A fungal phylogeny based on 82 complete genomes using the composition vector method

BMC Evolutionary Biology

Volumn 9, Issue 1, 2009, Pages

  Wang, Hao ^a   Xu, Zhao ^a   Gao, Lei ^b   Hao, Bailin ^a,c,d  

^a FUDAN UNIVERSITY   (China)

^b UNIVERSITY OF CALIFORNIA   (United States)

^c INSTITUTE OF THEORETICAL PHYSICS   (China)

^d SANTA FE INSTITUTE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

AJELLOMYCETACEAE; ARTICLE; ASCOMYCETES; ASPERGILLUS NIDULANS; CANDIDA GLABRATA; COMPOSITION VECTOR TREE; DOTHIDEOMYCETES; EUROTIALES; EUROTIOMYCETES; FUNGUS; GENOME; HISTOPLASMA; MAGNAPORTHE GRISEA; NOMENCLATURE; NONHUMAN; ONYGENACEAE; ONYGENALES; PARACOCCIDIOIDES; PEZIZOMYCOTINA; PHYLOGENETIC TREE; PHYLOGENY; PLECTOSPHAERELLACEAE; SACCHAROMYCOTINA; SEQUENCE ALIGNMENT; SORDARIALES; SORDARIOMYCETES; STANDARD; TREE OF LIFE; BIOLOGY; CLASSIFICATION; COMPARATIVE STUDY; DNA SEQUENCE; FUNGAL GENOME; GENETICS; GENOMICS; METHODOLOGY; MOLECULAR EVOLUTION;

AJELLOMYCES; AJELLOMYCETACEAE; CANDIDA GLABRATA; DOTHIDEOMYCETES; EMERICELLA NIDULANS; EUROTIALES; EUROTIOMYCETES; HYPOCREALES; MAGNAPORTHE GRISEA; ONYGENACEAE; ONYGENALES; PARACOCCIDIOIDES; PEZIZOMYCOTINA; SACCHAROMYCOTINA; SORDARIALES; SORDARIOMYCETES;

COMPUTATIONAL BIOLOGY; EVOLUTION, MOLECULAR; FUNGI; GENOME, FUNGAL; GENOMICS; PHYLOGENY; SEQUENCE ANALYSIS, DNA;

EID: 69949152972     PISSN: None     EISSN: 14712148     Source Type: Journal    
DOI: 10.1186/1471-2148-9-195     Document Type: Article

References (60)

