Comparative Genomic Analysis of 31 Genomes Reveals Genome Plasticity and Horizontal Gene Transfer.

species are oomycete plant pathogens that cause great economic and ecological impacts. The 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 species and 24 individual transcriptomes to study genetic relationships across the genus. o genome assemblies revealed variation in genome sizes, numbers of predicted genes, and in repetitive element content across the genus. A genus-wide comparison evaluated orthologous groups of genes. Predicted effector gene counts varied across species by effector family, genome size, and plant host range. Predicted numbers of apoplastic effectors increased as the host range of species increased. Predicted numbers of cytoplasmic effectors also increased with host range but leveled off or decreased in species that have enormous host ranges. With extensive sequencing across the 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 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 spp. We conclude that the 31 genomes presented here are essential for investigating genus-wide genomic associations in genus . [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.