The Pathogen-Host Interactions database (PHI-base): additions and future developments

Urban, Martin; Pant, Rashmi; Raghunath, Arathi; Irvine, Alistair G.; Pedro, Helder; Hammond‐Kosack, K. E.

doi:10.1093/nar/gku1165

Cited by 202 publications

(181 citation statements)

References 53 publications

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“…Information can be linked to the genome from other databases, such as the Pathogen-Host Interaction entries [47] to efficiently access phenotypic information from pathogenicity testing involving single and multiple gene deletion isolates generated mostly in the reference strain PH-1. The presentation in Ensembl fungi/PhytoPathdb will aid comparative genomics studies by the identification of homologous and orthologous genes with other representative fungal genomes which are continually increasing and being updated.…”

Section: Discussionmentioning

confidence: 99%

“…The Pathogen-Host Interactions database (PHI-base) stores molecular and biological information on pathogen genes for which mutant phenotypes in pathogen-host interactions have been tested experimentally [47]. PHIbase currently provides information on > 2,800 pathogen genes, involving~160 pathogenic species.…”

Section: Genes and Other Features Associated With The Proposed Ancienmentioning

confidence: 99%

“…As a consequence over the past decade, multiple Fusarium sequencing projects have taken place [3,4] or are currently in progress [5]. Although the haploid Fusarium genomes are small in size, typically [35][36][37][38][39][40][41][42][43][44][45][46][47][48][49][50] Mbp, for no Fusarium species is the complete genome sequence available. This is counter-intuitive to providing high quality genomic resources for research however a full spectrum of genomic resources currently exists.…”

Section: Introductionmentioning

confidence: 99%

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The completed genome sequence of the pathogenic ascomycete fungus Fusarium graminearum

et al. 2015

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Background: Accurate genome assembly and gene model annotation are critical for comparative species and gene functional analyses. Here we present the completed genome sequence and annotation of the reference strain PH-1 of Fusarium graminearum, the causal agent of head scab disease of small grain cereals which threatens global food security. Completion was achieved by combining (a) the BROAD Sanger sequenced draft, with (b) the gene predictions from Munich Information Services for Protein Sequences (MIPS) v3.2, with (c) de novo whole-genome shotgun re-sequencing, (d) re-annotation of the gene models using RNA-seq evidence and Fgenesh, Snap, GeneMark and Augustus prediction algorithms, followed by (e) manual curation.

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Section: Discussionmentioning

confidence: 99%

Section: Genes and Other Features Associated With The Proposed Ancienmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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The completed genome sequence of the pathogenic ascomycete fungus Fusarium graminearum

et al. 2015

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“…The data content has been continually updated (7). Since 2011, PHI-base has provided phenotypic annotation for over 100 crop plant infecting microbial pathogens into Ensembl Genomes (8) as part of the PhytoPath project (9).…”

Section: Introductionmentioning

confidence: 99%

PHI-base: a new interface and further additions for the multi-species pathogen–host interactions database

et al. 2016

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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. In addition, literature that indicates specific gene alterations that did not affect the disease interaction phenotype are curated to provide complete datasets for comparative purposes. Viruses are not included. Here we describe a revised PHI-base Version 4 data platform with improved search, filtering and extended data display functions. A PHIB-BLAST search function is provided and a link to PHI-Canto, a tool for authors to directly curate their own published data into PHI-base. The new release of PHI-base Version 4.2 (October 2016) has an increased data content containing information from 2219 manually curated references. The data provide information on 4460 genes from 264 pathogens tested on 176 hosts in 8046 interactions. Prokaryotic and eukaryotic pathogens are represented in almost equal numbers. Host species belong ∼70% to plants and 30% to other species of medical and/or environmental importance. Additional data types included into PHI-base 4 are the direct targets of pathogen effector proteins in experimental and natural host organisms. The curation problems encountered and the future directions of the PHI-base project are briefly discussed.

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“…phi-base.org) provides curated information on genes that affect the interaction between host and pathogens based on functional genetics studies with links to experimental evidence (Urban et al, 2015). A BLAST analysis against the nucleotide or predicted amino acid sequences in the database provides clues about whether pathogen genes expressed in planta are putative effectors, virulence factors or pathogenicity factors.…”

Section: Downstream Analysismentioning

confidence: 99%

Dual RNA-Sequencing to Elucidate the Plant-Pathogen Duel

Naidoo¹,

Visser²,

Zwart³

et al. 2018

Current Issues in Molecular Biology

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RNA-sequencing technology has been widely adopted to investigate host responses during infection with pathogens. Dual RNA-sequencing (RNA-seq) allows the simultaneous capture of pathogen-specific transcripts during infection, providing a more complete view of the interaction. In this review, we focus on the design of dual RNAseq experiments and the application of downstream data analysis to gain biological insight into both sides of the interaction. Recent literature in this area demonstrates the power of the dual RNA-seq approach and shows that it is not limited to model systems where genomic resources are available. Sequencing costs continue to decrease and single cell transcriptomics is becoming more feasible. In combination with proteomics and metabolomics studies, these technological advances are likely to contribute to our understanding of the temporal and spatial aspects of dynamic plant-pathogen interactions. A dual approach in plantaThe interaction between plants and pathogens is an active and dynamic process that can be likened to a duel. Plants have complex defence mechanisms that can be rendered ineffective when pathogens interfere with one of the various processes required for host defence. These processes include penetration resistance, recognition by Pattern Recognition Receptors (PRRs), phytohormone signalling pathways, secretory pathways, secondary metabolite production, and plant cell death (Dou and Zhou, 2012). Until recently, transcriptomic approaches have been applied in the host and pathogen separately to obtain the gene expression profile of each organism and gain insight into infection biology or host defence mechanisms.RNA sequencing (RNA-seq) is a powerful technology that does not rely on any prior knowledge of transcripts and can generate vast quantities of data with much smaller costs involved than for older techniques such as microarrays (Pareek et al., 2011;Wilhelm and Landry, 2009). An advantage of RNA-seq in the field of plant-pathogen interactions is that both plant and pathogen transcripts can be detected simultaneously and accurately in the same sample. This tactic, known as dual RNAseq, in planta RNA-seq, simultaneous RNA-seq, or comparative RNA-seq, is a relatively new technique both in the plant and medical fields. In plants, it allows for the study of plant-pathogen interactions in herbaceous crops Kunjeti et al., 2012;Lowe et al., 2014) as well as trees (Hayden et al., 2014;Liang et al., 2014;Teixeira et al., 2014). This review outlines technical considerations for dual RNA-seq experiments, summarizes recent insights drawn from such approaches in plant-pathogen interactions, and provides an

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The Pathogen-Host Interactions database (PHI-base): additions and future developments

Cited by 202 publications

References 53 publications

The completed genome sequence of the pathogenic ascomycete fungus Fusarium graminearum

The completed genome sequence of the pathogenic ascomycete fungus Fusarium graminearum

PHI-base: a new interface and further additions for the multi-species pathogen–host interactions database

Dual RNA-Sequencing to Elucidate the Plant-Pathogen Duel

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