1. The magnitude of fungal diversity: the 1.5 million species estimate revisited. DL Hawksworth, Mycol Res 2002 105 12 1422 1432 10.1017/ S0953756201004725
2. Assembling the fungal tree of life: progress, classification, and evolution of subcellular traits 1. F Lutzoni F Kauff C Cox D McLaughlin G Celio B Dentinger M Padamsee D Hibbett T James E Baloch, Am J Bot 2004 91 10 1446 1480 10.3732/ajb.91.10.1446
3. Reconstructing the early evolution of Fungi using a six-gene phylogeny. TY James F Kauff CL Schoch PB Matheny V Hofstetter CJ Cox G Celio C Gueidan E Fraker J Miadlikowska HT Lumbsch A Rauhut V Reeb AE Arnold A Amtoft JE Stajich K Hosaka GH Sung D Johnson B O'Rourke M Crockett M Binder JM Curtis JC Slot Z Wang AW Wilson A Schüssler JE Longcore K O'Donnell S Mozley-Standridge D Porter PM Letcher MJ Powell JW Taylor MM White GW Griffith DR Davies RA Humber JB Morton J Sugiyama AY Rossman JD Rogers DH Pfister D Hewitt K Hansen S Hambleton RA Shoemaker J Kohlmeyer B Volkmann-Kohlmeyer RA Spotts M Serdani PW Crous KW Hughes K Matsuura E Langer G Langer WA Untereiner R Lücking B Büdel DM Geiser A Aptroot P Diederich I Schmitt M Schultz R Yahr DS Hibbett F Lutzoni DJ McLaughlin JW Spatafora R Vilgalys, Nature 2006 443 7113 818 822 10.1038/nature05110 17051209 (Pubitemid 44622687)
4. A fungal phylogeny based on 42 complete genomes derived from supertree and combined gene analysis. DA Fitzpatrick ME Logue JE Stajich G Butler, BMC Evol Biol 2006 6 99 10.1186/1471-2148-6-99 17121679 (Pubitemid 44903742)
5. A higher-level phylogenetic classification of the Fungi. DS Hibbett M Binder JF Bischoff M Blackwell PF Cannon OE Eriksson S Huhndorf T James PM Kirk R Lücking HT Lumbsch F Lutzoni PB Matheny DJ McLaughlin MJ Powell S Redhead CL Schoch JW Spatafora JA Stalpers R Vilgalys MC Aime A Aptroot R Bauer D Begerow GL Benny LA Castlebury PW Crous YC Dai W Gams DM Geiser GW Griffith C Gueidan DL Hawksworth G Hestmark K Hosaka RA Humber KD Hyde JE Ironside U Köljalg CP Kurtzman KH Larsson R Lichtwardt J Longcore J Miadlikowska A Miller JM Moncalvo S Mozley-Standridge F Oberwinkler E Parmasto V Reeb JD Rogers C Roux L Ryvarden JP Sampaio A Schüssler J Sugiyama RG Thorn L Tibell WA Untereiner C Walker Z Wang A Weir M Weiss MM White K Winka YJ Yao N Zhang, Mycol Res 2007 111 Pt 5 509 547 10.1016/j.mycres.2007.03.004 17572334 (Pubitemid 46915419)
6. Evolutionary relationships within the fungi: analyses of nuclear small subunit rRNA sequences. TD Bruns R Vilgalys SM Barns D Gonzalez DS Hibbett DJ Lane L Simon S Stickel TM Szaro WG Weisburg, Mol Phylogenet Evol 1992 1 3 231 41 10.1016/1055-7903(92)90020-H 1342940
7. Broad phylogenomic sampling improves resolution of the animal tree of life. CW Dunn A Hejnol DQ Matus K Pang WE Browne SA Smith E Seaver GW Rouse M Obst GD Edgecombe MV Sørensen SHD Haddock A Schmidt-Rhaesa A Okusu RM Kristensen WC Wheeler MQ Martindale G Giribet, Nature 2008 452 7188 745 749 10.1038/nature06614 18322464
8. A decade of progress in plant molecular phylogenetics. V Savolainen MW Chase, Trends Genet 2003 19 12 717 724 10.1016/j.tig.2003.10.003 14642753 (Pubitemid 37464850)
9. Deuterostome phylogeny reveals monophyletic chordates and the new phylum Xenoturbellida. SJ Bourlat T Juliusdottir CJ Lowe R Freeman J Aronowicz M Kirschner ES Lander M Thorndyke H Nakano AB Kohn A Heyland LL Moroz RR Copley MJ Telford, Nature 2006 444 7115 85 88 10.1038/nature05241 17051155 (Pubitemid 44684760)
10. A phylogenomic analysis of the Ascomycota. B Robbertse JB Reeves CL Schoch JW Spatafora, Fungal Genet Biol 2006 43 10 715 725 10.1016/j.fgb.2006.05. 001 16781175 (Pubitemid 44292552)
11. Large-scale sequencing and the new animal phylogeny. H Philippe MJ Telford, Trends Ecol Evol 2006 21 11 614 620 10.1016/j.tree.2006.08.004 16919363 (Pubitemid 44528811)
12. Phylogenomics and the reconstruction of the tree of life. F Delsuc H Brinkmann H Philippe, Nat Rev Genet 2005 6 5 361 375 10.1038/nrg1603 15861208 (Pubitemid 40577180)
13. Whole Proteome Prokaryote Phylogeny Without Sequence Alignment: A K-String Composition Approach. J Qi B Wang B Hao, J Mol Evol 2004 58 1 11 10.1007/s00239-003-2493-7 14743310 (Pubitemid 38120400)
14. CVTree: a phylogenetic tree reconstruction tool based on whole gemomes. J Qi H Luo B Hao, Nucleic Acids Res 2004 32 Webserver W45 W47 10.1093/nar/gkh362 15215347 (Pubitemid 38997297)
