DESCRIPTION OF PHI-BASE
PHI-base is a web-accessible database that catalogues
experimentally verified pathogenicity, virulence and effector
genes from fungal, Oomycete and bacterial
pathogens, which infect animal, plant, fungal and insect
hosts. PHI-base is therfore an invaluable resource in the
discovery of genes in medically and agronomically important
pathogens, which may be potential targets for chemical
intervention. In collaboration with the FRAC team, PHI-base
also includes antifungal compounds and their target genes.
Each entry in PHI-base is curated by domain experts and is
supported by strong experimental evidence (gene disruption
experiments, STM etc), as well as literature references in
which the original experiments are described. Each gene in
PHI-base is presented with its nucleotide and deduced amino
acid sequence, as well as a detailed description of the
predicted protein's function during the host infection
process. To facilitate data interoperability, we have
annotated genes using controlled vocabularies and links to
external sources (Gene Ontology terms, EC Numbers, NCBI
taxonomy, EMBL, PubMed and FRAC).
PUBLICATIONS ON PHI-BASE
Winnenburg, R., Urban, M., Beacham, A., Baldwin, T.K., Holland, S., Lindeberg, M., Hansen, H., Rawlings, C., Hammond-Kosack, K.E., and Kohler, J.
(2008). PHI-base update: additions to the pathogen host interaction database. Nucleic Acids Res 36, D572-576.
PubMed:17942425
Baldwin, T.K., Winnenburg, R., Urban, M., Rawlings, C., Köhler, J. and Hammond-Kosack, K.E. 2006. The Pathogen-Host Interactions database (PHI-base) provides insights into generic and novel themes of pathogenicity. Mol Plant Microbe Interact. 19(12):1451-62
PubMed:17153929
Winnenburg, R., Baldwin, T.K., Urban, M., Rawlings, C., Köhler, J. and Hammond-Kosack, K.E. 2006. PHI-base: a new database for pathogen host interactions. Nucleic Acids Research. 34(Database issue):D459-D464
PubMed:16381911
PUBLICATIONS CITING PHI-BASE
Sexton AC, Howlett BJ. 2006. Parallels in fungal pathogenesis on plant and animal hosts. Eukaryot Cell. 5(12):1941-9
PubMed:17041185
O'Connell RJ, Panstruga R. 2006. Tete a tete inside a plant cell: establishing compatibility between plants and biotrophic fungi and oomycetes. New Phytol. 171(4):699-718
PubMed:16918543
van Baarlen P, van Belkum A, Summerbell RC, Crous PW, Thomma BP. 2007. Molecular mechanisms of pathogenicity: how do pathogenic microorganisms develop cross-kingdom host jumps? FEMS Microbiol Rev. 31(3):239-77
PubMed:17326816
Davies MN, Guan P, Blythe MJ, Salomon J, Toseland CP, Hattotuwagama C, Walshe V, Doytchinova IA, Flower DR. 2007.
Using databases and data mining in vaccinology. Expert Opinion on Drug Discovery 2(1):19-35
He et al (2008). The prediction of protein-protein interaction networks in rice blast
fungus. Bmc Genomics. 9, 519.
PubMed:18976500
Michielse, C.B., and Rep, M. (2009). Pathogen profile update: Fusarium oxysporum.
Molecular Plant Pathology 10, 311-324.
PubMed:19400835
PUBLICATIONS WHICH USED PHI-BASE FOR THE IDENTIFICATION OF PATHOGENICITY GENES
Jeon J, Park SY, Chi MH, Choi J, Park J, Rho HS, Kim S, Goh J, Yoo S, Choi J, Park JY, Yi M, Yang S, Kwon MJ, Han SS, Kim BR, Khang CH, Park B, Lim SE, Jung K, Kong S, Karunakaran M, Oh HS, Kim H, Kim S, Park J, Kang S, Choi WB, Kang S, Lee YH. 2007. Genome-wide functional analysis of pathogenicity genes in the rice blast fungus. Nat Genet. 39(4):561-5
PubMed:17353894
Scott DiGuistini, Steven G. Ralph, Young W. Lim, Robert Holt, Steven Jones, Jörg Bohlmann, Colette Breuil. 2007.
Generation and annotation of lodgepole pine and oleoresin-induced expressed sequences from the blue-stain fungus Ophiostoma clavigerum, a Mountain Pine Beetle-associated pathogen
FEMS Microbiology Letters. 267 (2):151-158
PubMed:17328114
Oeser et al (2009). Expressed sequence tags from the flower pathogen Claviceps purpurea. Molecular Plant Pathology. 10, 665-684.
