Other Resources


General Plant Pathology

  • Agrios, G. N. 1997. Plant Pathology. Academic Press, Inc., London.
  • de Bary, H. A. 1879. The Phenomenon of Symbiosis. Strasbourg.
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    • 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.
      • 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 set undofile
    • Jones et al., 2004. The diploid genome sequence of Candida albicans. Proc. Natl. Acad. Sci. U. S. A. 101:7329-7334.
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    • 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.broadinstitute.org/fungal genome initiative
    • Sanger Institute, 2005. Fungal genomes.
      Online: http://www.sanger.ac.uk/Projects/Fungi/


    Reviews on Pathogenicity citing PHI-base

    2024
    Baudin, M. et al, (2024). Pyricularia oryzae: Lab star and field scourge. Mol Plant Pathol doi: 10.1111/mpp.13449.
    Ji, W. et al, (2024). Algae blooms with resistance in fresh water: Potential interplay between Microcystis and antibiotic resistance genes. Sci Total Environ doi: 10.1016/j.scitotenv.2024.173528.
    Jing, J. et al, (2024). Strategies for tailoring functional microbial synthetic communities. ISME J doi: 10.1093/ismejo/wrae049.
    Rutherford, K. M. et al, (2024). PomBase: a Global Core Biodata Resource-growth, collaboration, and sustainability. Genetics doi: 10.1093/genetics/iyae007.
    Tan, K. L. S.S. B. Mohamad, (2024). Fungal Pathogen in Digital Age: Review on Current State and Trend of Comparative Genomics Studies of Pathogenic Fungi. Advancements of Microbiology doi: 10.2478/am-2024-0003.
    2023
    Bishnoi, R. et al, (2023). Genome engineering of disease susceptibility genes for enhancing resistance in plants. Funct. Integr. Genomics doi: 10.1007/s10142-023-01133-w.
    Gutierrez-Sanchez, A. et al, (2023). Virulence factors of the genus Fusarium with targets in plants. Microbiol Res doi: 10.1016/j.micres.2023.127506.
    Joshi, A. et al, (2023). Integrated Molecular and Bioinformatics Approaches for Disease-Related Genes in Plants. Plants (Basel) doi: 10.3390/plants12132454.
    Mostaffa, N. H. et al, (2023). Interactomics in plant defence: progress and opportunities. Mol. Biol. Rep. doi: 10.1007/s11033-023-08345-0.
    Rai, P. et al, (2023). Fungal effectors versus defense-related genes of B. juncea and the status of resistant transgenics against fungal pathogens. Front Plant Sci doi: 10.3389/fpls.2023.1139009.
    Zhao, Y. et al, (2023). Application of high-throughput sequencing technologies and analytical tools for pathogen detection in urban water systems: Progress and future perspectives. Sci Total Environ doi: 10.1016/j.scitotenv.2023.165867.
    2022
    Kang, S. et al, (2022). Genomics and Informatics, Conjoined Tools Vital for Understanding and Protecting Plant Health. Phytopathology doi: 10.1094/PHYTO-10-21-0418-RVW.
    Kumar, S. et al, (2022). Viral informatics: bioinformatics-based solution for managing viral infections. Brief Bioinform doi: 10.1093/bib/bbac326.
    Liu, Y.P. Xu, (2022). Quantitative and analytical tools to analyze the spatiotemporal population dynamics of microbial consortia. Curr Opin Biotechnol doi: 10.1016/j.copbio.2022.102754.
    Lv, J. et al, (2022). Computational models, databases and tools for antibiotic combinations. Brief Bioinform doi: 10.1093/bib/bbac309.
    Roe, A. L. et al, (2022). Considerations for determining safety of probiotics: A USP perspective. Regul Toxicol Pharmacol doi: 10.1016/j.yrtph.2022.105266.
    Saravanakumar, K. et al, (2022). Bioinformatics strategies for studying the molecular mechanisms of fungal extracellular vesicles with a focus on infection and immune responses. Brief Bioinform doi: 10.1093/bib/bbac250.
    Wu, Y. et al, (2022). Prediction of effector proteins and their implications in pathogenicity of phytopathogenic filamentous fungi: A review. Int. J. Biol. Macromol. doi: 10.1016/j.ijbiomac.2022.02.133.
