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).
PHI-base species list
(1) Several specific improvements to PHI-base are currently supported by a BBSRC BBR award called PhytoPath: an Integrated resource for comparative phytopathogen genomics (BB/1000488/1).
During phase 1 of this project, we have linked in a gene centric manner the European Bioinformatics Institute's (EBI's) new Ensembl Genomes Browser interface for priority crop and model phytopathogenic species of fungi and oomycetes. Further information on this joint Phytopath project is available at http://phytopathdb.org
(2) PHI-base has been given National Capability status in 2012 by BBSRC for its part in helping the UK deliver world-leading environmental research.
(3) In 2013 BBSRC awarded follow-up funds for the PhytoPath
project (Grant title: PhytoPath, an infrastructure for
hundreds of plant pathogen genomes, BB/K020056/1). This
award will allow to include additional pathosystems, curate
primary host targets of effectors, data on known
protein-protein interactions and their cellular locations during the period 2014 to 2016.
An important part during grant submission played the support
of the scientific community. In particular we would like to
thank the following researchers for writing letters of
Ken Hayes (University of Exeter), Pietro Spanu (Imperial
College) Mike Csukai (Syngenta, Jeallot's Hill), Matthew
Fisher (Imperial College) James Fountaine (Scottish
Agricultural College), Anna Avrova (The James Hutton
Institute), Rumiana Ray (University of Nottingham), Sophia
Tsoka (King's College, London), Steve Whisson (The James
Hutton Institute), Gero Steinberg (University of Exeter),
Hans Cools (Rothamsted Research), Jason Rudd (Rothamsted
Research), Leighton Pritchard (The James Hutton Institute)
and Laurence Bindschedler (Royal Holloway, London).
Regine Kahmann (Max Planck Inst. Terrestial Microbiology, DE), Rosie Bradshaw (Massey University, NZ), Antonio de Pietro (University of Cordoba, SP), Alexandre Amaral (EMBRAPA, BR based at RRes), Jan van Kan (Wageningen University, NL), John Manners (CSIRO Plant Industry, AUS), Barbara Howlett (University of Melbourne, AUS), Rohan Lowe (University of Melbourne, AUS), Martijn Rep (University of Amsterdam, NL), Pierre de Wit (University of Wageningen, NL), Eric Kemen (Max Planck Inst. Plant Breeding Res, DE), Daren Brown (USDA-ARS - Peoria, USA) and Frances Trail (Michigan State University, USA).
PUBLICATIONS ON PHI-BASE
Urban M, Pant R, Raghunath A, Irvine AG, Pedro H and Hammond-Kosack K (2015). The Pathogen-Host Interactions database: additons and future developments. Nucleic Acids Res 43 (Database Issue): D645-655. doi: 10.1093/nar/gku1165
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.
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
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
PUBLICATIONS CITING PHI-base - Total - 122 publications
Topic areas: original research articles describing single gene function studies and large scale forward genetics screens; characterisation of EST collections; full and partial genome annotation; protein-protein interaction mapping; inter-comparison of specific gene mutants within and between species; bioinformatics analysis; other databases on interactions and review articles.
Agrawal, Y. et al, (2015). Genome sequence, comparative analysis, and evolutionary insights into chitinases of entomopathogenic fungus Hirsutella thompsonii. Genome biology and evolution doi: 10.1093/gbe/evv037.
Castelhano Santos, N. et al, (2015). Pathogenicity phenomena in three model systems: from network mining to emerging system-level properties. Brief. Bioinform. doi: 10.1093/bib/bbt071
Comeau, A. M. et al, (2015). Functional annotation of the Ophiostoma novo-ulmi genome: Insights into the phytopathogenicity of the fungal agent of Dutch Elm Disease. Genome Biology and Evolution doi: 10.1093/gbe/evu281.
Dang, H. X. et al, (2015). The Alternaria genomes database: a comprehensive resource for a fungal genus comprised of saprophytes, plant pathogens, and allergenic species. BMC Genomics doi: 10.1186/s12864-015-1430-7.
Durmus, S. et al, (2015). A Review on Computational Systems Biology of Pathogen-Host Interactions. Frontiers in microbiology doi: 10.3389/fmicb.2015.00235
Jaramillo, V. D. et al, (2015). Identification of horizontally transferred genes in the genus Colletotrichum reveals a steady tempo of bacterial to fungal gene transfer. BMC Genomics doi: 10.1186/1471-2164-16-2
Małagocka, J. et al, (2015). Transcriptome of an entomophthoralean fungus (Pandora formicae) shows molecular machinery adjusted for successful host exploitation and transmission. Journal of Invertebrate Pathology doi: 10.1016/j.jip.2015.05.001.
Schulze, S et al (2015). Computation prediction of molecular pathogen-host interactions based on dual transcriptome data. Frontiers in Microbiology doi:10.3389/fmicb.2015.00065.
Subramanian, N. et al, (2015). Network representations of immune system complexity. Wiley interdisciplinary reviews. Systems biology and medicine doi: 10.1002/wsbm.1288.
