CFGP: A web-based, comparative fungal genomics platform

Nucleic Acids Research

Volumn 36, Issue SUPPL. 1, 2008, Pages

  Park, Jongsun ^a,b   Park, Bongsoo ^a,c   Jung, Kyongyong ^a,b   Jang, Suwang ^a   Yu, Kwangyul ^a   Choi, Jaeyoung ^a,b   Kong, Sunghyung ^a,b   Park, Jaejin ^a,b   Kim, Seryun ^a,b   Kim, Hyojeong ^a   Kim, Soonok ^a   Kim, Jihyun F ^d   Blair, Jaime E ^e   Lee, Kwangwon ^f   Kang, Seogchan ^c   Lee, Yong Hwan ^a,b,c  

^a Seoul National University   (South Korea)

^b Seoul National University   (South Korea)

^c PENNSYLVANIA STATE UNIVERSITY   (United States)

^d Korea Research Institute of Bioscience and Biotechnology (KRIBB)   (South Korea)

^e AMHERST COLLEGE   (United States)

^f Department of Obstetrics Gynecology   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; BIOINFORMATICS; COMPUTER INTERFACE; COMPUTER PROGRAM; DATA ANALYSIS; FUNGAL GENETICS; FUNGAL STRAIN; GENE IDENTIFICATION; GENE SEQUENCE; GENETIC ANALYSIS; GENOMICS; INFORMATION PROCESSING; INFORMATION SERVICE; NONHUMAN; PRIORITY JOURNAL; SACCHAROMYCES CEREVISIAE;

COMPUTATIONAL BIOLOGY; DATABASES, GENETIC; DNA, FUNGAL; FUNGAL PROTEINS; GENOME, FUNGAL; GENOMICS; INTERNET; SEQUENCE HOMOLOGY, NUCLEIC ACID; SOFTWARE; USER-COMPUTER INTERFACE;

SACCHAROMYCES CEREVISIAE;

EID: 38549176698     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkm758     Document Type: Article

References (67)