15. Prokaryote phylogeny without sequence alignment: from avoidance signature to composition distance. B Hao J Qi, J Bioinform Comput Biol 2004 2 1 19 10.1142/S0219720004000442 15272430 (Pubitemid 38996810)
16. Prokaryote phylogeny meets taxonomy: an exhaustive comparison of composition vector trees with systematic bacteriology. L Gao J Qi J Sun B Hao, Sci China C Life Sci 2007 50 5 587 599 10.1007/s11427-007-0084-3 17879055 (Pubitemid 47459905)
17. Whole genome molecular phylogeny of large dsDNA viruses using composition vector method. L Gao J Qi, BMC Evol Biol 2007 7 41 10.1186/1471-2148-7-41 17359548 (Pubitemid 46512734)
18. National Center for Biotechnology Information. ftp://ftp.ncbi.nih.gov/ genomes/
19. Dandruff-associated Malassezia genomes reveal convergent and divergent virulence traits shared with plant and human fungal pathogens. J Xu CW Saunders P Hu RA Grant T Boekhout EE Kuramae JW Kronstad YM Deangelis NL Reeder KR Johnstone M Leland AM Fieno WM Begley Y Sun MP Lacey T Chaudhary T Keough L Chu R Sears B Yuan TL Dawson, Proc Natl Acad Sci USA 2007 104 47 18730 18735 10.1073/pnas.0706756104 18000048 (Pubitemid 350210765)
20. A phylogenetic hypothesis of Ustilaginomycotina based on multiple gene analyses and morphological data. D Begerow M Stoll R Bauer, Mycologia 2006 98 6 906 916 10.3852/mycologia.98.6.906 17486967
21. A microscopist's view of heterobasidiomycete phylogeny. DJ McLaughlin EM Frieders H Lü Stud Mycol 1995 38 91 109
22. Archiascomycetes: detection of a major new lineage within the Ascomycota. H Nishida J Sugiyama, Mycoscience 1994 35 4 361 366 10.1007/BF02268506
23. Outline of Ascomycota-2007. HT Lumbsch SM Huhndorf, Myconet 2007 13 1 58
24. Loss of the flagellum happened only once in the fungal lineage: phylogenetic structure of kingdom Fungi inferred from RNA polymerase II subunit genes. YJ Liu MC Hodson BD Hall, BMC Evol Biol 2006 6 74 10.1186/1471-2148-6-74 17010206 (Pubitemid 44574348)
25. A five-gene phylogeny of Pezizomycotina. JW Spatafora GH Sung D Johnson C Hesse B O'Rourke M Serdani R Spotts F Lutzoni V Hofstetter J Miadlikowska V Reeb C Gueidan E Fraker T Lumbsch R Lücking I Schmitt K Hosaka A Aptroot C Roux AN Miller DM Geiser J Hafellner G Hestmark AE Arnold B Büdel A Rauhut D Hewitt WA Untereiner MS Cole C Scheidegger M Schultz H Sipman CL Schoch, Mycologia 2006 98 6 1018 1028 10.3852/mycologia.98.6.1018 17486977
26. Performance of four ribosomal DNA regions to infer higher-level phylogenetic relationships of inoperculate euascomycetes (Leotiomyceta). HT Lumbsch I Schmitt R Lindemuth A Miller A Mangold F Fernandez S Huhndorf, Mol Phylogenet Evol 2005 34 3 512 524 10.1016/j.ympev.2004.11.007 15683926 (Pubitemid 40427964)
27. Index Fungorum. http://www.indexfungorum.org/names/Names.asp
28. An overview of the systematics of the Sordariomycetes based on a four-gene phylogeny. N Zhang LA Castlebury AN Miller SM Huhndorf CL Schoch KA Seifert AY Rossman JD Rogers J Kohlmeyer B Volkmann-Kohlmeyer GH Sung, Mycologia 2006 98 6 1076 1087 10.3852/mycologia.98.6.1076 17486982
29. International Code for Botanic Nomenclature. http://ibot.sav.sk/icbn/ main.htm
30. A comparison of three fission yeast mitochondrial genomes. CE Bullerwell J Leigh L Forget BF Lang, Nucleic Acids Res 2003 31 2 759 768 10.1093/nar/gkg134 12527786 (Pubitemid 36175966)
31. Molecular systematics of the Coronophorales and new species of Bertia, Lasiobertia and Nitschkia. SM Huhndorf AN Miller FA Fernández, Mycol Res 2004 108 Pt 12 1384 1398 10.1017/S0953756204001273 15757174 (Pubitemid 40198909)
32. Multi-gene phylogenies indicate ascomal wall morphology is a better predictor of phylogenetic relationships than ascospore morphology in the Sordariales (Ascomycota, Fungi). AN Miller SM Huhndorf, Mol Phylogenet Evol 2005 35 60 75 10.1016/j.ympev.2005.01.007 15737582 (Pubitemid 40281403)
33. The phylogeny of plant and animal pathogens in the Ascomycota. M Berbee, Physiol Mol Plant Pathol 2001 59 4 165 187 10.1006/pmpp.2001.0355 (Pubitemid 34000020)
34. Aspergillus nidulans Genome and a Comparative Analysis of Genome Evolution in Aspergillus. A Rokas JE Galagan, The Aspergilli: Genomics, Medical Aspects, Biotechnology, and Research New York: CRC Press, Osmani SA, Goldman GH, 2007 43 54