Troncoso, L. L. et al, (2015). Characterization and comparative analysis of a simian foamy virus complete genome isolated from Brazilian capuchin monkeys. Virus research doi: 10.1016/j.virusres.2015.05.022.
Urban, M. et al, (2015). Whole-genome analysis of Fusarium graminearum insertional mutants identifies virulence associated genes and unmasks untagged chromosomal deletions. BMC genomics doi: 10.1186/s12864-015-1412-9.
Bleves S, Dunger I, Walter MC et al (2014). HoPaCI-DB: host-Pseudomonas and Coxiella interaction database. Nucleic Acids Res. doi: 10.1093/nar/gkt925
de Castro, P. A. et al, (2014). ChIP-seq reveals a role for CrzA in the Aspergillus fumigatus high-osmolarity glycerol response (HOG) signalling pathway. Molecular Microbiology doi: 10.1111/mmi.12785.
Dyawanapelly, S. et al, (2014). RNA interference-based therapeutics: molecular platforms for infectious diseases. Journal of biomedical nanotechnology doi: 10.1166/jbn.2014.1929
Gao, S. et al, (2014). Genome sequence and virulence variation-related transcriptome profiles of Curvularia lunata, an important maize pathogenic fungus. BMC Genomics doi: 10.1186/1471-2164-15-627
Ghosh, S. et al, (2014). Identification and functional analysis of AG1-IA specific genes of Rhizoctonia solani. Current genetics doi: 10.1007/s00294-014-0438-x.
Guo L, Han L, Yang L et al. (2014). Genome and transcriptome analysis of the fungal pathogen Fusarium oxysporum f. sp. cubense causing banana vascular wilt disease. PLoS One. doi: 10.1371/journal.pone.0095543
Hane, J. K. et al, (2014). Genome sequencing and comparative genomics of the broad host-range pathogen Rhizoctonia solani AG8. PLoS genetics doi: 10.1371/journal.pgen.1004281
Hayden, K. J. et al, (2014). Dual RNA-seq of the plant pathogen Phytophthora ramorum and its tanoak host. Tree Genet Genomes doi: 10.1007/s11295-014-0698-0
Hu, X. et al, (2014). Trajectory and genomic determinants of fungal-pathogen speciation and host adaptation. Proc. Natl. Acad. Sci. U. S. A. doi: 10.1073/pnas.1412662111
Ke, X. et al, (2014). Transcriptome profiling to identify genes involved in pathogenicity of Valsa mali on apple tree. Fungal Genet. Biol. doi: 10.1016/j.fgb.2014.04.004
Kersey PJ, Allen JE, Christensen M et al (2014). Ensembl Genomes 2013: scaling up access to genome-wide data. Nucleic Acids Res.doi: 10.1093/nar/gkt979
Pattemore, J. A. et al, (2014). The genome sequence of the biocontrol fungus Metarhizium anisopliae and comparative genomics of Metarhizium species. BMC Genomics doi: 10.1186/1471-2164-15-660
Rech, G. E. et al, (2014). Natural Selection on Coding and Noncoding DNA Sequences Is Associated with Virulence Genes in a Plant Pathogenic Fungus. Genome Biology and Evolution doi: 10.1093/gbe/evu192
Soliai MM, Meyer SE, Udall JA et al. (2014). De novo genome assembly of the fungal plant pathogen Pyrenophora semeniperda. PLoS One. doi: 10.1371/journal.pone.0087045
Srivastava SK, Huang X, Brar HK et al. (2014). The genome sequence of the fungal pathogen Fusarium virguliforme that causes sudden death syndrome in soybean. PLoS One doi: 10.1371/journal.pone.0081832
Staats, C. C. et al, (2014). Comparative genome analysis of entomopathogenic fungi reveals a complex set of secreted proteins. BMC Genomics doi: 10.1186/1471-2164-15-822
Talhinhas, P. et al, (2014). Overview of the functional virulent genome of the coffee leaf rust pathogen Hemileia vastatrix with an emphasis on early stages of infection. Frontiers in plant science doi: 10.3389/fpls.2014.00088
Yu, M. et al, (2014). De novo sequencing and transcriptome analysis of Ustilaginoidea virens by using Illumina paired-end sequencing and development of simple sequence repeat markers. Gene doi: 10.1016/j.gene.2014.06.008
Zhang, Y. et al (2014), Specific adaptation of Ustilaginoidea virens in occupying host florets revealed by comparative and functional genomics. Nature communications, doi: 10.1038/ncomms4849
Andersson K, Meerupati T, Levander F et al. (2013). Proteome of the Nematode-Trapping Cells of the Fungus Monacrosporium haptotylum. Appl. Environ. Microbiol. doi: 10.1128/AEM.01390-13
Cai Z, Li G, Lin C et al. (2013). Identifying pathogenicity genes in the rubber tree anthracnose fungus Colletotrichum gloeosporioides through random insertional mutagenesis. Microbiol Res. doi: 10.1016/j.micres.2013.01.005
Chang, D. et al (2013), A multi-omic analysis of an Enterococcus faecium mutant reveals specific genetic mutations and dramatic changes in mRNA and protein expression. BMC Microbiol. doi: 10.1186/1471-2180-13-304
Chen, C. et al (2013), Genome comparison of two Magnaporthe oryzae field isolates reveals genome variations and potential virulence effectors. BMC Genomics, doi: 10.1186/1471-2164-14-887 4.