PubMed:19694956
Takahara et al (2009). Flow cytometric purification of Colletotrichum higginsianum biotrophic hyphae from Arabidopsis leaves for stage-specific
transcriptome analysis. Plant J 59, 672-683
PubMed:19392696
Kleemann et al (2008). Identification of soluble secreted proteins from appressoria of Colletotrichum higginsianum by analysis of expressed sequence
tags. Microbiology 154, 1204-1217.
PubMed:18375813
Haegi et al (2008). Histological and molecular analysis of Rdg2a barley resistance to leaf stripe. Molecular Plant Pathology. 9, 463-478.
PubMed:18705861
Frezal et al (2008). Four years of DNA barcoding: current advances and prospects. Infect Genet Evol . 8, 727-736. Pubmed 18573351
PubMed:18573351
Bouzidi et al (2007). Expressed Sequence Tags from the oomycete Plasmopara halstedii, an obligate parasite of the sunflower. BMC Microbiol. 7,
110. Pubmed 18062809
PubMed:18062809
Yockteng et al (2007). Expressed sequences tags of the anther smut fungus, Microbotryum violaceum, identify mating and pathogenicity genes. Bmc
Genomics. 8, 272.
PubMed:17692127
Staal, J., and Dixelius, C. (2007). Tracing the ancient origins of plant innate immunity. Trends Plant Sci . 12, 334-342.
PubMed:17644465
Xiang et al (2007). PHIDIAS: a pathogen-host interaction data integration and analysis system. Genome Biol. 8, R150.
PubMed:17663773
van Baarlen et al (2007). Molecular mechanisms of pathogenicity: how do pathogenic microorganisms develop cross-kingdom host jumps? FEMS Microbiol
Rev. 31, 239-277.
PubMed:17326816
Hane et al (2007). Dothideomycete plant interactions illuminated by genome sequencing and EST analysis of the wheat pathogen Stagonospora nodorum.
Plant Cell. 19, 3347-3368. PubMed:18024570
Bolton, M.D., and Thomma, B.P.H.J. (2008). The complexity of nitrogen metabolism and nitrogen-regulated gene expression in plant pathogenic fungi.
Physiological and Molecular Plant Pathology. 72, 104-110. Pubmed: not available. DOI: 10.1016/j.pmpp.2008.07.001
ORAL PRESENTATIONS ON PHI-BASE
2009
Kim Hammond-Kosack, Martin Urban, Andrew Beacham, Neil Brown, Catherine Cavanet, Mansoor Saqi, Chris Rawlings and John Antoniw Using genomics to
reveal the enemy.s weapons. BA festival of Science, University of Surrey, Guildford, Sept 2009
2008
Kim Hammond-Kosack, Thomas Baldwin, Andrew Beacham, Martin Urban, Rainer Winnenburg, Jacob Koehler, Mansoor Saqi and Chris Rawlings. Novel ways to
explore sequenced fungal genomes. European Fungal Genetics Conference, Edinburgh, UK April 2008
Andrew Beacham, Catherine Cavanet, Jan Taubert, Martin Urban, John Antoniw, Chris Rawlings and Kim Hammond-Kosack. Analysis of the newly sequenced
Fusarium genomes using PHI-base and ONDEX. 10th International Fusarium and Fusarium genomics workshop. Alghero, Sardinia, Italy, Sept 2008
Kim Hammond-Kosack, Thomas Baldwin, Martin Urban, Rainer Winnenburg, Jacob Koehler, Mansoor Saqi and Chris Rawlings. The Plant Pathogen 'Omics world
- where is it taking us? EBI-EMBL joint workshop, Cambridge, UK Oct 2008
Kim Hammond-Kosack and John Antoniw. An inter-comparison of the pathogenicity, virulence and effector gene complement of the six Dothidiomycete
genomes. Dothidiomycetes genome jamboree, DOE, Joint Genome Institute, Walnut Creek, California, USA Nov 2008
Kim Hammond-Kosack, Martin Urban, Andrew Beacham, Neil Brown, Catherine Cavanet, Mansoor Saqi, Chris Rawlings and John Antoniw How can molecular
genetic information on plant pathogens benefit disease management. British Society for Plant Pathology, Presidential conference, Queen Mary College,
London, Dec 2008.
