The populations of the potato and tomato late blight pathogen, Phytophthora infestans, in the US are well known for emerging repeatedly as novel clonal lineages. These successions of dominant clones have historically been named US1 through US24, in order of appearance, since their first characterization using molecular markers. Hypothetically, these lineages can emerge by descent from prior lineages or as novel, independent lineages.
Phytophthora infestans US lineage diagnostic single nucleotide polymorphisms (SNP) data:
We tested for the presence of phylogenetic relationships using a population of 33 whole genome sequences including dominant US clonal lineages as well as available samples from global populations. We analyzed ancestry of the whole mitochondrial genome and samples of nuclear loci including supercontig 1.1 and 1.5 as well as several previously characterized coding regions. We found support for a shared mitochondrial and nuclear haplotype in the US11 and US18 lineages derived from either a common ancestor or one of the lineages. The other nuclear haplotype assort independently providing evidence for recombination. However, we found no support for emergence of any other lineages from a common ancestor shared with any other lineage. Each of the US clonal lineages fit a model where populations of new clonal lineages emerge via migration from a source population that is sexual in nature and potentially located in central Mexico or elsewhere. This work provides novel insights into patterns of emergence of clonal lineages in plant pathogen genomes.
- Phytophthora infestans supercontig_1.1 variantsData
Phytophthora infestans supercontig_1.1 variants: Sequence data for...
- Phytophthora infestans supercontig_1.5 variantsData
Phytophthora infestans supercontig_1.5 variants: Sequence data for...
- Phytophthora infestans SSR datacsv
Phytophthora infestans SSR data: Microsatellite data for a population of...
PITG_Supercontig_1.MT_noindels.fasta: Whole genome mitochondrial for a...
Phytophthora infestans alignment for predicted gene NEP1 (PITG_00142)....
Phytophthora infestans alignment for the gene￼ Beta-tubulin (PITG_00156)....
Phytophthora infestans alignment for predicted gene trafficking protein...
Phytophthora infestans alignment for predicted gene serin S09X (PITG_04066...
Phytophthora infestans alignment for predicted gene SNARE (PITG_04424)....
Phytophthora infestans alignment for a conserved hypothetical protein (...
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005:037 - Department of Agriculture - Research and Education
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005:00 - Department of Agriculture