    Zhang, Z. et al, (2022). Metagenome Analysis of the Bacterial Characteristics in Invasive Klebsiella Pneumoniae Liver Abscesses. Front. Cell. Infect. Microbiol. doi: 10.3389/fcimb.2022.812542.
    2021
    Dong, A. Y. et al, (2021). Bioinformatic tools support decision-making in plant disease management. Trends Plant Sci doi: 10.1016/j.tplants.2021.05.001.
    Johns, L. E. et al, (2021). Nutrient sensing and acquisition in fungi: mechanisms promoting pathogenesis in plant and human hosts. Fungal Biology Reviews doi: 10.1016/j.fbr.2021.01.0021749-4613/.
    Mores, A. et al, (2021). Genomic Approaches to Identify Molecular Bases of Crop Resistance to Diseases and to Develop Future Breeding Strategies. Int. J. Mol. Sci. doi: 10.3390/ijms22115423.
    Jaiswal, S. et al, (2020). Systems Biology Approaches for Therapeutics Development Against COVID-19. Front. Cell. Infect. Microbiol. doi: 10.3389/fcimb.2020.560240.
    2020
    Jaiswal, S. et al, (2020). Systems Biology Approaches for Therapeutics Development Against COVID-19. Front. Cell. Infect. Microbiol. doi: 10.3389/fcimb.2020.560240.
    Kanja, C.K. E. Hammond-Kosack, (2020). Proteinaceous effector discovery and characterization in filamentous plant pathogens. Mol Plant Pathol doi: 10.1111/mpp.12980.
    Li, J. et al, (2020). Contents, Construction Methods, Data Resources, and Functions Comparative Analysis of Bacteria Databases. Int J Biol Sci doi: 10.7150/ijbs.39289.
    Muggia, L. et al, (2020). An Overview of Genomics, Phylogenomics and Proteomics Approaches in Ascomycota. Life (Basel) doi: 10.3390/life10120356.
    Neik, T. X. et al, (2020). Understanding Host-Pathogen Interactions in Brassica napus in the Omics Era. Plants (Basel) doi: 10.3390/plants9101336.
    Rampersad, S. N., (2020). Pathogenomics and Management of Fusarium Diseases in Plants. Pathogens doi: 10.3390/pathogens9050340.
    Urban, M. et al, (2020). PHI-base: the pathogen-host interactions database. Nucleic Acids Res doi: 10.1093/nar/gkz904.
    Verheggen, K. et al, (2020). Anatomy and evolution of database search engines-a central component of mass spectrometry based proteomic workflows. Mass Spectrom Rev doi: 10.1002/mas.21543.
    Zhang, R. et al, (2020). Traditional Chinese Medicine and Gut Microbiome: Their Respective and Concert Effects on Healthcare. Front Pharmacol doi: 10.3389/fphar.2020.00538.
    Argemi, X. et al, (2019). Coagulase-Negative Staphylococci Pathogenomics. Int. J. Mol. Sci. doi: 10.3390/ijms20051215.
    2019
    Argemi, X. et al, (2019). Coagulase-Negative Staphylococci Pathogenomics. Int. J. Mol. Sci. doi: 10.3390/ijms20051215.
    Consortium, O.T. Gabaldon, (2019). Recent trends in molecular diagnostics of yeast infections: from PCR to NGS. FEMS Microbiol Rev doi: 10.1093/femsre/fuz015.
    Consortium, O.T. Gabaldon, (2019). Recent trends in molecular diagnostics of yeast infections: from PCR to NGS. FEMS Microbiol Rev doi: 10.1093/femsre/fuz015.
    Dunn, N. A. et al, (2019). Apollo: Democratizing genome annotation. PLoS Comput Biol doi: 10.1371/journal.pcbi.1006790.
    Martin-Galiano, A. J.M. J. McConnell, (2019). Using Omics Technologies and Systems Biology to Identify Epitope Targets for the Development of Monoclonal Antibodies Against Antibiotic-Resistant Bacteria. Front Immunol doi: 10.3389/fimmu.2019.02841.
    Pedro, H. et al, (2019). Collaborative Annotation Redefines Gene Sets for Crucial Phytopathogens. Front Microbiol doi: 10.3389/fmicb.2019.02477.
    Sayers, S. et al, (2019). Victors: a web-based knowledge base of virulence factors in human and animal pathogens. Nucleic Acids Res doi: 10.1093/nar/gky999.
    Chagas, F. O. et al, (2018). Chemical signaling involved in plant-microbe interactions. Chem Soc Rev doi: 10.1039/c7cs00343a.
    2018
    Chagas, F. O. et al, (2018). Chemical signaling involved in plant-microbe interactions. Chem Soc Rev doi: 10.1039/c7cs00343a.
