High-Quality Genome of the Tree Pathogen Phytophthora plurivora —A Novel Resource for Epidemiological Research

• Published in: PhytoFrontiers Vol. 3; no. 4; pp. 888 - 892
• Main Authors: Tsykun, T., Mishra, B., Ploch, S., Briseño, R. I. Alcalá, Prospero, S., Grünwald, N. J., Thines, M.
• Format: Journal Article
• Language: English
• Published: The American Phytopathological Society 01.12.2023
• Subjects: chromosome level; disease-causing agent; Fagus sylvatica; oomycetes
• ISSN: 2690-5442; 2690-5442
• DOI: 10.1094/PHYTOFR-05-23-0065-A

Phytophthora plurivora can affect a range of ecologically and silviculturally important tree species, including European beech ( Fagus sylvatica), a common late successional tree species native to Europe. Here, we report on the high-quality genome of P. plurivora strain TJ71 (CBS 124093). We sequenced it using Oxford Nanopore MinION and PacBio Sequel II long-read sequencing with 80× coverage, chromatin conformation capture (Hi-C) sequencing with 400× coverage, and DNBSEQ 150-bp paired-end short reads sequencing with 200× coverage. This complex sequencing approach allowed for assembly of the genome at the chromosome level. Specifically, the P. plurivora genome resulted in 18 scaffolds of 47 Mbp total size with 95% completeness of the eukaryotic gene set as implemented in BUSCO. This is a considerable improvement relative to the previous NCBI reference genome of P. plurivora (NMPK00000000.1) with ∼41 Mbp organized in 1,898 scaffolds with 93.8% eukaryotic BUSCO completeness. This high-quality genome provides a valuable resource for further evolutionary, epidemiological, and population genomic studies. [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 .