2007
Kim Hammond-Kosack, Martin Urban, Jason Rudd and Kostya Kanyuka Comparative genomics of pathogenesis and innate immunity. Joint Rothamsted
Research - Institute of Animal Health Workshop, held at The Compton Laboratory, England, May 2007
2006
Jacob Köhler, Rainer Winnenburg, Chris Rawlings, Thomas Baldwin, Martin Urban and Kim Hamond-Kosack
Pathogen-Host Interactions Database (Phi-Base)
COGEME interest group meeting, 7th - 8th November 2006, Chancellors Hotel and Conference Centre, Manchester, UK
Thomas K. Baldwin, Rainer Winnenburg, Martin Urban, Chris Rawlings, Jacob Köhler and Kim E. Hammond-Kosack
PHI-base: A database of experimentally verified pathogenicity, virulence and effector genes in fungal and Oomycete pathogens of animals and plants
8th European Conference on Fungal Genetics in the Symposium "Mechanisms of human pathogenesis" 8th & 11th April 2006, Vienna, Austria
Online:Conference
Presentation
2005
Thomas Baldwin, Rainer Winnenburg, Jacob Köhler, Martin Urban and Kim Hammond-Kosack
Bioinformatic and molecular genetic tools for identifying genes involved in pathogenicity
XVI Molecular Biology of Plant Pathogens meeting, Ambleside 19-21th September 2005
ESF-EMBO Symposium on Comparative Genomics of Eukaryotic Microorganisms, Sant Feliu de Guixols, Spain. November 2005
(Oral and poster presentations)
Thomas Baldwin, Rainer Winnenburg, Jacob Köhler, Martin Urban and Kim Hammond-Kosack
Bioinformatic and molecular genetic tools for identifying genes involved in the pathogenicity of Fusarium graminearum on wheat ears
COGEME users meeting - Manchester University November 2005
Online:(http://www.cogeme.man.ac.uk/)
FUTURE DEVELOPMENTS FOR PHI-BASE FROM 2010 ONWARDS
PHASE 1 - Development of a prototype self-entry data curation interface
PHASE 2 - Beta testing of the curation interface for several species
PHASE 3 - Development of tools to permit basic pathogen comparative analysis directly within PHI-base
We intend to show relationships between proteins in PHI-base using network representations where the nodes represent the proteins and the edges
reflect the degree of sequence similarity between the proteins. The nodes in these clusters of related proteins would be colour and shape coded
according to whether the pathogens were plant/animal and according to phenotype (see beneath for prototype image using the ONDEX (Kohler et al, (2006)
Bioinformatics, 22:1383-90) data integration and visualisation software). The curation tool would automatically assign a new sequence to a cluster (if
related) thereby allowing the annotator to view its biological context. Additionally the user would be able to select groups of related proteins and
retrieve the corresponding sequences and perform multiple sequence alignments. This would allow the patterns of sequence conservation to be examined
in the context of the type of pathogen and the associated phenotype.
Figure: Part of an Ondex screenshot showing a cluster of related
sequences from PHI-base (triangles) coloured according to outcome (phenotype) and
showing relationships to associated KEGG pathways (stars). The PHI-base
proteins were clustered using MCL clustering. Some edges in the graph are not
shown for increased clarity. We hope to develop a link from the proposed curation
tool to an Ondex web service to allow a new putative sequence involved in a
pathogen-host interaction to be assigned to a cluster (if appropriate) and the
Ondex graph returned. Inspection of the graph would then allow the curator to
view the context of the new sequence in relation to existing PHI-base sequences
and pathway information.
The tightly connected cluster are polygalacturinases (part of glycosyl hydrolase
28 family)
Mappings to KEGG - include Pentose and Glucuronate interconversion, Starch and
sucrose metabolism, Aminosugars metabolism. Some edges are not shown for
clarity.
RELATED WORK
General Plant Pathology
Agrios, G. N. 1997. Plant Pathology. Academic Press, Inc., London.
de Bary, H. A. 1879. The Phenomenon of Symbiosis. Strasbourg.
Shaner, G., Stromberg, E. L., Lacy, G. H., Barker, K. R., and Pirone, T. P. 1992. Nomenclature and concepts of pathogenicity and virulence. Annu. Rev. Phytopathol. 30:47-66.
