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ARS Home » Pacific West Area » Corvallis, Oregon » Horticultural Crops Disease and Pest Management Research Unit » Research » Publications at this Location » Publication #385649
Research Project: Integrated Disease Management of Exotic and Emerging Plant Diseases of Horticultural Crops

Location: Horticultural Crops Disease and Pest Management Research Unit

Title: High quality, phased genomes sequences of phytophthora ramorum clonal lineages NA1 and EU1

Author
item CARLESON, NICHOLAS - Oregon State University
item Press, Caroline
item Grunwald, Niklaus - Nik

Submitted to: bioRxiv
Publication Type: Pre-print Publication
Publication Acceptance Date: 6/23/2021
Publication Date: 6/23/2021
Citation: Carleson, N.C., Press, C.M., Grunwald, N.J. 2021. High quality, phased genomes sequences of phytophthora ramorum clonal lineages NA1 and EU1. bioRxiv. 2021.06.23.449625. https://doi.org/10.1101/2021.06.23.449625.
DOI: https://doi.org/10.1101/2021.06.23.449625

Interpretive Summary: The water mold Phytophthora ramorum is the causal agent of sudden oak death in West Coast. This pathogen invaded Oregon forests as two distinct genetic lineages, NA1 and EU1, causing epidemics in Oregon forests. Here, we report on two high-quality genomes of individuals belonging to the NA1 and EU1 clonal lineages respectively, using long-read sequencing technology. The current genome assemblies are much improved relative to previously published genomes with larger continuous assemblies into fewer scaffolds and equally high completeness of gene calls. These high-quality genomes provide a valuable resource for studying the genetics, evolution, and adaptation of the sudden oak death pathogen.

Technical Abstract: Phytophthora ramorum is the causal agent of sudden oak death in West Coast forests and currently two clonal lineages, NA1 and EU1, cause epidemics in Oregon forests. Here, we report on two high-quality genomes of individuals belonging to the NA1 and EU1 clonal lineages respectively, using PacBio long-read sequencing. The NA1 strain Pr102, originally isolated from coast live oak in California, is the current reference genome and was previously sequenced independently using either Sanger (P. ramorum v1) or PacBio (P. ramorum v2) technology. The EU1 strain PR-15-019 was obtained from tanoak in Oregon. These two genomes have a total size of 57.5 Mb, with a contig N50 length of ~3.5-3.6 Mb and encode ~15,300 predicted protein-coding genes. Genomes were assembled into 27 and 28 scaffolds with 95% BUSCO scores and are considerably improved relative to the current JGI reference genome with 2,575 or the PacBio genomes with 1,512 scaffolds. These high-quality genomes provide a valuable resource for studying the genetics, evolution, and adaptation of these two clonal lineages.