PHYMYCO-DB: A Curated Database for Analyses of Fungal Diversity and Evolution

PLoS ONE

Volumn 7, Issue 9, 2012, Pages

  Mahé, Stéphane ^a,b   Duhamel, Marie ^a,b,c   Le Calvez, Thomas ^a,b,e   Guillot, Laetitia ^b,d   Sarbu, Ludmila ^b,d   Bretaudeau, Anthony ^b,d   Collin, Olivier ^b,d   Dufresne, Alexis ^a,b   Kiers, E Toby ^c   Vandenkoornhuyse, Philippe ^a,b  

^a UNIVERSITÉ DE RENNES 1   (France)

^b UNIVERSITÉ EUROPÉENNE DE BRETAGNE   (France)

^c VU UNIVERSITY AMSTERDAM   (Netherlands)

^d UNIVERSITÉ DE RENNES 1   (France)

^e AQUASIM   (France)

Author keywords

[No Author keywords available]

Indexed keywords

ELONGATION FACTOR 1; SMALL SUBUNIT RIBOSOMAL RNA;

ARTICLE; AUTOMATION; CHYTRIDIOMYCETES; DEEP SEA; EF1 ALPHA GENE; EVOLUTION; FUNGUS; GENE SEQUENCE; INFORMATION STORAGE; MARKER GENE; MICROBIAL DIVERSITY; PHYLOGENY; PHYMYCO DATABASE; SEQUENCE ALIGNMENT; SEQUENCE DATABASE; SSU RRNA GENE; TAXONOMY;

BASE SEQUENCE; DATABASES, NUCLEIC ACID; EVOLUTION, MOLECULAR; FUNGI; GENETIC VARIATION; INTERNET; MOLECULAR SEQUENCE DATA; PHYLOGENY; RNA, RIBOSOMAL; SEQUENCE ALIGNMENT;

CHYTRIDIOMYCOTA; FUNGI;

EID: 84866389483     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0043117     Document Type: Article

References (55)

