropica 40: 405-408.
4. Janzen DH, Hallwachs W, Blandin P, Burns JM, Cadiou JM, et al. (2009) Integration of DNA barcoding into an ongoing inventory of complex tropical biodiversity. Mol Ecol Res 9 (s1): 1-26.
5. Seifert KA, (2009) Progress towards DNA barcoding of fungi. Mol Ecol Res 9 (s1): 83-89.
6. Hawksworth DL, (2001) The magnitude of fungal diversity: the 1.5 million species estimate revisited. Mycol Res 105: 1422-1432.
7. Hawksworth DL, (2004) Fungal diversity and its implications for genetic resource collections. Stud Mycol 50: 9-18.
8. O'Brien HE, Parrent JL, Jackson JA, Moncalvo JM, Vilgalys R, (2005) Fungal community analysis by large-scale sequencing of environmental samples. Appl Environ Microb 71: 5544-5550.
9. Schmitt JP, Mueller GM, (2007) An estimate of the lower limit of global fungal diversity. Biodivers Conserv 16: 99-111.
10. Blackwell M, (2011) The Fungi: 1, 2, 3... 5.1 million species? Am J Bot 98: 426-438.
11. Kirk PM, Cannon PF, Minter DW, Stalpers JA, (2008) Dictionary of the Fungi, 10th Edition. Wallingford CABI Publishing.
12. Smith MA, Fisher BL, Hebert PDN, (2005) DNA barcoding for effective biodiversity assessment of a hyperdiverse arthropod group: the ants of Madagascar. Phil Trans R Soc B 360: 1825-1834.
13. Vences M, Thomas M, Bonett RM, Vieites DR, (2005) Deciphering amphibian diversity through DNA barcoding: chances and challenges. Phil Trans R Soc B 360: 1859-1868.
14. Ward RD, Zemlak TS, Innes BH, Last PR, Hebert PDN, (2005) DNA barcoding Australia's fish species. Phil Trans R Soc B 360: 1847-1857.
15. Chase MW, Cowan RS, Hollingsworth PM, van den Berg C, Madriñan S, et al. (2007) A proposal for a standardised protocol to barcode all land plants. Taxon 56: 295-299.
16. Kress WJ, Erickson D, (2007) A two-locus global DNA barcode for land plants: The coding rbcL gene complements the non-coding trnH-psbA spacer region. PLoS ONE 2: e508.
17. Newmaster SG, Fazekas AJ, Ragupathy S, (2006) DNA barcoding in land plants: evaluation of rbcL in a multigene tiered approach. Can J Bot 84: 335-341.
18. Lahaye R, van der Bank M, Bogarin D, Warner J, Pupulin F, et al. (2008) DNA barcoding the floras of biodiversity hotspots. Proc Natl Acad Sci U S A 105: 2923-2928.
19. Hollingsworth ML, Clark A, Forrest LL, Richardson JE, Pennington RT, et al. (2009) Selecting barcoding loci for plants: evaluation of seven candidate loci with species-level sampling in three divergent groups of land plants. Mol Ecol Res 9: 439-457.
20. Geiser DM, Klich MA, Frisvad JC, Peterson SW, Varga J, et al. (2007) The current status of species recognition and identification in Aspergillus. Stud Mycol 59: 1-10.
21. Seifert KA, Samson RA, Dewaard JR, Houbraken J, Lévesque CA, et al. (2007) Prospects for fungus identification using CO1 DNA barcodes, with Penicillium as a test case. Proc Natl Acad Sci U S A 104: 3901-3906.
22. Nguyen HDT, Seifert KA, (2008) Description and DNA barcoding of three new species of Leohumicola from South Africa and the United States. Persoonia 21: 57-69.
23. Gilmore SR, Gräfenhan T, Louis-Seize G, Seifert KA, (2009) Multiple copies of cytochrome oxidase 1 in species of the fungal genus Fusarium. Mol Ecol Res 9 (s1): 90-98.
24. Vialle A, Feau N, Allaire M, Didukh M, Martin M, et al. (2009) In silico evaluation of mitochondrial genes as DNA barcode for Basidiomycota. Mol Ecol Res 9 (s1): 99-113.
25. Gonzalaz P, Barroso G, Labarère J, (1998) Molecular analysis of the split cox1 gene from the Basidiomycota Agrocybe aegerita: relationship of its introns with homologous Ascomycota introns and divergence levels from common ancestral copies. Gene 220: 45-53.