    Figueroa, M. et al, (2018). A review of wheat diseases-a field perspective. Mol Plant Pathol doi: 10.1111/mpp.12618.
    Jones, D. A. et al, (2018). Bioinformatic prediction of plant-pathogenicity effector proteins of fungi. Curr Opin Microbiol doi: 10.1016/j.mib.2018.01.017.
    Lacasta, J. et al, (2018). Agricultural recommendation system for crop protection. Comput Electron Agr doi: 10.1016/j.compag.2018.06.049.
    Naidoo, S. et al, (2018). Dual RNA-Sequencing to Elucidate the Plant-Pathogen Duel. Curr Issues Mol Biol doi: 10.21775/cimb.027.127.
    Ravet, K. et al, (2018). The power and potential of genomics in weed biology and management. Pest Manag Sci doi: 10.1002/ps.5048.
    2017
    A ylward, J. et al, (2017). A plant pathology perspective of fungal genome sequencing. IMA Fungus doi: 10.5598/imafungus.2017.08.01.01.
    Hassani-Pak, K.C. Rawlings, (2017). Knowledge Discovery in Biological Databases for Revealing Candidate Genes Linked to Complex Phenotypes. J Integr Bioinform doi: 10.1515/jib-2016-0002.
    Motaung, T. E. et al, (2017). Large-scale molecular genetic analysis in plant-pathogenic fungi: a decade of genome-wide functional analysis. Mol Plant Pathol doi: 10.1111/mpp.12497.
    Schatschneider, S. et al, (2017). Systems and synthetic biology perspective of the versatile plant-pathogenic and polysaccharide-producing bacterium Xanthomonas campestris. Microbiology (Reading) doi: 10.1099/mic.0.000473.
    Urban, M. et al, (2017). PHI-base: a new interface and further additions for the multi-species pathogen-host interactions database. Nucleic Acids Res doi: 10.1093/nar/gkw1089.
    2016
    Armijo, G. et al, (2016). Grapevine Pathogenic Microorganisms: Understanding Infection Strategies and Host Response Scenarios. Front Plant Sci doi: 10.3389/fpls.2016.00382.
    Bakour, S. et al, (2016). Identification of virulence factors and antibiotic resistance markers using bacterial genomics. Future Microbiol doi: 10.2217/fmb.15.149.
    Brown, N. A. et al, (2016). The trans-kingdom identification of negative regulators of pathogen hypervirulence. FEMS Microbiol Rev doi: 10.1093/femsre/fuv042.
    Cairns, T. C. et al, (2016). New and Improved Techniques for the Study of Pathogenic Fungi. Trends Microbiol doi: 10.1016/j.tim.2015.09.008.
    Dix, A. et al, (2016). Use of systems biology to decipher host-pathogen interaction networks and predict biomarkers. Clin Microbiol Infect doi: 10.1016/j.cmi.2016.04.014.
    Imam, J. et al, (2016). Plant Microbe Interactions in Post Genomic Era: Perspectives and Applications. Front Microbiol doi: 10.3389/fmicb.2016.01488.
    Li, H.Z. D. Zhang, (2016). Systems understanding of plant-pathogen interactions through genome-wide protein-protein interaction networks. Frontiers of Agricultural Science and Engineering doi: 10.15302/J-Fase-2016100.
    Pan, A. et al, (2016). Computational analysis of protein interaction networks for infectious diseases. Brief Bioinform doi: 10.1093/bib/bbv059.
    Sen, R. et al, (2016). A review on host-pathogen interactions: classification and prediction. Eur J Clin Microbiol-//-Eur J Clin Microbiol doi: 10.1007/s10096-016-2716-7.
    Sonah, H. et al, (2016). Computational Prediction of Effector Proteins in Fungi: Opportunities and Challenges. Front Plant Sci doi: 10.3389/fpls.2016.00126.
    Tian, S. et al, (2016). Molecular aspects in pathogen-fruit interactions: Virulence and resistance. Postharvest Biology and Technology doi: 10.1016/j.postharvbio.2016.04.018.
    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.
    Before 2015
    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.
    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

Version: 4.17 release - Last revision: 01/05/2024

PHI-base is funded by the Biotechnology and Biological Sciences Research Council (BBSRC, UK) and is being developed and maintained by scientists at Rothamsted Research.
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