1. Vandenkoornhuyse P, Baldauf SL, Leyval C, Straczek J, Young JPW, (2002a) Extensive fungal diversity in plant roots. Science 295: 2051.
2. Purvis A, Hector A, (2000) Getting the measure of biodiversity. Nature 405: 212-219.
3. Taylor JW, Jacobson DJ, Kroken S, Kasuga T, Geiser DM, (2000) Phylogenetic species recognition and species concept in fungi. Fung Genet Biol 31: 21-32.
4. Vandenkoornhuyse P, Husband R, Daniell TJ, Watson IJ, Duck JM, et al. (2002b) Arbuscular mycorrhizal community composition associated with two plant species in a grassland ecosystem. Mol Ecol 11: 1555-1564.
5. Jones MDM, Forn I, Gadelha C, Egan MJ, Bass D, et al. (2011) Discovery of novel intermediate forms redefines the fungal tree of life. Nature 474: 200-203.
6. Powell JR, Monaghan MT, Öpik M, Rillig MC, (2011) Evolutionary criteria outperform operational approaches in producing ecologically relevant fungal species inventories. Molecular Ecology 20: 655-666.
7. Hawksworth DL, Rossman AY, (1997) Where are all the undescribed fungi? Phytopath 87: 888-891.
8. Blackwell M, (2011) The Fungi: 1, 2, 3.. 5.1 million species? Am J Bot 98: 426-438.
9. Woese CR, (2000) Interpreting the universal phylogenetic tree. Proc Natl Acad Sci USA 97: 8392-8396.
10. Pace NR, (2009) Mapping the Tree of Life: Progress and Prospects. Microbiology and Mol Biol Rev 73: 565-576.
11. Choi IG, Kim SH, (2007) Global extent of horizontal gene transfer. Proc Natl Acad Sci USA 104: 4489-4494.
12. Boon E, Zimmerman E, Lang BF, Hijri M, (2010) Intra-isolate genome variation in arbuscular mycorrhizal fungi persists in the transcriptome. J Evol Biol 23: 1519-1527.
13. Sanders IR, Alt M, Groppe K, Boller T, Wiemken A, (1995) Identification of ribosomal DNA polymorphisms among and within spores of the Glomales- Applications to study on the genetic diversity of Arbuscular Mycorrhizal fungal communities. New Phytol 130: 419-427.
14. Lim YW, Sturrock R, Leal I, Pellow K, Yamaguchi T, et al. (2008) Distinguishing homokaryons and heterokaryons in Phellinus sulphurascens using pairing tests and ITS polymorphisms. Antonie van Leeuwenhoek 93: 99-110.
15. Benson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, Sayers EW, (2011) GenBank. Nucl Acids Res 39: D32-D37.
16. Kulikova T, Akhtar R, Aldebert P, Althorpe N, Andersson M, et al. (2007) The EMBL nucleotide sequence database in 2006. Nucl Acids Res 35: D16-D20.
17. Kaminuma E, Kosuge T, Kodama Y, Aono H, Mashima J, et al. (2011) DDBJ progress report. Nucl Acids Res 39: D22-D27.
18. Avise JC (2004) Molecular Markers, Natural History, and Evolution. Sunderland, Massachusetts: Sinauer Associates.
19. Baldauf SL, (1999) A search for the origins of Animals and Fungi: comparing and combining molecular data. Am Nat 154: S178-S188.
20. Baldauf SL, Roger AJ, Wenk-Siefert I, Doolitle WF, (2000) A kingdom-level phylogeny of eukaryotes based on combined protein data. Science 290: 972-977.
21. Helgason T, Watson IJ, Young JPW, (2003) Phylogeny of the Glomerales and Diversisporales (Fungi: Glomeromycota) from actin and elongation factor 1-alpha sequences. FEMS Microb Let 229: 127-132.
22. Baldauf SL, Palmer JD, (1993) Animals and fungi are each others closest relatives: congruent evidence from multiple proteins. Proc Natl Acad Sci USA 90: 11558-11562.
23. Moon CD, Miles CO, Jarlfors U, Schardl CL, (2002) The evolutionary origins of three new Neotyphodium endophyte species from grasses indigenous to the Southern Hemisphere. Mycologia 94: 694-711.
24. Tanabe Y, Saikawa M, Watanabe MM, Sugiyama J, (2004) Molecular phylogeny of Zygomycota based on EF-1α and RBP1 sequences: limitations and utility of alternative markers to rDNA. Mol Phyl Evol 30: 438-449.
25. Bidartondo MI, (2008) Preserving accuracy in GenBank. Science 319: 1616.
26. Bridge PD, Roberts PJ, Spooner BM, Panchal G, (2003) On the unreliability of published DNA sequences. New Phytol 160: 43-48.
27. Vilgalys R, (2003) Taxonomic misidentification in public DNA databases. New Phytol 160: 4-5.
28. Bridge PD, Spooner BM, Roberts PJ, (2004) Reliability and use of published sequence data. New Phytol 161: 15-17.
