Skip to main content
ARS Home » Pacific West Area » Corvallis, Oregon » Horticultural Crops Disease and Pest Management Research Unit » Research » Publications at this Location » Publication #404664
Research Project: Knowledge Based Tools for Exotic and Emerging Diseases of Small Fruit and Nursery Crops

Location: Horticultural Crops Disease and Pest Management Research Unit

Title: High quality genome of the tree pathogen Phytophthora plurivora - a novel resource for epidemiological research

Author
item TSYKA, T - Goethe University
item MISHRA, B - Biodiversity And Climate Research Centre (BIK-F)
item PLOCH, S - Biodiversity And Climate Research Centre (BIK-F)
item ALCALA-BRISENO, R - Oregon State University
item PROSPERO, S - Swiss Federal Research Institute Wsl
item Grunwald, Niklaus - Nik
item THINES, M - Goethe University

Submitted to: PhytoFrontiers
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 5/24/2023
Publication Date: 5/29/2023
Citation: Tsyka, T., Mishra, B., Ploch, S., Alcala-Briseno, R.I., Prospero, S., Grunwald, N.J., Thines, M. 2023. High quality genome of the tree pathogen Phytophthora plurivora - a novel resource for epidemiological research. PhytoFrontiers. https://doi.org/10.1094/PHYTOFR-05-23-0065-A.
DOI: https://doi.org/10.1094/PHYTOFR-05-23-0065-A

Interpretive Summary: Phytophthora plurivora and Phytopohthora cambivora are two plant pathogens affecting forest tree species. Both pathogens cause severe disease on European beech, a common tree native to Europe. Here, we report on high-quality genome assemblies for both pathogens. The high quality and completeness of these two genomes provides a crucial, novel resource for further research.

Technical Abstract: Phytophthora plurivora and P. cambivora can affect range of ecologically and silviculturally important tree species. Both pathogens are known to cause disease on European beech (Fagus sylvatica), a common late successional tree native to Europe. Here, we report on high-quality genomes of both pathogen species, P. ×cambivora strain TJ197 (CBS 141218 isolate) and P. plurivora strain TJ71 (CBS 124093 isolate). We sequenced their DNA using Oxford Nanopore MinION and PacBio Sequel II long-read sequencing with 80x coverage, chromatin conformation capture (Hi-C) sequencing with 400x coverage and DNBSEQ 150bp paired-end short reads sequencing with 200x coverage. This complex sequencing approach allowed assembly of the genomes to near-chromosome level. Specifically, the P. plurivora genome resulted in 18 scaffolds of 47 Mbp total size with 95% BUSCO eukaryotic gene coverage. The P. cambivora genome was assembled into 12 scaffolds of ~312 Mbp total size with 97% BUSCO  support. This is a considerable improvement relative to the previous reference genomes P. plurivora  (NMPK00000000.1 accession) and P. x cambivora (GCA_000443045.1 accession) with ~41 Mbp and ~231 Mbp assembled into 1,898 and 19,533 scaffolds with 93.8% and 93.0 % BUSCO’s coverage, respectively. The high quality and completeness of these two genomes provide a crucial, novel resource for further evolutionary, epidemiological, and population genomic research.