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

Abstract

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. [Figure: see text] Copyright © 2023 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.

Keywords

• chromosome level
• disease-causing agent
• Fagus sylvatica
• oomycetes