35. BROAD-FGI Aspergillus Comparative Database. http://www.broad.mit.edu/ annotation/genome/aspergillus-group/MultiHome.html
36. Phylogenetic relationships in Aspergillus based on rDNA sequence analysis. SW Peterson, Integration of Modern Taxonomic Methods for Penicillium and Aspergillus Classification Amsterdam: Harwood Academic Publishers, Samson RA, Pitt JI, 2000 323 355
37. Paracoccidioides brasiliensis and paracoccidioidomycosis: molecular approaches to morphogenesis, diagnosis, epidemiology, taxonomy and genetics. G San-Blas G Nĩo-Vega T Iturriaga, Med Mycol 2002 40 3 225 242 10.1080/714031110 12146752
38. Paracoccidioides brasiliensis: phylogenetic and ecological aspects. E Bagagli RC Theodoro SMG Bosco JG McEwen, Mycopathologia 2008 165 4-5 197 207 10.1007/s11046-007-9050-7 18777629 (Pubitemid 351606078)
39. The Ajellomycetaceae, a new family of vertebrate-associated Onygenales. W Untereiner J Scott F Naveau L Sigler J Bachewich A Angus, Mycologia 2004 96 4 812 821 10.2307/3762114
40. Species concepts and biodiversity in Trichoderma and Hypocrea: from aggregate species to species clusters? I Druzhinina CP Kubicek, J Zhejiang Univ Sci B 2005 6 2 100 112 10.1631/jzus.2005.B0100 15633245 (Pubitemid 40232918)
41. Members of the Fusarium solani species complex that cause infections in both humans and plants are common in the environment. N Zhang K O'Donnell DA Sutton FA Nalim RC Summerbell AA Padhye DM Geiser, J Clin Microbiol 2006 44 6 2186 2190 10.1128/JCM.00120-06 16757619 (Pubitemid 43902174)
42. BROAD-FGI Fusarium Comparative Database. http://www.broad.mit.edu/ annotation/genome/fusarium-group/MultiHome.html
43. Genome sequence of the lignocellulose-bioconverting and xylose-fermenting yeast Pichia stipitis. TW Jeffries IV Grigoriev J Grimwood JM Laplaza A Aerts A Salamov J Schmutz E Lindquist P Dehal H Shapiro YS Jin V Passoth PM Richardson, Nat Biotechnol 2007 25 3 319 326 10.1038/nbt1290 17334359 (Pubitemid 46398771)
44. Genome-scale approaches to resolving incongruence in molecular phylogenies. A Rokas BL Williams N King SB Carroll, Nature 2003 425 6960 798 804 10.1038/nature02053 14574403 (Pubitemid 37355944)
45. Phylogenomics: the beginning of incongruence? O Jeffroy H Brinkmann F Delsuc H Philippe, Trends Genet 2006 22 4 225 231 10.1016/j.tig.2006.02.003 16490279
46. Phylogenetic circumscription of Saccharomyces, Kluyveromyces and other members of the Saccharomycetaceae, and the proposal of the new genera Lachancea, Nakaseomyces, Naumovia, Vanderwaltozyma and Zygotorulaspora. CP Kurtzman, FEMS Yeast Res 2003 4 3 233 245 10.1016/S1567-1356(03)00175-2 14654427 (Pubitemid 37494721)
47. Multiple rounds of speciation associated with reciprocal gene loss in polyploid yeasts. DR Scannell KP Byrne JL Gordon S Wong KH Wolfe, Nature 2006 440 7082 341 345 10.1038/nature04562 16541074
48. Phylogenetics of Saccharomycetales, the ascomycete yeasts. SO Suh M Blackwell CP Kurtzman MA Lachance, Mycologia 2006 98 6 1006 1017 10.3852/mycologia.98.6.1006 17486976
49. Compositional bias may affect both DNA-based and protein-based phylogenetic reconstructions. PG Foster DA Hickey, J Mol Evol 1999 48 3 284 290 10.1007/PL00006471 10093217
50. Weighted neighbor joining: a likelihood-based approach to distance-based phylogeny reconstruction. WJ Bruno ND Socci AL Halpern, Mol Biol Evol 2000 17 189 197 10666718
51. PHYLIP-Phylogeny Inference Package (Version 3.2). J Felsenstein, Cladistics 1989 5 164 166
52. Test Data Sets and Evaluation of Gene Prediction Programs on the Rice Genome. H Li L Gao L Fang T Liu HH Li Y Li LJ Fang HM Xie WM Zheng JS Liu Z Xu J Jin YD Li ZX Xing SG Gao BL Hao, J Comput Sci & Technol 2005 20 4 446 53 10.1007/s11390-005-0446-x (Pubitemid 43257719)
53. Beijing Gene Finder. http://tlife.fudan.edu.cn/bgf/
54. Board Institute Fungal Genome Initiative. http://www.broad.mit.edu/ annotation/fgi/
55. Department of Energy Joint Genome Institute. http://genome.jgi-psf.org/
56. Resources for Fungal Comparative Genomics. http://fungal.genome.duke.edu/
57. Fungal Genome Research. http://fungalgenomes.org/
58. Assembling the Fungal Tree of Life Project. http://aftol.org
59. Myconet. http://www.fieldmuseum.org/myconet
60. NCBI taxonomy browser. http://www.ncbi.nlm.nih.gov/Taxonomy/