1. Hawksworth, D.L. (1991) The fungal dimension of biodiversity: Magnitude, significance, and conservation. Mycol. Res., 95, 641-655.
2. Van der Heijden, M.G.A., Klironomos, J.N., Ursic, M., Moutoglis, P., Streitwolf-Engel, R., Boller, T., Wiemken, A. and Sanders, I.R. (1998) Mycorrhizal fungal diversity determines plant biodiversity, ecosystem variability and productivity. Nature, 396, 69.
3. Demain, A.L. (2000) Microbial biotechnology. Trends Biotechnol., 18, 26-31.
4. Agrios, G.N. (2005) edn. Plant Pathology, 5th edn. Academic Press, San Diego.
5. Denning, D.W. (1998) Invasive aspergillosis. Clin. Infect. Dis., 26, 781-805.
6. Kwon-Chung, K.J., Varma, A. and Howard, D.H. (1990) Ecology of Cryptococcus neoformans and prevalence of its two varieties in AIDS and non-AIDS associated Cryptococcosis. In Vanden Bossche, H., Mackenzie, D.W.R., Cauwenbergh, G., Van Custem, J., Drouhet, E. and Dupont, B. (eds), Mycoses in AIDS Patients. Plenum Press, New York, pp. 103-113.
7. Galagan, J.E., Henn, M.R., Ma, L.J., Cuomo, C.A. and Birren, B. (2005) Genomics of the fungal kingdom: Insights into eukaryotic biology. Genome Res., 15, 1620-1631.
8. Goffeau, A., Barrell, B.G., Bussey, H., Davis, R.W., Dujon, B., Feldmann, H., Galibert, F., Hoheisel, J.D., Jacq, C. et al. (1996) Life with 6000 genes. Science, 274, 546, 563-547.
9. Park, J., Kim, H., Kim, S., Kong, S., Park, J., Kim, S., Han, H., Park, B., Jung, K. et al. (2006) A comparative genome-wide analysis of GATA transcription factors in fungi. Genomics Inform., 4, 147-160.
10. Metzker, M.L. (2006) Emerging technologies in DNA sequencing. Genome Res., 15, 1767-1776.
11. James, T.Y., Kauff, F., Schoch,C.L., Matheny, P.B., Hofstetter, V., Cox, C.J., Celio, G., Gueidan, C., Fraker, E. et al. (2006) Reconstructing the early, evolution of fungi using a six-gene phylogeny. Nature, 443, 818-822
12. Hibbett, D.S., Binder, M., Bischoff, J.F., Blackwell, M., Cannon, P.F., Eriksson, O.E., Huhndorf, S., James, T., Kirk, P.M. et al. (2007) A higher-level phylogenetic classification of the Fungi. Mycol. Res. 111, 509-547.
13. Fitzpatrick, D.A., Logue, M.E., Stajich, J. E. and Butler, G. (2006) A fungal phylogeny, based on 42 complete genomes derived from supertree and combined gene analysis. BMC Evol. Biol., 6, 99.
14. Kroken, S., Glass, N.L., Taylor, J.W., Yoder, O.C. and Turgeon, B.G. (2003) Phylogenomic analysis of type I polyketide synthase genes in pathogenic and saprobic ascomycetes. Proc. Natl Acad. Sci. USA, 100, 15670-15675.
15. Kamper, J., Kahmann, R., Bolker, M., Ma, L.J., Brefort, T., Saville, B.J., Banuett, F., Kronstad, J.W., Gold, S.E. et al. (2006) Insights from the genome of the biotrophic fungal plant pathogen Ustilago maydis. Nature, 444, 97-101.
16. Jeon, J., Park, S.Y., Chi, M.H., Choi, J., Park, J., Rho, H.S., Kim, S., Goh, J., Yoo, S. et al. (2007) Genome-wide functional analysis of pathogenicity genes in the rice blast fungus. Nat. Genet, 39 561-565.
17. Galagan, J.E., Calvo, S.E., Cuomo, C., Ma, L.J., Wortman, J.R., Batzoglou, S., Lee, S.I., Basturkmen, M., Spevak, C.C. et al. (2005) Sequencing of Aspergillus nidulans and comparative analysis with A. fumigatus and A. oryzae. Nature, 438, 1105-1115.
18. Payne, G.A., Nierman, W.C., Wortman, J.R., Pritchard, B.L., Brown, D., Dean, R.A., Bhatnagar, D., Cleveland, T.E., Machida, M. et al. (2006) Whole genome comparison of Aspergillus flavus and A. oryzae. Med. Mycol., 44(Suppl.), 9-11.
19. Dujon, B., Sherman, D., Fischer, G., Durrens, P., Casaregola, S., Lafontaine, I., De Montigny, J., Marck, C., Neuveglise, C. et al. (2004) Genome evolution in yeasts. Nature, 430, 35-44.
20. Kellis, M., Birren, B.W. and Lander, E.S. (2004) Proof and evolutionary analysis of ancient genome duplication in the yeast Saccharomyces cerevisiae. Nature, 428, 617-624.
21. Cornell, M., Paton, N.W., Hedeler, C., Kirby, P., Delneri, D., Hayes, A. and Oliver, S.G. (2003) GIMS: An integrated data storage and analysis environment for genomic and functional data. Yeast, 20, 1291-1306.
22. Price, E.W. and Carbone, I. (2005) SNAP: Workbench management tool for evolutionary population genetic analysis. Bioinformatics, 21 402-404.
23. Rice, P., Longden, I. and Bleasby, A. (2000) EMBOSS: The European Molecular Biology Open Software Suite. Trends Genet., 16, 276-277.
24. Choi, K., Ma, Y, Choi, J.H. and Kim, S. (2005) PLATCOM: A platform for computational comparative genomics. Bioinformatics, 21, 2514-2516.