Cools HJ, Hammond-Kosack KE. (2013). Exploitation of genomics in fungicide research: current status and future perspectives. Mol Plant Pathol. doi: 10.1111/mpp.12001
Danchin EG, Arguel MJ, Campan-Fournier A et al (2013). Identification of novel target genes for safer and more specific control of root-knot nematodes from a pan-genome mining. PLoS Pathog. doi: 10.1371/journal.ppat.1003745
De la Iglesia D, Garcia-Remesal M, de la Calle G et al. (2013). The impact of computer science in molecular medicine: enabling high-throughput research. Curr Top Med Chemi PMID: 23548020
Khoshraftar S, Hung S, Khan S et al. (2013). Sequencing and annotation of the Ophiostoma ulmi genome. BMC Genomics. doi: 10.1186/1471-2164-14-162
Kshirsagar M, Carbonell J, Klein-Seetharaman J. (2013). Multitask learning for host-pathogen protein interactions. Bioinformatics. doi: 10.1093/bioinformatics/btt245
Lefebvre F, Joly DL, Labbe C et al. (2013). The transition from a phytopathogenic smut ancestor to an anamorphic biocontrol agent deciphered by comparative whole-genome analysis. Plant Cell. doi: 10.1105/tpc.113.113969
Liu X, Zhang X, Tang WH et al. (2013). eFG: an electronic resource for Fusarium graminearum. Database (Oxford). doi: 10.1093/database/bat042
Luo, S et al (2013). The tetraspanin gene MaPls1 contributes to virulence by affecting germination, appressorial function and enzymes for cuticle degradation in the entomopathogenic fungus, Metarhizium acridum.Environmental Microbiology doi: 10.1111/1462-2920.12166
Lysenko et al (2013) Network-based data integration for selecting candidate virulence associated proteins in the cereal infecting fungus Fusarium graminearum. PLoS ONE. doi: 10.1371/journal.pone.0067926
Mukherjee S, Sambarey A, Prashanthi K, Chandra N. (2013). Current trends in modeling host-pathogen interactions. Data Mining and Knowledge Discovery. doi: 10.1002/widm.1085
Sperschneider, J. et al (2013), A comparative hidden Markov model analysis pipeline identifies proteins characteristic of cereal-infecting fungi. BMC Genomics doi: 10.1186/1471-2164-14-807
Tekir, S. D.K. O. Ulgen (2013), Systems biology of pathogen-host interaction: Networks of protein-protein interaction within pathogens and pathogen-human interactions in the post-genomic era. Biotechnology journal 8, 85
Thakur K, Chawla V, Bhatti S et al. (2013). De novo transcriptome sequencing and analysis for Venturia inaequalis, the devastating apple scab pathogen. PLoS One. doi: 10.1371/journal.pone.0053937
Urban, M.K. Hammond-Kosack (2013), in Fusarium genomics and molecular and cellular biology, D. Brown, R. H. Proctor, Eds. (Norwich: Horizon Scientific Press 2013), pp. 43-79.
Vogel KJ, Moran NA. (2013). Functional and evolutionary analysis of the genome of an obligate fungal symbiont. Genome Biol Evol. doi: 10.1093/gbe/evt054
Xiao-chen B, Jing Y, Sheng-qi W. (2013). Systems biology approach for virus-host interaction and host- directed antiviral strategy. International Journal of AUTOMATION AND COMPUTING. doi: 10.3867/j.issn.1000-3002.2013.02.001
Zhou H, Jin J, Wong L. (2013). Progress in computational studies of host-pathogen interactions. J Bioinform Comput Biol. doi: 10.1142/S0219720012300018
Arnold R, Boonen K, Sun MG, Kim PM. (2012). Computational analysis of interactomes: current and future perspectives for bioinformatics approaches to model the host-pathogen interaction space. Methods. doi: 10.1016/j.ymeth.2012.06.011
Bakkerena G, Songa X, Panwar V et al. (2012). Functional genomic approaches in cereal rusts. Canadian Journal of Plant Pathology. doi: 10.1080/07060661.2012.664567
Bennett, L. et al, Detection of multi-clustered genes and community structure for the plant pathogenic fungus Fusarium graminearum, vol. LNCS 7605 (2012), vol. LNCS 7605 pp. 69-86.
