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Multi-species Conserved Sequences

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Next-generation sequencing technologies have created large genomic databases of a variety of animals and plants. Ever since the human genome project was completed, scientists studied the genome of primates, mammals, and other phylogenetically distant living beings. Such large-scale studies have provided new insights into the evolutionary relationship between organisms.
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Updated: Oct 13, 2025

High-Throughput Transcriptome Analysis for Investigating Host-Pathogen Interactions

High-Throughput Transcriptome Analysis for Investigating Host-Pathogen Interactions

Published on: March 5, 2022

PHI-base in 2022: a multi-species phenotype database for Pathogen-Host Interactions.

Martin Urban¹, Alayne Cuzick¹, James Seager¹

¹Department of Biointeractions and Crop Protection, Rothamsted Research, Harpenden AL5 2JQ, UK.

Nucleic Acids Research

|November 17, 2021

Summary

This summary is machine-generated.

The Pathogen-Host Interactions Database (PHI-base) manually curates verified pathogenicity, virulence, and effector genes from diverse pathogens and their hosts. This resource aids in comparative analysis and identifying intervention targets in important species.

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Area of Science:

Microbiology
Genomics
Bioinformatics

Background:

The Pathogen-Host Interactions Database (PHI-base) has been a crucial resource since 2005.
It manually curates experimentally verified data on pathogenicity, virulence, and effector genes.
PHI-base covers fungal, bacterial, and protist pathogens infecting a wide range of hosts.

Purpose of the Study:

To present phenotype information on pathogenicity and effector genes and their host interactions.
To facilitate comparative analyses for discovering candidate intervention targets.
To provide an updated and expanded dataset of pathogen-host interactions.

Main Methods:

Manual curation of experimentally verified gene data.
Inclusion of specific gene alterations affecting host interaction phenotypes.
Data dissemination to major biological databases like UniProtKB, FungiDB, and Ensembl Genomes.

Main Results:

Version 4.12 (September 2021) contains 4387 references, information on 8411 genes from 279 pathogens, and 18,190 interactions.
A 24% increase in gene content since Version 4.8 (September 2019).
Bacterial and fungal pathogens constitute the majority (54:46 split), with plants as the primary host type (54%).

Conclusions:

PHI-base is an invaluable resource for understanding pathogen-host interactions.
It supports the discovery of novel targets for medical and agricultural interventions.
A forthcoming gene-centric version (5.0) will enhance data accessibility and utility.