25. Lee, D., Choi, J.H., Dalkilic, M.M. and Kim, S. (2006) COMPAM: visualization of combining pairwise alignments for multiple genomes. Bioinformatics, 22, 242-244.
26. Siepel, A., Farmer, A., Tolopko, A., Zhuang, M., Mendes, P., Beavis, W. and Sobral, B. (2001) ISYS: A decentralized, component-based approach to the integration of heterogeneous bioinformatics resources. Bioinformatics, 17, 83-94.
27. McGinnis, S. and Madden, T.L. (2004) BLAST: At the core of a powerful and diverse set of sequence analysis tools. Nucleic Acids Res., 32, W20-W25.
28. Thompson, J.D., Higgins, D.G. and Gibson, T.J. (1994) CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res., 22, 4673-4680.
29. Mulder, N.J., Apweiler, R., Attwood, T.K., Bairoch, A., Bateman, A., Binns, D., Bradley, P., Bork, P., Bucher, P. et al. (2005) InterPro, progress and status in 2005. Nucleic Acids Res., 33 D201-D205.
30. Bendtsen, J.D., Nielsen, H., von Heijne, G. and Brunak, S. (2004) Improved prediction of signal peptides: SignalP 3.0. J. Mol. Biol. 340, 783-795.
31. Nakai, K. and Horton, P. (1999) PSORT: A program for detecting sorting signals in proteins and predicting their subcellular localization. Trends Biochem. Sci., 24, 34-36.
32. Wickware, P. (2000) Next-generation biologists must straddle computation and biology. Nature, 404, 683-684.
33. Blair, J.E., Shah, P. and Hedges, S.B. (2005) Evolutionary sequence analysis of complete eukaryote genomes. BMC Bioinformatics, 6 53.
34. Schell, M.A., Karmirantzou, M., Snel, B., Vilanova, D., Berger, B, Pessi, G., Zwahlen, M.C., Desiere, F., Bork, P. et al. (2002) The genome sequence of Bifidobacterium longum reflects its adaptation to the human gastrointestinal tract. Proc. Natl Acad. Sci. USA, 99, 14422-14427.
35. Bentley, S.D., Chater, K.F., Cerdeno-Tarraga, A.M., Challis, G.L., Thomson, N.R., James, K.D., Harris, D.E., Quail, M.A., Kieser, H. et al. (2002) Complete genome sequence of the model actinomycete Streptomyces coelicolor A3(2). Nature, 417, 141-147.
36. Blattner, F.R., Plunkett, G. 3rd, Bloch, C.A., Perna, N.T., Burland, V., Riley, M., Collado-Vides, J., Glasner, J.D., Rode, C.K. et al. (1997) The complete genome sequence of Escherichia coli K-12. Science, 277, 1453-1474.
37. Paulsen, I.T., Press, C.M., Ravel, J., Kobayashi, D.Y., Myers, G.S., Mavrodi, D.V., DeBoy R.T., Seshadri, R., Ren, Q. et al. (2005) Complete genome sequence of the plant commensal Pseudomonas fluorescens Pf-5. Nat. Biotechnol., 23, 873-878.
38. Douglas, S.E. and Penny, S.L. (1999) The plastid genome of the cryptophyte alga, Guillardia theta: Complete sequence and conserved synteny groups confirm its common ancestry with red algae. J. Mol. Evol., 48, 236-244.
39. Myler, P.J., Beverley, S.M., Cruz, A.K., Dobson, D.E., Ivens, A.C., McDonagh, P.D., Madhubala, R., Martinez-Calvillo, S., Ruiz, J.C. et al. (2001) The Leishmania genome project: New insights into gene organization and function. Med. Microbiol. Immumol., 190, 9-12.
40. Nierman, W.C., Pain, A., Anderson, M.J., Wortman, J.R., Kim, H.S., Arroyo, J., Berriman, M., Abe, K., Archer, D.B. et al. (2005) Genomic sequence of the pathogenic and allergenic filamentous fungus Aspergillus fumigatus. Nature, 438, 1151-1156.
41. Machida, M., Asai, K., Sano, M., Tanaka, T., Kumagai, T., Terai, G., Kusumoto, K., Arima, T., Akita, O. et al. (2005) Genome sequencing and analysis of Aspergillus oryzae. Nature, 438, 1157-1161.
42. Cuomo, C. Güldener, U., Xu, J., Trail, F., Turgeon, B., Di, P.A., Walton, J., Ma, L., Baker, S. et al. (2007) The Fusarium graminearum genome reveals a link between localized polymorphism and pathogen specialization. Science, 317, 1400-1402.
43. Dean, R.A., Talbot, N.J., Ebbole, D.J., Farman, M.L., Mitchell, T.K., Orbach, M.J., Thon, M., Kulkarni, R., Xu, J.R. et al. (2005) The genome sequence of the rice blast fungus Magnaporthe grisea. Nature 434, 980-986.
44. Borkovich, K.A., Alex, L.A., Yarden, O., Freitag, M., Turner, G.E., Read, N.D., Seiler, S., Bell-Podersen, D., Paietta, J. et al. (2004) Lessons from the genome sequence of Neurospora crassa: tracing the path from genomic blueprint to multicellular organism. Microbiol. Mol. Biol. Rev., 68, 1-108.
45. Jones, T., Federspiel, N.A., Chibana, H., Dungan, J., Kalman, S., Magee, B.B., Newport, G., Thorstenson, Y.R., Agabian, N. et al. (2004) The diploid genome sequenee of Candida albicans. Proc. Natl Acad. Sci. USA, 101, 7329-7334.