Fernandez D, Tisserant E, Talhinhas P, et al. (2012) 454-pyrosequencing of Coffea arabica leaves infected by the rust fungus Hemileia vastatrix reveals in planta-expressed pathogen-secreted proteins and plant functions in a late compatible plant-rust interaction. Mol Plant Pathol doi: 10.1111/j.1364-3703.2011.00723.x
Garcia-Garcia J, Schleker S, Klein-Seetharaman J, Oliva B. (2012). BIPS: BIANA Interolog Prediction Server. A tool for protein-protein interaction inference. Nucleic Acids Res. doi: 10.1093/nar/gks553
Gonzalez-Fernandez R, Jorrin-Novo JV (2012) Contribution of proteomics to the study of plant pathogenic fungi. J Proteome Res doi: 10.1021/pr200873p
He M, Hu J, Xia Y. (2012). Large scale expressed sequence tag (EST) analysis of Metarhizium acridum infecting Locusta migratoria reveals multiple strategies for fungal adaptation to the host cuticle. Curr Genet. doi: 10.1007/s00294-012-0382-6
Hu J, Chen C, Peever T et al. (2012). Genomic characterization of the conditionally dispensable chromosome in Alternaria arborescens provides evidence for horizontal gene transfer. BMC Genomics. doi: 10.1186/1471-2164-13-171
Hulsegge B, Smits MA, te Pas MF, Woelders H. (2012). Contributions to an animal trait ontology. J Anim Sci. doi: 10.2527/jas.2011-4251
Islam MS, Haque MS, Islam MM et al (2012). Tools to kill: genome of one of the most destructive plant pathogenic fungi Macrophomina phaseolina. BMC Genomics. doi: 10.1186/1471-2164-13-493
Kour A, Greer K, Valent B et al. (2012). MGOS: development of a community annotation database for Magnaporthe oryzae. Mol Plant Microbe Interact. doi: 10.1094/MPMI-07-11-0183
Lu T, Yao B, Zhang C. (2012). DFVF: database of fungal virulence factors. Database (Oxford). doi: 10.1093/database/bas032
Marcet-Houben M, Ballester AR, de la Fuente B et al. (2012). Genome sequence of the necrotrophic fungus Penicillium digitatum, the main postharvest pathogen of citrus. BMC Genomics. doi: 10.1186/1471-2164-13-646
Schleker S, Garcia-Garcia J, Klein-Seetharaman J, Oliva B. (2012). Prediction and comparison of Salmonella-human and Salmonella-Arabidopsis interactomes. Chem Biodivers. doi: 10.1002/cbdv.201100392
Talas F, Würschum T, Reif JC, Parzies HK, Miedaner T. (2012). Association of single nucleotide polymorphic sites in candidate genes with aggressiveness and deoxynivalenol production in Fusarium graminearum causing wheat head blight. BMC Genet. doi: 10.1186/1471-2156-13-14
Tanh T, Joshi S, Warren S, et al. (2012) Literature mining of host-pathogen interactions: comparing feature-based supervised learning and language-based approaches. Bioinformatics. doi: 10.1093/bioinformatics/bts04
Tekir SD, Ulgen KO. (2012). Systems biology of pathogen-host interaction: networks of protein-protein interaction within pathogens and pathogen-human interactions in the post-genomic era. Biotechnol J. doi: 10.1002/biot.201200110
Thieu T, Joshi S, Warren S, Korkin D. (2012). Literature mining of host-pathogen interactions: comparing feature-based supervised learning and language-based approaches. Bioinformatics. doi: 10.1093/bioinformatics/bts042
Vargas WA, Martin JM, Rech GE et al. (2012). Plant defense mechanisms are activated during biotrophic and necrotrophic development of Colletotricum graminicola in maize. Plant Physiol. doi: 10.1104/pp.111.190397
Xiao-Gang Z, Chun-Xin Y, Yu-Mei D. (2012). Progress on nitrogen regulation gene expression of plant pathogenic fungi under nitrogen starvation. HEREDITAS. doi: 10.3724/SP.J.1005.2012.00848
Zheng LL, Li YX, Ding J et al. (2012). A comparison of computational methods for identifying virulence factors. PLoS One. doi: 10.1371/journal.pone.0042517
Zhou XG, Yao CX, Ding YM et al. (2012). Progress on nitrogen regulation gene expression of plant pathogenic fungi under nitrogen starvation. Yi Chuan. PMID: 22805210
Zhu S, Cao YZ, Jiang C et al. (2012). Sequencing the genome of Marssonina brunnea reveals fungus-poplar co-evolution. BMC Genomics. doi: 10.1186/1471-2164-13-382
