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Data from: Genomic analyses of dominant US clonal lineages of Phytophthora infestans reveals a shared ancestry for US11 and US18 and a lack of recently shared ancestry for all other US lineages

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.

Dataset Info

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Knaus, Brian
Tabima, Javier
Judelson, Howard
Grünwald, Niklaus
Product Type
Genome/Genetics Data
Contact Name
Grunwald, Niklaus
Contact Email
Public Access Level
Primary Article

Knaus, B. J., Tabima, J. F., Davis, C. E., Judelson, H. S. and Grünwald, N. J. (2016). Genomic Analyses of Dominant U.S. Clonal Lineages of Phytophthora infestans Reveals a Shared Common Ancestry for Clonal Lineages US11 and US18 and a Lack of Recently Shared Ancestry Among All Other U.S. Lineages. Phytopathology, 106(11), 1393-1403

Funding Source(s)
Agricultural Research Service
Dataset DOI (digital object identifier)
Program Code
005:037 - Department of Agriculture - Research and Education
Bureau Code
005:00 - Department of Agriculture
ARIS Log Number
322 568
Modified Date
Release Date
Ag Data Commons Keywords: 
  • Agroecosystems & Environment
  • Agroecosystems & Environment
  • Invasive species
  • Genomics & Genetics
  • Genomics & Genetics
  • Genome
  • Genomics & Genetics
  • Variants
  • Plants & Crops
  • Plants & Crops
  • Plant health
State or Territory: 
ISO Topic(s):