46. Dietrich, F.S., Voegeli, S., Brachat, S., Lerch, A., Gates, K., Steiner, S., Mohr, C., Pohlmann, R., Luedi, P. et al. (2004) The Ashbya gossypii genome as a tool for mapping the ancient Saccharomyces cerevisiae genome. Science, 304, 304-307.
47. Kellis, M. Patterson, N., Endrizzi, M., Birren, B. and Lander, E.S. (2003) Sequencing and comparison of yeast species to identify genes and regulatory elements. Nature, 423, 241-254.
48. Cliften, P., Sudarsanam, P., Desikan, A., Fulton, L., Fulton, B., Majors, J., Waterston, R., Cohen, B.A. and Johnston, M. (2003) Finding functional features in Saccharomyces genomes by phylogenetic footprinting. Science, 301, 71-76.
49. Jeffries, T.W., Grigoriev, I.V., Grimwood, J., Laplaza, J.M., Aerts, A., Salamov, A., Schmutz, J., Lindquist, E., Dehal, P. et al. (2007) Genome sequence of the lignocellulose-bioconverting and xylose-fermenting yeast Pichia stipitis. Nat. biotechnol., 25 319-326.
50. Wood, V., Gwilliam, R., Rajandream, M.A., Lyne, M., Lyne, R., Stewart, A., Sgouros, J., Peat, N., Hayles, J. et al. 2002) The genome sequence of Schizosaccharomyces pombe. Nature, 415, 871-880.
51. Martinez, D., Larrondo, L.F., Putnam, N., Gelpke, M.D., Huang, K., Chapman, J., Helfenbein, K.G., Ramaiya, P., Detter, J.C. et al. (2004) Genome sequence of the lignocellulose degrading fungus Phanerochaete chrysosporium strain RP78. Nat. Biotechnol., 22, 695-700.
52. Loftus, B.J., Fung, E., Roncaglia, P., Rowley, D., Amedeo, P., Bruno, D., Vamathevan, J., Miranda, M., Anderson, I.J. et al. (2005) The genome of the basidiomycetous yeast and human pathogen Gryptococcus neoformans Science, 307, 1321-1324.
53. Katinka, M.D., Duprat, S., Cornillot, E., Metenier, G., Thomarat, F., Prensier, G., Barbe, V., Peyretaillade, E., Brottier, P. et al. (2001) Genome sequence and gene compaction of the eukaryote parasite Encephalitozoon cuniculi. Nature, 414, 450-453.
54. Tyler, B.M., Tripathy, S., Zhang, X., Dehal, P., Jiang, R.H., Aerts, A., Arredondo, F.D., Baxter, L., Bensasson, D. et al. (2006) Phytophthora genome sequences uncover evolutionary origins and mechanisms of pathogenesis. Science, 313, 1261-1266.
55. AGI. (2000) Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature, 408, 796-815.
56. IRGSP. (2005) The map-based sequence of the rice genome. Nature, 436, 793-800.
57. Yu, J., Hu, S., Wang, J., Wong, G.K., Li, S., Liu, B., Deng, Y., Dai, L., Zhou, Y. et al. (2002) A draft sequence of the rice genome ( Oryza sativa L. ssp. indica). Science, 296, 79-92.
58. Tuskan, G.A., Difazio, S., Jansson, S., Bohlmann, J., Grigoriev, I., Hellsten, U., Putnam, N., Ralph, S., Rombauts, S. et al. (2006) The genome of black cottonwood, Populus trichocarpa (Torr. & Gray). Science, 313, 1596-1604.
59. Holt, R.A., Subramanian, G.M., Halpern, A., Sutton, G.G., Charlab, R., Nusskern, D.R., Wincker, P., Clark, A.G., Ribeiro, J.M. et al. (2002) The genome sequence of the malaria mosquito Anopheles gambiae. Science, 298, 129-149.
60. Kornberg, T.B. and Krasnow, M.A. (2000) The Drosophila genome sequence: Implications for biology and medicine. Science, 287 2218-2220.
61. Darling, J.A., Reitzel, A.R., Burton, P.M., Mazza, M.E., Ryan, J.F., Sullivan, J.C. and Finnerty, J.R. (2005) Rising starlet: The starlet sea anemone, Nematostella vectensis. Bioessays, 27, 211-221.
62. CSC. (1998) Genome sequence of the nematode C. elegans: A platform for investigating biology. Science, 282, 2012-2018.
63. Dehal, P., Satou, Y., Campbell, R.K., Chapman, J., Degnan, B., De Tomaso, A., Davidson, B., Di Gregorio, A., Gelpke, M. et al. (2002) The draft genome of Ciona intestinalis: Insights into chordate and vertebrate origins. Science, 298, 2157-2167.
64. Waterston, R.H., Lindblad-Toh, K., Birney, E., Rogers, J., Abril, J.F., Agarwal, P., Agarwala, R., Ainscough, R., Alexandersson, M. et al. (2002) Initial sequencing and comparative analysis of the mouse genome. Nature, 420, 520-562.
65. Lander, E.S., Linton, L.M., Birren, B., Nusbaum, C., Zody, M.C., Baldwin, J., Devon, K., Dewar, K., Doyle, M., et al. (2001) Initial sequencing and analysis of the human genome. Nature, 409, 860-921.
66. Garrity, G.M. (2001) Bergey's Manual of Systematic Bacteriology, 2nd edn. New York, Springer.
67. Adl, S.M., Simpson, A.G., Farmer, M.A., Andersen, R.A., Anderson, O.R., Barta, J.R., Bowser S.S., Brugerolle, G., Fensome, R.A. et al. (2005) The new higher level classification of eukaryotes with emphasis on the taxonomy of protists. J. Eukaryot. Microbiol., 52, 399-451.