Antoniw J, Beacham AM, Baldwin TK, et al. (2011) OmniMapFree: A unified tool to visualise and explore sequenced genomes. BMC Bioinformatics doi: 10.1186/1471-2105-12-447
Doehlemann et al (2011). Two linked genes encoding a secreted effector and a membrane protein are essential for Ustilago maydis-induced tumour formation. Molecular Microbiology. doi: 10.1111/j.1365-2958.2011.07728.x
Driscoll T, Gabbard J, Mao C, et al.(2011) Integration and visualization of host-pathogen data related to infectious diseases. Bioinformatics doi:10.1093/bioinformatics/btr391
Gao et al (2011). Genome sequencing and comparative transcriptomics of the model entomopathogenic fungi Metarhizium anisopliae and M. acridum. Plos Genetics. doi: 10.1371/journal.pgen.1001264
Hamilton JP, Neeno-Eckwall EC, Adhikari BN et al (2011). The Comprehensive Phytopathogen Genomics Resource: a web-based resource for data-mining plant pathogen genomes. Database. doi: 10.1093/database/bar053
Kozhenkov et al (2011). BiologicalNetworks--tools enabling the integration of multi-scale data for the host-pathogen studies. BMC Syst Biol. doi: 10.1186/1752-0509-5-7
Lucas (2011). Advances in plant disease and pest management. Journal of Agricultural Science. doi: 10.1017/s0021859610000997
Yang J, Wang, L, Ji X, et al.(2011) Genomic and proteomic analyses of the fungus Arthrobotrys oligospora provide insights into nematode-trap formation. PLoS Pathogens doi: 10.1371/journal.ppat.1002179
van de Wouw and Howlett (2011). Fungal pathogenicity genes in the age of 'omics'. Mol Plant Pathol. doi: 10.1111/j.1364-3703.2010.00680.x
Baldwin et al (2010). A partial chromosomal deletion caused by random plasmid integration resulted in a reduced virulence phenotype in Fusarium graminearum. Molecular Plant-Microbe Interactions. doi: 10.1094/mpmi-23-8-1083
Flower et al (2010). Computer aided selection of candidate vaccine antigens. Immunome research. doi: 10.1186/1745-7580-6-S2-S1
Javier Fernandez-Acero et al (2010). 2-DE proteomic approach to the Botrytis cinerea secretome induced with different carbon sources and plant-based elicitors. Proteomics. doi: 10.1002/pmic.200900408
Kim et al (2010). Combining ChIP-chip and expression profiling to model the MoCRZ1 mediated circuit for Ca(2+)/calcineurin signaling in the rice blast fungus. Plos Pathogens. doi: 10.1371/journal.ppat.1000909
Kumar and Nanduri (2010). HPIDB - a unified resource for host-pathogen interactions. BMC Bioinformatics. doi: 10.1186/1471-2105-11-s6-s16
Lowe et al (2010). A combined (1)H nuclear magnetic resonance and electrospray ionization mass spectrometry analysis to understand the basal metabolism of plant-pathogenic Fusarium spp. Molecular Plant-Microbe Interactions. doi: 10.1094/mpmi-04-10-0092
Sanchez-Rodriguez et al (2010). The Potential for pathogenicity was present in the ancestor of the Ascomycete subphylum Pezizomycotina. BMC Evolutionary Biology. doi: 10.1186/1471-2148-10-318
Sintchenko (2010). Informatics for infectious disease research and control. in: Infectious Disease Informatics. doi: 10.1007/978-1-4419-1327-2_1
Huser et al (2009). Discovery of pathogenicity genes in the crucifer anthracnose fungus Colletotrichum higginsianum using random insertional mutagenesis. Molecular Plant-Microbe Interactions. doi: 10.1094/mpmi-22-2-0143
Korves and Colosimo (2009). Controlled vocabularies for microbial virulence factors. Trends in Microbiology. doi: 10.1016/j.tim.2009.04.002
Li et al (2009). Towards a comprehensive HBV-human interaction map. 2009 International Joint Conference on Bioinformatics
Oeser et al (2009). Expressed sequence tags from the flower pathogen Claviceps purpurea. Mol Plant Pathol. doi: 10.1111/j.1364-3703.2009.00560.x
Soderlund (2009). Computational techniques for elucidating plant-pathogen interactions from large-scale experiments on fungi and oomycetes. Briefings in Bioinformatics. doi: 10.1093/bib/bbp053
Sun, C. et al (2009), Protein Subcellular Localization Prediction for Fusarium graminearum. L. Chen, X. S. Zhang, L. Y. Wu, Y. Wang, Eds., Optimization and Systems Biology, vol. 11, pp. 254-260.
