Members of the Phytophthora genus are responsible for many important diseases in agricultural and natural ecosystems. Phytophthora ramorum causes devastating diseases of oak and tanoak stands in U.S. forests and larch in the United Kingdom. The four evolutionary lineages involved express different virulence phenotypes on plant hosts, and characterization of gene content is foundational to understanding the basis for these differences. Recent discovery of P. ramorum at its candidate center of origin in Asia provides a new opportunity for investigating the evolutionary history of the species. We assembled high-quality genome sequences of six P. ramorum isolates representing three lineages from Asia and three causing epidemics in Western U.S. forests. The six genomes were assembled into 13 putative chromosomes. Analysis of structural variation revealed multiple chromosome fusion and fission events. Analysis of putative virulence genes revealed variations in effector gene composition among the sequenced lineages. We further characterized their evolutionary history and inferred a contraction of crinkler-encoding genes in the subclade of Phytophthora containing P. ramorum. There were losses of multiple families and a near complete loss of paralogs in the largest core crinkler family in the ancestor of P. ramorum and sister species P. lateralis. Secreted glycoside hydrolase enzymes showed a similar degree of variation in abundance among genomes of P. ramorum lineages as that observed among several Phytophthora species. We found plasticity among genomes from multiple lineages in a Phytophthora species and provide insights into the evolutionary history of a class of anciently conserved effector genes. [Formula: see text] Copyright © 2025 The Author(s). This is an open access article distributed under the CC BY 4.0 International license.

Center for Environmental and Societal Sustainability Gifu University Gifu 501 1193 Japan

Department of Agricultural Sciences University of Sassari 07100 Sassari Italy

Department of Botany and Plant Pathology Oregon State University Corvallis OR 97331 U S A

Forest Research Alice Holt Lodge Farnham Surrey GU10 4LH U K

Forestry and Forest Products Research Institute Tsukuba Ibaraki 305 8687 Japan

Horticultural Crops Disease and Pest Management Research Unit USDA Agricultural Research Service Corvallis OR 97330 U S A

Laboratory of Molecular and Cellular Biology Department of Bioregulation and Bio interaction Tokyo University of Agriculture and Technology Fuchu Tokyo 183 8509 Japan

Mendel University in Brno Faculty of Forestry and Wood Technology Phytophthora Research Centre 613 00 Brno Czech Republic

Citace poskytuje Crossref.org