ArticlePLoS pathogens2022
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.
Article in PLoS pathogens, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
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22 citing papers in PubMed, 39 citations in OpenAlex.
- Eukaryotic metagenome-assembled genomes recovered from deep metagenomic sequencing of the seagrass,Microbial genomics · 2026Article
- Oomycete plant pathogens: biology, pathogenesis and emerging control strategies.Nature reviews. Microbiology · 2026Review
- Parallel adaptation and admixture drive the evolution of virulence in the grapevine downy mildew pathogen.PLoS pathogens · 2026Article
- Powdery Scab of Potato: An Evaluation of Current Molecular Resources.Environmental microbiology reports · 2026Review
- Phylogenomics of Plasmopara halstedii Reveals Genomic Regions Associated With the Breakdown of Sunflower Downy Mildew Resistance Genes.Molecular ecology · 2026Article
- Chromosome-scale assembly and annotation of Phytophthora capsici isolate BYA5.Scientific data · 2026Article
- Pathogenicity and virulence ofVirulence · 2025Review
- Bioluminescent imaging of an oomycete pathogen empowers chemical selections and rational fungicide applications.Plant methods · 2025Article
- Recombination landscape and karyotypic variations revealed by linkage mapping in the grapevine downy mildew pathogen Plasmopara viticola.G3 (Bethesda, Md.) · 2025Article
- Gene Editing and Protein Tagging in the Oomycete Phytophthora infestans Using CRISPR-Cas12a.Methods in molecular biology (Clifton, N.J.) · 2025Article
- RNA Silencing Strategies in Phytophthora: Experimental Guidelines and Insights.Methods in molecular biology (Clifton, N.J.) · 2025Article
- A pangenome analysis reveals the center of origin and evolutionary history of Phytophthora infestans and 1c clade species.PloS one · 2025Article
- Promoter Analysis and Dissection Using Reporter Genes, Comparative Genomics, and Gel Shift Assays in Phytophthora.Methods in molecular biology (Clifton, N.J.) · 2025Article
- Pangenome graph analysis reveals extensive effector copy-number variation in spinach downy mildew.PLoS genetics · 2024Article
- Viable protoplast isolation, organelle visualization and transformation of the globally distributed plant pathogen Phytophthora cinnamomi.Protoplasma · 2024Article
- Evolution of Phytophthora infestans on its potato host since the Irish potato famine.Nature communications · 2024Article
- Transcription factor binding specificities of the oomycete Phytophthora infestans reflect conserved and divergent evolutionary patterns and predict function.BMC genomics · 2024Article
- Comparative genomics of the closely related fungal genera Cryptococcus and Kwoniella reveals karyotype dynamics and suggests evolutionary mechanisms of pathogenesis.PLoS biology · 2024Article
- Complete telomere-to-telomere genomes uncover virulence evolution conferred by chromosome fusion in oomycete plant pathogens.Nature communications · 2024Article
- Comparative genomics ofbioRxiv : the preprint server for biology · 2024Article
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4 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
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.
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