Karyotype variation, spontaneous genome rearrangements affecting chemical insensitivity, and expression level polymorphisms in the plant pathogen Phytophthora infestans revealed using its first chromosome-scale assembly

Natural isolates of the potato and tomato pathogen Phytophthora infestans exhibit substantial variation in virulence, chemical sensitivity, ploidy, and other traits. A chromosome-scale assembly was developed to expand genomic resources for this oomyceteous microbe, and used to explore the basis of variation. Using PacBio and Illumina data, a long-range linking library, and an optical map, an assembly was created and coalesced into 15 pseudochromosomes spanning 219 Mb using SNP-based genetic linkage data. De novo gene prediction combined with transcript evidence identified 19,981 protein-coding genes, plus about eight thousand tRNA genes. The chromosomes were comprised of a mosaic of gene-rich and gene-sparse regions plus very long centromeres. Genes exhibited a biased distribution across chromosomes, especially members of families encoding RXLR and CRN effectors which clustered on certain chromosomes. Strikingly, half of F1 progeny of diploid parents were polyploid or aneuploid. Substantial expression level polymorphisms between strains were identified, much of which could be attributed to differences in chromosome dosage, transposable element insertions, and adjacency to repetitive DNA. QTL analysis identified a locus on the right arm of chromosome 3 governing sensitivity to the crop protection chemical metalaxyl. Strains heterozygous for resistance often experienced megabase-sized deletions of that part of the chromosome when cultured on metalaxyl, increasing resistance due to loss of the sensitive allele. This study sheds light on diverse phenomena affecting variation in P. infestans and relatives, helps explain the prevalence of polyploidy in natural populations, and provides a new foundation for biologic and genetic investigations. Author summary Strains of the oomycete Phytophthora infestans from nature vary in traits including aggressiveness and chemical resistance, and range from diploid to tetraploid. What causes such variation in this important potato and tomato pathogen is largely unknown. To study this we generated the species' first chromosome-scale assembly and employed it to study karyotypic, transcriptomic, and phenotypic variation between strains. Intriguingly, we found that about half of progeny of diploid parents were polyploid or aneuploid. Many expression level polymorphisms between strains resulted from karyotype differences, transposon insertions, and the influence of repetitive DNA flanking genes. We also used SNPs to map loci determining sensitivity to a popular crop protection chemical, and found that a loss of heterozygosity affecting one locus often occurred which increased resistance. We also observed that the genome was organized into a montage of intermingled gene-dense and gene-sparse zones, with long pericentric regions.