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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 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 genome at the chromosome level. Specifically, the Phytophthora 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 genomes 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.

The goal of biosecurity is to minimize the risk of introduction and transmission of infectious diseases to people, animals, and plants. This is achieved by accurately identifying pathogens and instituting appropriate methods to prevent their introduction, reemergence, and/or spread. However, disease is dynamic, and biosecurity needs to continually change to keep pace as pathogens evolve. As described in this chapter, a basic understanding of evolution is central in considering how genetic changes and their associated phenotypes can alter the disease presentation of pathogens. In addition, evolution leaves a trail of genetic information that can be leveraged to inform biosecurity because the spatiotemporal patterns of these past changes provide clues as to how the pathogen might be spreading. This chapter aims to provide insights into how various genetic alterations occur, the background on how these are informative for biosecurity, and illustrations of applications to real-world examples. Evolution underlies the abilities of pathogens to adapt, emerge, and to cause epidemics.