Systems Biology and Intelligent Computing Proceedings. doi: 10.1109/ijcbs.2009.49
Takahara et al (2009). Flow cytometric purification of Colletotrichum higginsianum biotrophic hyphae from Arabidopsis leaves for stage-specific transcriptome analysis. Plant Journal. doi: 10.1111/j.1365-313X.2009.03896.x
Zhao et al (2009). FPPI: Fusarium graminearum protein-protein interaction database. Journal of Proteome Research. doi: 10.1021/pr900415b
Bolton and Thomma (2008). The complexity of nitrogen metabolism and nitrogen-regulated gene expression in plant pathogenic fungi. Physiological and Molecular Plant Pathology. doi: 10.1016/j.pmpp.2008.07.001
Frezal and Leblois (2008). Four years of DNA barcoding: Current advances and prospects. Infection Genetics and Evolution. doi: 10.1016/j.meegid.2008.05.005
Haegi et al (2008). Histological and molecular analysis of Rdg2a barley resistance to leaf stripe. Mol Plant Pathol. doi: 10.1111/j.1364-3703.2008.00479.x
He et al (2008). The prediction of protein-protein interaction networks in rice blast fungus. Bmc Genomics. doi: 10.1186/1471-2164-9-519
Jeon et al (2008). Functional genomics in the rice blast fungus to unravel the fungal pathogenicity. Journal of Zhejiang University-Science B. doi: 10.1631/jzus.B0860014
Kleemann et al (2008). Identification of soluble secreted proteins from appressoria of Colletotrichum higginsianum by analysis of expressed sequence tags. Microbiology-Sgm. doi: 10.1099/mic.0.2007/014944-0
Soanes et al (2008). Comparative genome analysis of filamentous fungi reveals gene family expansions associated with fungal pathogenesis. Plos One. doi: 10.1371/journal.pone.0002300
Bouzidi et al (2007). Expressed sequence tags from the oomycete Plasmopara halstedii an obligate parasite of the sunflower. BMC Microbiol. doi: 10.1186/1471-2180-7-110
Davies et al (2007). Using databases and data mining in vaccinology. Expert opinion on Drug Discovery. doi: 10.1517/174604220.127.116.11
DiGuistini et al (2007). Generation and annotation of lodgepole pine and oleoresin-induced expressed sequences from the blue-stain fungus Ophiostoma clavigeruma mountain pine beetle-associated pathogen. Fems Microbiology Letters. doi: 10.1111/j.1574-6968.2006.00565.x
Dickman (2007). Subversion or coersion? Pathogenic deteminants in fungal phytopathogens. Fungal Biology Reviews. doi: 10.1016/j.fbr.2007.06.003
Hane et al (2007). Dothideomycete-plant interactions illuminated by genome sequencing and EST analysis of the wheat pathogen Stagonospora nodorum. Plant Cell. doi: 10.1105/tpc.107.052829
Jeon et al (2007). Genome-wide functional analysis of pathogenicity genes in the rice blast fungus. Nature Genetics. doi: 10.1038/ng2002
Staal and Dixelius (2007). Tracing the ancient origins of plant innate immunity. Trends in Plant Science. doi: 10.1016/j.tplants.2007.06.014
Williamson et al (2007). Botrytis cinerea: the cause of grey mould disease. Mol Plant Pathol. doi: 10.1111/j.1364-3703.2007.00417.x
Xiang et al (2007). PHIDIAS: a pathogen-host interaction data integration and analysis system. Genome Biol. doi: 10.1186/gb-2007-8-7-r150
Yockteng et al (2007). Expressed sequences tags of the anther smut fungus Microbotryum violaceum identify mating and pathogenicity genes. BMC Genomics. doi: 10.1186/1471-2164-8-272
van Baarlen et al (2007). Molecular mechanisms of pathogenicity: how do pathogenic microorganisms develop cross-kingdom host jumps? FEMS Microbiology Reviews. doi: 10.1111/j.1574-6976.2007.00065.x
van der Does and Rep (2007). Virulence genes and the evolution of host specificity in plant-pathogenic fungi. Mol Plant Microbe Interact. doi: 10.1094/MPMI-20-10-1175
Kohler et al (2006). Graph-based analysis and visualization of experimental results with ONDEX. Bioinformatics. doi: 10.1093/bioinformatics/bt/081
Kohler et al (2006). Ontology based text indexing and querying for the semantic web. Knowledge-Based Systems. doi: 10.1016/j.knosys.2006.04.015
O'Connell and Panstruga (2006). Tete a tete inside a plant cell: establishing compatibility between plants and biotrophic fungi and oomycetes. New Phytologist. doi: 10.1111/j.1469-8137.2006.01829.x
Sexton and Howlett (2006). Parallels in fungal pathogenesis on plant and animal hosts. Eukaryotic cell. doi: 10.1128/ec.00277-06
PRESENTATIONS AND POSTERS ON PHI-BASE
Urban M, Antoniw J, Martins N, Lysenko A, Grzebyta J,
Janowska-Sedja E, Saqi M, Hammond-Kosack K. Using the phenotypic information in the PHI-base
database to explore pathogen genomes. 27th Fungal Genetics Conference, Asilomar, March
Same poster presented at The Agriscience Symposium
'Biological and Chemical Approaches Towards Combating
Resistance in Agriculture, held at Imperial college, London
on 26th Sep 2013. Sponsored by the Royal Society of
Chemistry, Biological & Medicinal Chemistry Sector and
Posters on PHI-base and Phytopath resources and 2 additional demonstration/user engagement sessions. 11th European Conference on fungal genetics, 30 March - 2 April 2012, Marburg, Germany.
K. Hammond-Kosack, J. Grzebyta, M. Urban, M. Saqi. The Phytopath/PHI-base resource. 18th UK PhD conference Molecular Biology of Plant Pathogens (MBPP), Reading University, 16th - 17th April 2012.