Sequenced Fungal and Oomycete Genomes
Tyler et al., 2006. Phytophthora genome sequences uncover evolutionary origins and mechanisms of
pathogenesis. Science 313(5791):1261-6.
PubMed:16946064
Kamper et al., 2006. Insights from the genome of the biotrophic fungal plant pathogen Ustilago maydis. Nature 444(7115):97-101.
PubMed:17080091
Dean et al., 2005. The genome sequence of the rice blast fungus Magnaporthe
grisea. Nature 434:980-6.
PubMed:15846337
Dietrich et al., 2004. The Ashbya gossypii genome as a tool for mapping the
ancient Saccharomyces cerevisiae genome. Science 304:304-7.
PubMed:15001715
Galagan et al., 2003. The genome sequence of the filamentous fungus
Neurospora crassa. Nature 422:859-68.
PubMed:12712197
Goffeau et al., 1996. Life with 6000 Genes. Science 274:546-566.
PubMed:8849441
Jones et al., 2004. The diploid genome sequence of Candida albicans.
Proc. Natl. Acad. Sci. U. S. A. 101:7329-7334.
PubMed:15123810
Génolevures 2005. Genomic exploration of the hemiascomycete yeasts.
Online:http://cbi.labri.fr/Genolevures/index.php
Joint Genome Institute 2005. Eukaryotic Genomes.
Online:http://genome.jgi-psf.org/euk_cur1.html
Broad Institute 2005. Fungal Genome Initiative (FGI).
Online:http://www.broad.mit.edu/annotation/fungi/fgi/
Sanger Institute, 2005. Fungal genomes.
Online:http://www.sanger.ac.uk/Projects/Fungi/
Reviews on Pathogenicity
Ellis, J.G., Rafiqi, M., Gan, P., Chakrabarti, A., and Dodds, P.N. (2009). Recent progress in discovery and functional analysis of effector proteins
of fungal and oomycete plant pathogens. Curr. Opinion in Plant Biol. 12, 399-405.
PubMed:19540152
Hogenhout, S.A., Van der Hoorn, R.A.L., Terauchi, R., and Kamoun, S. (2009). Emerging Concepts in Effector Biology of Plant-Associated Organisms.
Mol. Plant-Microbe Interactions 22, 115-122.
PubMed:19132864
Stergiopoulos, I., and de Wit, P.J.G.M. (2009). Fungal Effector Proteins. Annual Rev. of Phytopathol. 47, 233-263.
PMID: 19400631
PubMed:19400631
Sexton AC, Howlett BJ., 2006. Parallels in fungal pathogenesis on plant and animal hosts. Eukaryot Cell. 5(12):1941-9
PubMed:17041185
Feldbrugge, M., Kamper, J., Steinberg, G., and Kahmann, R., 2004. Regulation of mating and pathogenic development in Ustilago maydis. Curr
Opin Microbiol. 7:666-72.
PubMed:15556041
Talbot, NJ, 2003. On the trail of a cereal killer: Exploring the biology of Magnaporthe grisea. Annu Rev Microbiol. 57:177-202
PubMed:14527276
Idnurm, A., and Howlett, B. J., 2001. Pathogenicity genes of phytopathogenic fungi. Mol. Plant Pathol. 2:241-255.
Laugé, R., and De Wit, P. J., 1998. Fungal avirulence genes: structure and possible functions. Fungal Genet Biol. 24:285-97.
PubMed:9756710
Knogge, W., 1996. Fungal infections of plants. Plant Cell 8:1711-1722.
PubMed:12239359
Ontologies
Torto-Alalibo, T., Collmer, C. W. and Gwinn-Giglio, M., 2009. The Plant-Associated Microbe Gene Ontology (PAMGO) Consortium:
community development of new Gene Ontology terms describing biological processes involved in microbe-host interactions.
BMC Microbiology 9 (Suppl I): SI. Review.
PubMed:19278549
Gene-Ontology-Consortium., 2006. The Gene Ontology (GO) project in 2006. Nucl. Acids Res. 34:D322-D326.
PubMed:16381878
PAMGO - Plant-Associated Microbe Gene Ontologies (2005) A collaborative effort has establishment of 585 terms in the GO Biological Process ontology. Four hundred and seventy two (472) of these terms, have recently incorporated into the Biological Process ontology describe more specific processes involved in the interaction between microbes and their hosts.
Featured below are some high order terms developed by PAMGO, which can be accessed from the Gene Ontology browser (AMIGO: http://www.godatabase.org).
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