In:
PLOS Pathogens, Public Library of Science (PLoS), Vol. 18, No. 10 ( 2022-10-10), p. e1010869-
Kurzfassung:
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.
Materialart:
Online-Ressource
ISSN:
1553-7374
DOI:
10.1371/journal.ppat.1010869
DOI:
10.1371/journal.ppat.1010869.g001
DOI:
10.1371/journal.ppat.1010869.g002
DOI:
10.1371/journal.ppat.1010869.g003
DOI:
10.1371/journal.ppat.1010869.g004
DOI:
10.1371/journal.ppat.1010869.g005
DOI:
10.1371/journal.ppat.1010869.g006
DOI:
10.1371/journal.ppat.1010869.g007
DOI:
10.1371/journal.ppat.1010869.g008
DOI:
10.1371/journal.ppat.1010869.g009
DOI:
10.1371/journal.ppat.1010869.g010
DOI:
10.1371/journal.ppat.1010869.s001
DOI:
10.1371/journal.ppat.1010869.s002
DOI:
10.1371/journal.ppat.1010869.s003
DOI:
10.1371/journal.ppat.1010869.s004
DOI:
10.1371/journal.ppat.1010869.s005
DOI:
10.1371/journal.ppat.1010869.s006
DOI:
10.1371/journal.ppat.1010869.s007
DOI:
10.1371/journal.ppat.1010869.s008
DOI:
10.1371/journal.ppat.1010869.s009
DOI:
10.1371/journal.ppat.1010869.s010
DOI:
10.1371/journal.ppat.1010869.s011
DOI:
10.1371/journal.ppat.1010869.s012
DOI:
10.1371/journal.ppat.1010869.s013
DOI:
10.1371/journal.ppat.1010869.s014
DOI:
10.1371/journal.ppat.1010869.s015
DOI:
10.1371/journal.ppat.1010869.s016
DOI:
10.1371/journal.ppat.1010869.s017
DOI:
10.1371/journal.ppat.1010869.r001
DOI:
10.1371/journal.ppat.1010869.r002
DOI:
10.1371/journal.ppat.1010869.r003
DOI:
10.1371/journal.ppat.1010869.r004
Sprache:
Englisch
Verlag:
Public Library of Science (PLoS)
Publikationsdatum:
2022
ZDB Id:
2205412-1
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