Large-Scale Bioinformatical Analysis of Host Factors Commonly Induced by <i>Phytophthora</i> Infection

Abstract

Oomycetes of the genus Phytophthora are devastating plant pathogens that affect many commercially important plants. Considerable efforts have been made to investigate the transcriptional response of individual plant species to Phytophthora infection, often showing a concerted upregulation of pathogen-response (PR) gene families, which are also induced upon infection by fungi and other biotic and even non-biotic stressors. For many of the upregulated factors, a biological role has not been firmly established. Here, we performed a large-scale exploratory bioinformatical function prediction of protein-coding genes, which are consistently upregulated by Phytophthora infection in multiple hosts. By integrating four very different transcriptomics datasets derived from three different plants ( Arabidopsis, soybean, and cocoa), a core set of upregulated sequence clusters was derived, which represents a multi-gene/multispecies response to Phytophthora infections. We annotated 309 upregulated multi-gene clusters and subjected the encoded proteins to bioinformatical analysis. Besides the expected PR genes, several novel gene families without known links to biotic stress were found to be strongly induced in all tested datasets. Among the most prominent response genes are two families of putatively secreted peptides and a family of predicted mitochondrial complex IV-associated proteins. Interestingly, the latter sequences are related to the mammalian NDUFA4 family, which also contains members with constitutive and pathogen-induced expression. This recurrent functional diversification points toward an important role of complex IV regulation within the biotic defense response in multiple kingdoms. [Formula: see text] Copyright © 2026 The Author(s). This is an open access article distributed under the CC BY 4.0 International license .