26. Haridas S, Gantt JS, (2010) The mitochondrial genome of the wood-degrading basidiomycete Trametes cingulata. FEMS Microbiol Lett 308: 29-34.
27. Férandon C, Moukha S, Callac P, Benedetto JP, Castroviejo M, et al. (2011) The Agaricus bisporus cox1 gene: The longest mitochondrial gene and the largest reservoir of mitochondrial group I introns. PLoS One 5: e14048.
28. Lee SB, Taylor JW, (1990) Isolation of DNA from fungal mycelia and single spores. In: Innis M, Gelfand D, Sninsky J, White T, editors. PCR Protocols: A Guide to Methods and Applications Orlando Academic Press pp. 282-287.
29. Zolan ME, Pukkila PJ, (1986) Inheritance of DNA methylation in Coprinus cinereus. Mol Cell Biol 6: 195.
30. Dentinger BTM, Margaritescu S, Moncalvo JM, (2010) Rapid and reliable high-throughput methods of DNA extraction for use in barcoding and molecular systematics of mushrooms. Mol Ecol Res 10: 628-633.
31. White TJ, Bruns T, Lee S, Taylor J, (1990) Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenies. In: Innis M, Gelfand D, Sninsky J, White T, editors. PCR Protocols: A Guide to Methods and Applications Orlando Academic Press pp. 315-322.
32. Gardes M, Bruns TD, (1993) ITS primers with enhanced specificity for basidiomycetes- application to the identification of mycorrhizae and rusts. Mol Ecol 2: 113-118.
33. Ratnasingham S, Hebert PDN, (2007) BOLD: The Barcode of Life Data System. Mol Ecol Notes 7: 355-364.
34. Benson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, Wheeler DL, (2005) GenBank. Nucleic Acids Res 33: D34-D38.
35. Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA, et al. (2007) Clustal W and Clustal X version 2.0. Bioinformatics 23: 2947-2948.
36. Galtier N, Gouy M, Gautier C, (1996) SEAVIEW and PHYLO_WIN: two graphic tools for sequence alignment and molecular phylogeny. Comput Appl Biosci 12: 543-548.
37. Gouy M, Guindon S, Gascuel O, (2010) SeaView version 4: a multiplatform graphical user interface for sequence alignment and phylogenetic tree building. Mol Biol Evol 27: 221-224.
38. Posada D, (2008) jModelTest: Phylogenetic Model Averaging. Mol Biol Evol 25: 1253-1256.
39. Guindon S, Gascuel O, (2003) A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst Biol 52: 696-704.
40. Anisimova M, Gascuel O, (2006) Approximate likelihood ratio test for branches: A fast, accurate and powerful alternative. Syst Biol 55: 539-552.
41. Swofford DL, (2003) PAUP* Phylogenetic Analysis Using Parsimony (* and other methods), Version 4. Sunderland Sinauer.
42. Nilsson RH, Kristiansson E, Ryberg M, Hallenberg N, Larsson KH, (2008) Intraspecific ITS variability in the Kingdom Fungi as expressed in the international sequence databases and its implications for molecular species identification. Evol Bioinform Online 4: 193-201.
43. Edgar RC, (2004) MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 32: 1792-97.
44. Hibbett DS, Binder M, Bischoff JF, Blackwell M, Cannon PF, et al. (2007) A higher-level phylogenetic classification of the Fungi. Mycol Res 111: 509-547.
45. Dentinger BTM, Ammirati JF, Both EE, Desjardin DE, Halling RE, et al. (2010) Molecular phylogenetics of porcini mushrooms (Boletus section Boletus). Mol Phylogenet Evol 57: 1276-1292.
46. Kõljalg U, Larsson KH, Abarenkov K, Nilsson RH, Alexander IJ, et al. (2005) UNITE: a database providing web-based methods for the molecular identification of ectomycorrhizal fungi. New Phytol 166: 1063-1068.
47. Begerow D, Nilsson H, Unterseher M, Maier W, (2010) Current state and perspectives of fungal DNA barcoding and rapid identification procedures. Appl Microbiol Biot 87: 99-108.
48. Bruns TD, Arnold AE, Hughes KW, (2008) Fungal networks made of humans: UNITE, FESIN, and frontiers in fungal ecology. New Phytol 177: 586-588.