J. Lucas, J. Grzebyta, M. Urban, M. Saqi and K. E. Hammond-Kosack. The pathogen-host interactions database: new developments. The Center for Biomedical Informatics, State University of Campinas, Brazil, 16th Dec 2011
J. Grzebyta, A. Splendiani, M. Urban, K. E. Hammond-Kosack, C. J. Rawlings and M. Saqi. Towards a computational representation of host-pathogen interaction networks. Second SICSA Workshop on Biological Networks, 21st Oct 2011
M. Saqi, Andrea Splendiani, J. Grzebyta, M. Urban, M. Defoin-Platel, E. Janowska-Sejda, C. Rawlings and K. E. Hammond-Kosack. Gene discovery for improved resistance to pests and pathogens. Monogram workshop Session V, Sutton Bonnington, Nottingham UK, 11-13th April 2011
E. Janowska-Sejda , M. Defoin-Platel, K. E. Hammond-Kosack , M. Urban , S. Tsoka and M. Saqi. A systems biology approach to explore host-pathogen interactions through the use and further development of PHI-base database and newly sequenced pathogen genomes. Molecular Biology of Plant Pathogens Conference , Exeter, UK, 17th - 19th September 2010.
J. Grzebyta, A. Splendiani, M. Urban, K. E. Hammond-Kosack, C. J. Rawlings and M. Saqi. PHI-base 4: A new approach for capturing host-pathogen interactions. Molecular Biology of Plant Pathogens Conference , Exeter, UK, 17th - 19th September 2010.
K. Hammond-Kosack, M. Urban, J. Rudd, H. Cools and J. Antoniw. The plant pathogen 'omics world where is it taking us in developing novel options to control fungal diseases ? 9th International Mycology Congress (IMC9), Edinburgh, UK, 1-6 August 2010
A. Beacham, J. Antoniw, A. Freeman, M. Urban, K. Hammond-Kosack. The identification of a virulence factor enriched micro-region in the Fusarium graminearum genome. 9th International Mycology Congress (IMC9), Edinburgh, UK, 1-6 August 2010
K. Hammond-Kosack, M. Urban, A. Beacham, N. Brown, C. Cavanet, M. Saqi, C. Rawlings and J. Antoniw. Using genomics to
reveal the enemy's weapons. BA festival of Science, University of Surrey, Guildford, Sept 2009
K. Hammond-Kosack, T. Baldwin, A. Beacham, M. Urban, R. Winnenburg, J. Koehler, M. Saqi and C. Rawlings. Novel ways to
explore sequenced fungal genomes. European Fungal Genetics Conference, Edinburgh, UK April 2008
A. Beacham, C. Cavanet, J. Taubert, M. Urban, J. Antoniw, C. Rawlings and K. 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
K. Hammond-Kosack, T. Baldwin, M. Urban, R. Winnenburg, J. Koehler, M. Saqi and C. Rawlings. The plant pathogen 'omics world
- where is it taking us? EBI-EMBL joint workshop, Cambridge, UK Oct 2008
K. Hammond-Kosack and J. 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
K. Hammond-Kosack, M. Urban, A. Beacham, N. Brown, C. Cavanet, M. Saqi, C. Rawlings and J. 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.
K. Hammond-Kosack, M. Urban, J. Rudd and K. Kanyuka Comparative genomics of pathogenesis and innate immunity. Joint Rothamsted
Research - Institute of Animal Health Workshop, held at The Compton Laboratory, England, May 2007
J. Köhler, R. Winnenburg, C. Rawlings, T. Baldwin, M. Urban and K. Hamond-Kosack
Pathogen-Host Interactions Database (Phi-Base)
COGEME interest group meeting, 7th - 8th November 2006, Chancellors Hotel and Conference Centre, Manchester, UK
T. K. Baldwin, R. Winnenburg, M. Urban, C. Rawlings, J. Köhler and K. 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
T. Baldwin, R. Winnenburg, J. Köhler, M. Urban and K. 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)
T. Baldwin, R. Winnenburg, J. Köhler, M. Urban and K. 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
FUTURE DEVELOPMENTS FOR PHI-BASE FROM 2011 ONWARDS
PHASE 1 - Link the new ENSEMBL genome browser interface to the contents of PHI-base in a gene centric manner - achieved October 2011
PHASE 2 - Train others in the data curation process to clear the peer-reviewed paper backlog - on track
PHASE 3 - Development of a prototype self-entry data curation interface
PHASE 4 - Beta testing of the curation interface for several species
PHASE 5 - Launch the new database scheme as PHI-base version 4
PHASE 6 - 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
Mappings to KEGG - include Pentose and Glucuronate interconversion, Starch and
sucrose metabolism, Aminosugars metabolism. Some edges are not shown for
PHI-BASE SPECIES LIST
PHI-base species list
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
