Comparative Genomic Analysis of 31 <i>Phytophthora</i> Genomes Reveals Genome Plasticity and Horizontal Gene Transfer

Abstract

<i>Phytophthora</i> species are oomycete plant pathogens that cause great economic and ecological impacts. The <i>Phytophthora</i> genus includes over 180 known species, infecting a wide range of plant hosts, including crops, trees, and ornamentals. We sequenced the genomes of 31 individual <i>Phytophthora</i> species and 24 individual transcriptomes to study genetic relationships across the genus. <i>De nov</i>o genome assemblies revealed variation in genome sizes, numbers of predicted genes, and in repetitive element content across the <i>Phytophthora</i> genus. A genus-wide comparison evaluated orthologous groups of genes. Predicted effector gene counts varied across <i>Phytophthora</i> species by effector family, genome size, and plant host range. Predicted numbers of apoplastic effectors increased as the host range of <i>Phytophthora</i> species increased. Predicted numbers of cytoplasmic effectors also increased with host range but leveled off or decreased in <i>Phytophthora</i> species that have enormous host ranges. With extensive sequencing across the <i>Phytophthora</i> genus, we now have the genomic resources to evaluate horizontal gene transfer events across the oomycetes. Using a machine-learning approach to identify horizontally transferred genes with bacterial or fungal origin, we identified 44 candidates over 36 <i>Phytophthora</i> species genomes. Phylogenetic reconstruction indicates that the transfers of most of these 44 candidates happened in parallel to major advances in the evolution of the oomycetes and <i>Phytophthora</i> spp. We conclude that the 31 genomes presented here are essential for investigating genus-wide genomic associations in genus <i>Phytophthora</i>. [Formula: see text] Copyright © 2023 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.