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Since 2005, the Pathogen-Host Interactions Database (PHI-base) has manually curated experimentally verified pathogenicity, virulence and effector genes from fungal, bacterial and protist pathogens, which infect animal, plant, fish, insect and/or fungal hosts. PHI-base (www.phi-base.org) is devoted to the identification and presentation of phenotype information on pathogenicity and effector genes and their host interactions. Specific gene alterations that did not alter the in host interaction phenotype are also presented. PHI-base is invaluable for comparative analyses and for the discovery of candidate targets in medically and agronomically important species for intervention. Version 4.12 (September 2021) contains 4387 references, and provides information on 8411 genes from 279 pathogens, tested on 228 hosts in 18, 190 interactions. This provides a 24% increase in gene content since Version 4.8 (September 2019). Bacterial and fungal pathogens represent the majority of the interaction data, with a 54:46 split of entries, whilst protists, protozoa, nematodes and insects represent 3.6% of entries. Host species consist of approximately 54% plants and 46% others of medical, veterinary and/or environmental importance. PHI-base data is disseminated to UniProtKB, FungiDB and Ensembl Genomes. PHI-base will migrate to a new gene-centric version (version 5.0) in early 2022. This major development is briefly described.

Scientific communication is facilitated by a data-driven, scientifically sound taxonomy that considers the end-user's needs and established successful practice. In 2013, the Fusarium community voiced near unanimous support for a concept of Fusarium that represented a clade comprising all agriculturally and clinically important Fusarium species, including the F. solani species complex (FSSC). Subsequently, this concept was challenged in 2015 by one research group who proposed dividing the genus Fusarium into seven genera, including the FSSC described as members of the genus Neocosmospora, with subsequent justification in 2018 based on claims that the 2013 concept of Fusarium is polyphyletic. Here, we test this claim and provide a phylogeny based on exonic nucleotide sequences of 19 orthologous protein-coding genes that strongly support the monophyly of Fusarium including the FSSC. We reassert the practical and scientific argument in support of a genus Fusarium that includes the FSSC and several other basal lineages, consistent with the longstanding use of this name among plant pathologists, medical mycologists, quarantine officials, regulatory agencies, students, and researchers with a stake in its taxonomy. In recognition of this monophyly, 40 species described as genus Neocosmospora were recombined in genus Fusarium, and nine others were renamed Fusarium. Here the global Fusarium community voices strong support for the inclusion of the FSSC in Fusarium, as it remains the best scientific, nomenclatural, and practical taxonomic option available.

Zymoseptoria tritici is the causal agent of Septoria tritici blotch (STB) disease of wheat. Z. tritici is an apoplastic fungal pathogen, which does not penetrate plant cells at any stage of infection, and has a long initial period of symptomless leaf colonisation. During this phase it is unclear to what extent the fungus can access host plant nutrients or communicate with plant cells. Several important primary and secondary metabolite pathways in fungi are regulated by the post-translational activator phosphopantetheinyl transferase (Ppt) which provides an essential co-factor for lysine biosynthesis and the activities of non-ribosomal peptide synthases (NRPS) and polyketide synthases (PKS). To investigate the relative importance of lysine biosynthesis, NRPS-based siderophore production and PKS-based DHN melanin biosynthesis, we generated deletion mutants of ZtPpt. The ∆ZtPpt strains were auxotrophic for lysine and iron, non-melanised and non-pathogenic on wheat. Deletion of the three target genes likely affected by ZtPpt loss of function (Aar- lysine; Nrps1-siderophore and Pks1- melanin), highlighted that lysine auxotrophy was the main contributing factor for loss of virulence, with no reduction caused by loss of siderophore production or melanisation. This reveals Ppt, and the lysine biosynthesis pathway, as potential targets for fungicides effective against Z. tritici.

The pathogen-host interactions database (PHI-base) is available at www.phi-base.org. PHI-base contains expertly curated molecular and biological information on genes proven to affect the outcome of pathogen-host interactions reported in peer reviewed research articles. PHI-base also curates literature describing specific gene alterations that did not affect the disease interaction phenotype, in order to provide complete datasets for comparative purposes. Viruses are not included, due to their extensive coverage in other databases. In this article, we describe the increased data content of PHI-base, plus new database features and further integration with complementary databases. The release of PHI-base version 4.8 (September 2019) contains 3454 manually curated references, and provides information on 6780 genes from 268 pathogens, tested on 210 hosts in 13,801 interactions. Prokaryotic and eukaryotic pathogens are represented in almost equal numbers. Host species consist of approximately 60% plants (split 50:50 between cereal and non-cereal plants), and 40% other species of medical and/or environmental importance. The information available on pathogen effectors has risen by more than a third, and the entries for pathogens that infect crop species of global importance has dramatically increased in this release. We also briefly describe the future direction of the PHI-base project, and some existing problems with the PHI-base curation process.

