{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,30]],"date-time":"2026-09-30T20:40:26Z","timestamp":1790800826774,"version":"4.1.0"},"update-to":[{"DOI":"10.1371\/journal.ppat.1010869","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2022,10,20]],"date-time":"2022-10-20T00:00:00Z","timestamp":1666224000000}}],"reference-count":122,"publisher":"Public Library of Science (PLoS)","issue":"10","license":[{"start":{"date-parts":[[2022,10,10]],"date-time":"2022-10-10T00:00:00Z","timestamp":1665360000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/publicdomain\/zero\/1.0\/"}],"funder":[{"DOI":"10.13039\/100000001","name":"National Science Foundation","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100000001","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100005825","name":"National Institute of Food and Agriculture","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100005825","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000001","name":"National Science Foundation","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100000001","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["www.plospathogens.org"],"crossmark-restriction":false},"short-container-title":["PLoS Pathog"],"abstract":"<jats:p>\n                    Natural isolates of the potato and tomato pathogen\n                    <jats:italic>Phytophthora infestans<\/jats:italic>\n                    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.\n                    <jats:italic>De novo<\/jats:italic>\n                    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\n                    <jats:italic>P<\/jats:italic>\n                    .\n                    <jats:italic>infestans<\/jats:italic>\n                    and relatives, helps explain the prevalence of polyploidy in natural populations, and provides a new foundation for biologic and genetic investigations.\n                  <\/jats:p>","DOI":"10.1371\/journal.ppat.1010869","type":"journal-article","created":{"date-parts":[[2022,10,10]],"date-time":"2022-10-10T13:58:59Z","timestamp":1665410339000},"page":"e1010869","update-policy":"https:\/\/doi.org\/10.1371\/journal.ppat.corrections_policy","source":"Crossref","is-referenced-by-count":46,"title":["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"],"prefix":"10.1371","volume":"18","author":[{"given":"Michael E. H.","family":"Matson","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Qihua","family":"Liang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Stefano","family":"Lonardi","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7865-6235","authenticated-orcid":true,"given":"Howard S.","family":"Judelson","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"340","published-online":{"date-parts":[[2022,10,10]]},"reference":[{"key":"ppat.1010869.ref001","doi-asserted-by":"crossref","first-page":"158","DOI":"10.1016\/j.mib.2019.11.001","article-title":"A titanic drug resistance threat in Cryptococcus neoformans","volume":"52","author":"H Zafar","year":"2019","journal-title":"Curr Opin Microbiol"},{"issue":"4","key":"ppat.1010869.ref002","doi-asserted-by":"crossref","first-page":"601","DOI":"10.1111\/ppa.13166","article-title":"Mechanisms of powdery mildew resistance of wheat\u2014a review of molecular breeding","volume":"69","author":"YC Kang","year":"2020","journal-title":"Plant Pathol"},{"key":"ppat.1010869.ref003","doi-asserted-by":"crossref","DOI":"10.1186\/s12864-018-4598-9","article-title":"Mapping QTL for white striping in relation to breast muscle yield and meat quality traits in broiler chickens","volume":"19","author":"E Pampouille","year":"2018","journal-title":"BMC Genomics"},{"issue":"7789","key":"ppat.1010869.ref004","doi-asserted-by":"crossref","first-page":"179","DOI":"10.1038\/s41586-019-1879-7","article-title":"A brief history of human disease genetics","volume":"577","author":"M Claussnitzer","year":"2020","journal-title":"Nature"},{"issue":"1","key":"ppat.1010869.ref005","doi-asserted-by":"crossref","first-page":"70","DOI":"10.1016\/j.cell.2019.02.032","article-title":"Genomic analysis in the age of human genome sequencing","volume":"177","author":"T Lappalainen","year":"2019","journal-title":"Cell"},{"key":"ppat.1010869.ref006","doi-asserted-by":"crossref","first-page":"57","DOI":"10.1016\/j.gde.2015.09.001","article-title":"The two-speed genomes of filamentous pathogens: waltz with plants","volume":"35","author":"SM Dong","year":"2015","journal-title":"Curr Opin Genet Dev"},{"key":"ppat.1010869.ref007","doi-asserted-by":"crossref","first-page":"175","DOI":"10.1016\/bs.adgen.2020.03.001","article-title":"Recent advances in oomycete genomics","volume":"105","author":"J McGowan","year":"2020","journal-title":"Adv Genet"},{"key":"ppat.1010869.ref008","first-page":"562","volume-title":"Phytophthora diseases worldwide","author":"DC Erwin","year":"1996"},{"issue":"7262","key":"ppat.1010869.ref009","doi-asserted-by":"crossref","first-page":"393","DOI":"10.1038\/nature08358","article-title":"Genome sequence and analysis of the Irish potato famine pathogen Phytophthora infestans","volume":"461","author":"BJ Haas","year":"2009","journal-title":"Nature"},{"issue":"3","key":"ppat.1010869.ref010","doi-asserted-by":"crossref","first-page":"1074","DOI":"10.1111\/nph.17828","article-title":"Oomycete intracellular effectors: specialised weapons targeting strategic plant processes","volume":"233","author":"G. 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