29. Hawksworth DL, (2004) 'Misidentification' in fungal DNA sequence databanks. New Phytol 161: 13-15.
30. Hawksworth DL, (2009) Separate name for fungus's sexual stage may cause confusion. Nature 458: 29.
31. Holst-Jensen A, Vrålstad T, Schumacher T, (2004) On reliability. New Phytol 161: 11-13.
32. Nilsson RH, Ryberg M, Kristiansson E, Abarenkov K, Larsson KH, et al. (2006) Taxonomic reliability of DNA sequences in public sequence databases: a fungal perspective. PloS One 1: e59.
33. 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.
34. Öpik M, Vanatoa A, Vanatoa E, Moora M, Davison J, et al. (2010) The online database MaarjAM reveals global and ecosystemic distribution patterns in arbuscular mycorrhizal fungi (Glomeromycota). New Phytol 188: 223-241.
35. Cole JR, Wang Q, Cardenas E, Fish J, Chai B, et al. (2009) The Ribosomal Database Project: Improved alignments and new tools for rRNA analysis. Nucl Acids Res 37: D141-D145.
36. Pruesse E, Quast C, Knittel K, Fuchs BM, Ludwig W, (2007) SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB. Nucl Acids Res 35: 7188-7196.
37. DeSantis TZ, Hugenholtz P, Larsen N, Rojas M, Brodie EL, et al. (2006) Greengenes, a Chimera-Checked 16S rRNA Gene Database and Workbench Compatible with ARB. Appl Env Microb 72: 5069-5072.
38. 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.
39. Bhattacharya D, Friedl T, Helms G, (2002) Vertical evolution and intragenic spread of lichen-fungal group I intron. J Mol Evol 55: 74-84.
40. Felsenstein J (2004) Inferring phylogenies. Sinauer Associates, Sunderland, Massachusetts.
41. Posada D, Crandall KA, (1998) MODELTEST: testing the model of DNA substitution. Bioinformatics 14: 817-818.
42. Bar-Hen A, Mariadassou M, Poursat MA, Vandenkoornhuyse P, (2008) Influence function for robust phylogenetic reconstructions. Mol Biol Evol 25: 869-873.
43. Vandenkoornhuyse P, Leyval C, (1998) SSU rDNA sequencing and PCR-fingerprinting reveal genetic variation within Glomus mossae. Mycologia 90: 791-797.
44. White TJ, Bruns T, Lee S, Taylor J (1990) Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics. In: Innis MA, Gelfand DH, Sninsky JJ, White TJ editors. PCR protocols, a guide to methods and applications. San Diego, California Academic Press pp. 315-322.
45. Le Calvez T, Burgaud G, Mahé S, Barbier G, Vandenkoornhuyse P, (2009) Fungal diversity in deep-sea hydrothermal ecosystems. Appl Env Microb 75: 6415-6421.
46. Simmons DR, James TY, Meyer AF, Longcore JE, (2009) Lobulomycetales, a new order in the Chytridiomycota. Mycological Res 113: 450-460.
47. Lutzoni F, Kauff F, Cox CJ, McLaughlin D, Celio G, et al. (2004) Assembling the fungal tree of life: progress, classification, and evolution of subcellular traits. American J Bot 91: 1446-1480.
48. Abarenkov K, Nilsson RH, Larsson KH, Alexander IJ, Eberhardt U, et al. (2010a) The UNITE database for molecular identification of fungi- recent updates and future perspectives. New Phytol 186: 281-285.
49. Abarenkov K, Tedersoo L, Nilsson RH, Vellak K, Saar I, et al. (2010b) PlutoF-a Web Based Workbench for Ecological and Taxonomic Research, with an Online Implementation for Fungal ITS Sequences. Evol Bioinformatics 6: 189-196.
50. Schoch CL, Seifert KA, Huhndorf S, Robert V, Spouge JL, et al. (2012) Nuclear ribosomal internal transcribed spacer (ITS) region as a universal DNA barecode marker for fungi. Proc Natl Acad Sci USA 109: 6241-6246.
51. Anderson IC, Parkin PI, (2007) Detection of active soil fungi by RT-PCR amplification of precursor rRNA molecules. J Microb Meth 68: 248-253.
52. Xu P, Han Y, Wu J, Lv H, Qiu L, et al. (2007) Phylogenetic Analysis of the Sequences of rDNA Internal Transcribed Spacer (ITS) of Phytophthora sojae. J Genet Genom 34: 180-188.
53. D'Auria G, Pushker R, Rodriguez-Valera F, (2006) IWoCS analyzing ribosomal intergenic transcribed spacers configuration and taxonomic relationships. Bioinformatics 22: 527-531.
54. Bass D, Howe A, Brown N, Barton H, Demidova M, et al. (2007) Yeast forms dominate fungal diversity in the deep oceans. Proc Royal Soc B 274: 3069-3077.
55. 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.