The mating locus within the F. venenatum and F. graminearum genomes. F. venenatum A3/5 contains only the MAT1–1 locus confirming heterothallism and the requirement for a complementary sexual partner. Whilst homothallic F. graminearum possesses both the MAT1–1 and MAT1–2 loci and hence does not require a complementary partner for sexual reproduction. Gene designations: A) FGRRES_08887, B) FGRRES_08888_M, C) FGRRES_08889_M, D) FGRRES_08894, E) FVRRES_05564, F) FGRRES_15525, G) FGRRES_13273_M. (PDF 90 kb)

Co-inoculation of F. venenatum with plant-pathogenic Fusaria in vitro and in vivo. (A) Carrot agar plate inoculated with agar plugs of strains Fv A3/5, two isolates of Fg (PH1 and 602), and Fc UK99. A barrage line between strains is visible at day 6. (B) F. culmorum and F. venenatum spores where mixed in equal amounts and co-inoculated into two spikelets at anthesis. As a control, water was inoculated (C) F. venenatum spores were sprayed onto wheat heads at the booting stage to potentially prime plant defence responses, followed by point-inoculation with F. culmorum spores of two heads per spike" should be "two spikelets per head at anthesis. (D) Wheat plants were treated as in C. Just after inoculaton with F. culmorum, wheat heads were sprayed once more with F. venenatum spores until run-off. Error bars show standard deviation, nâ =â 6. (PDF 111Â kb)

A figure locating the positions of Fusarium venenatum species-specific genes versus NCBI, in relation to sequences predicted to be the secretome, tRNA, and transposons. (PDF 144Â kb)

Programs used for detecting transmembrane helix positions (PDF 34 kb)

Programs used for detecting transmembrane helix positions (PDF 34 kb)

Pathogen-Host interaction data is core to our understanding of disease processes and their molecular/genetic bases. Facile access to such core data is particularly important for the plant sciences, where individual genetic and phenotypic observations have the added complexity of being dispersed over a wide diversity of plant species vs. the relatively fewer host species of interest to biomedical researchers. Recently, an international initiative interested in scholarly data publishing proposed that all scientific data should be ?FAIR?Findable, Accessible, Interoperable, and Reusable. In this work, we describe the process of migrating a database of notable relevance to the plant sciences?the Pathogen-Host Interaction Database (PHI-base)?to a form that conforms to each of the FAIR Principles. We discuss the technical and architectural decisions, and the migration pathway, including observations of the difficulty and/or fidelity of each step. We examine how multiple FAIR principles can be addressed simultaneously through careful design decisions, including making data FAIR for both humans and machines with minimal duplication of effort. We note how FAIR data publishing involves more than data reformatting, requiring features beyond those exhibited by most life science Semantic Web or Linked Data resources. We explore the value-added by completing this FAIR data transformation, and then test the result through integrative questions that could not easily be asked over traditional Web-based data resources. Finally, we demonstrate the utility of providing explicit and reliable access to provenance information, which we argue enhances citation rates by encouraging and facilitating transparent scholarly reuse of these valuable data holdings.

Name and 2D structure of the 10 retained compounds (PDF 108 kb)

A phylogenetic tree of 904 identified common proteins (see Additional file 3) using F. solani, F. oxysporum, F. verticillioides, F. mangiferae, F. fujikuroi, F. proliferatum, F. poae, F. venenatum, F. langsethiae, F. graminearum and F. pseudograminearum. The substitution rate is on each branch and 100% branch support was found from 100 bootstraps. Type A, B, or A/B trichothecene producers were labelled. The tree was rooted to F. solani. (PDF 104Â kb)

A phylogenetic tree of 904 identified common proteins (see Additional file 3) using F. solani, F. oxysporum, F. verticillioides, F. mangiferae, F. fujikuroi, F. proliferatum, F. poae, F. venenatum, F. langsethiae, F. graminearum and F. pseudograminearum. The substitution rate is on each branch and 100% branch support was found from 100 bootstraps. Type A, B, or A/B trichothecene producers were labelled. The tree was rooted to F. solani. (PDF 104Â kb)

Biological growth characteristics of F. venenatum compared to its close pathogenic relative F. graminearum. (A) Appearance of inoculated wheat head of cv. Bobwhite, 21 days after plug inoculations (dpi) with F. venenatum (Fv), (B) mock inoculation with water, (C) with F. graminearum (Fg). The white arrow indicates the inoculation points. (D) Appearance of wheat head 16 days after spray inoculation (dsi) with Fv, (E) mock spray inoculation with water, (F) spray inoculation with Fg. (G) Wheat seeds collected from a typical spray inoculated wheat head at 21 dsi with Fv, (H) mock spray with water, (I) with Fg. (J) Fv macrospores, (K) Fg macrospores. (L) Fv and (M) Fg growth on PDB plate at 6 days. (N) Fv inoculated tomato fruit at 4 days, (O) water control, (P) Fg. (Q) Fv inoculated tomato fruit at 12 days, (R) water control, (S) Fg. Bars in J, K: 10 μm. (PDF 268 kb)

Biological growth characteristics of F. venenatum compared to its close pathogenic relative F. graminearum. (A) Appearance of inoculated wheat head of cv. Bobwhite, 21 days after plug inoculations (dpi) with F. venenatum (Fv), (B) mock inoculation with water, (C) with F. graminearum (Fg). The white arrow indicates the inoculation points. (D) Appearance of wheat head 16 days after spray inoculation (dsi) with Fv, (E) mock spray inoculation with water, (F) spray inoculation with Fg. (G) Wheat seeds collected from a typical spray inoculated wheat head at 21 dsi with Fv, (H) mock spray with water, (I) with Fg. (J) Fv macrospores, (K) Fg macrospores. (L) Fv and (M) Fg growth on PDB plate at 6 days. (N) Fv inoculated tomato fruit at 4 days, (O) water control, (P) Fg. (Q) Fv inoculated tomato fruit at 12 days, (R) water control, (S) Fg. Bars in J, K: 10 μm. (PDF 268 kb)