Cantu D, Segovia V, MacLean D et al (2013). Genome analyses of the wheat yellow (stripe) rust pathogen Puccinia striiformis f. sp. tritici reveal polymorphic and haustorial expressed secreted proteins as candidate effectors. BMC Genomics. doi: 10.1186/1471-2164-14-270
Wicker T, Oberhaensli S, Parlange Fet al (2013). The wheat powdery mildew genome shows the unique evolution of an obligate biotroph. Nat Genet. doi: 10.1038/ng.2704
Gardiner DM, McDonald MC, Covarelli L, Solomon PS et al (2012). Comparative pathogenomics reveals horizontally acquired novel virulence genes in fungi infecting cereal hosts. PLoS Pathog. doi: 10.1371/journal.ppat.1002952
de Wit PJ, van der Burgt A, Okmen B et al (2012).The genomes of the fungal plant pathogens Cladosporium fulvum and Dothistroma septosporum reveal adaptation to different hosts and lifestyles but also signatures of common ancestry. PLoS Genet. doi: 10.1371/journal.pgen.1003088
Amselem J, Cuomo CA, van Kan JA et al (2011). Genomic analysis of the necrotrophic fungal pathogens Sclerotinia sclerotiorum and Botrytis cinerea PLoS Genet. doi: 10.1371/journal.pgen.1002230
Duplessis S, Cuomo CA, Lin YC et al (2011). Obligate biotrophy features unraveled by the genomic analysis of rust fungi. Proc Natl Acad Sci U S A. doi: 10.1073/pnas.1019315108
Goodwin et al (2011). Finished genome of the fungal wheat pathogen Mycosphaerella graminicola reveals dispensome structure, chromosome plasticity, and stealth pathogenesis. PLoS Genet. doi: 10.1371/journal.pgen.1002070
Ma LJ, van der Does HC, Borkovichet KA al (2010).
Comparative genomics reveals mobile pathogenicity
chromosomes in Fusarium oxysporum. Nature. doi: 10.1038/nature08850
Spanu et al (2010). Genome expansion and gene loss in powdery mildew fungi reveal tradeoffs in extreme parasitism. Science. doi: 10.1126/science.1194573
Tyler et al., 2006. Phytophthora genome sequences uncover evolutionary origins and mechanisms of
pathogenesis. Science 313(5791):1261-6.
Kamper et al., 2006. Insights from the genome of the biotrophic fungal plant pathogen Ustilago maydis. Nature 444(7115):97-101.
Dean et al., 2005. The genome sequence of the rice blast fungus Magnaporthe
grisea. Nature 434:980-6.
Dietrich et al., 2004. The Ashbya gossypii genome as a tool for mapping the
ancient Saccharomyces cerevisiae genome. Science 304:304-7.
Galagan et al., 2003. The genome sequence of the filamentous fungus
Neurospora crassa. Nature 422:859-68.
Goffeau et al., 1996. Life with 6000 Genes. Science 274:546-566.
Jones et al., 2004. The diploid genome sequence of Candida albicans.
Proc. Natl. Acad. Sci. U. S. A. 101:7329-7334.
Génolevures 2005. Genomic exploration of the hemiascomycete yeasts.
Joint Genome Institute 2005. Eukaryotic Genomes.
Broad Institute 2005. Fungal Genome Initiative (FGI).
Online:http://www.broadinstitute.org/fungal genome initiative
Sanger Institute, 2005. Fungal genomes.
Reviews on Pathogenicity
Ma LJ, Geiser DM, Proctor RH et al (2013). Fusarium pathogenomics Annu Rev Microbiol. doi: 10.1146/annurev-micro-092412-155650
Dean R, Van Kan JA, Pretorius ZA, Hammond-Kosack KE, DiPietro A, et al. (2012) The Top 10 fungal pathogens in molecular plant pathology. Mol Plant Pathol 13:414-430, doi:10.1111/j.1364-3703.2010.00680.x
Raffaele S, Kamoun S. (2012). Genome evolution in filamentous plant pathogens: why bigger can be better
Nat Rev Microbiol. doi: 10.1038/nrmicro2790.
van de Wouw and Howlett (2011). Fungal pathogenicity genes in the age of 'omics'. Mol Plant Pathol 12:507-514, doi:10.1111/j.1364-3703.2010.00680.x
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.
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.
Stergiopoulos, I., and de Wit, P.J.G.M. (2009). Fungal Effector Proteins. Annual Rev. of Phytopathol. 47, 233-263.
Sexton AC, Howlett BJ., 2006. Parallels in fungal pathogenesis on plant and animal hosts. Eukaryot Cell. 5(12):1941-9
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.
Talbot, NJ, 2003. On the trail of a cereal killer: Exploring the biology of Magnaporthe grisea. Annu Rev Microbiol. 57:177-202
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.
Knogge, W., 1996. Fungal infections of plants. Plant Cell 8:1711-1722.
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.
Gene-Ontology-Consortium., 2006. The Gene Ontology (GO) project in 2006. Nucl. Acids Res. 34:D322-D326.
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).