title: 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.
abstract: Populations of the potato and tomato late-blight pathogen Phytophthora infestans are well known for emerging 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 through divergence from other U.S. lineages, recombination among lineages, or as novel, independent lineages originating outside the United States. We tested for the presence of phylogenetic relationships among U.S. lineages using a population of 31 whole-genome sequences, including dominant U.S. clonal lineages as well as available samples from global populations. We analyzed ancestry of the whole mitochondrial genome and samples of nuclear loci, including supercontigs 1.1 and 1.5 as well as several previously characterized coding regions. We found support for a shared ancestry among lineages US11 and US18 from the mitochondrial genome as well as from one nuclear haplotype on each supercontig analyzed. The other nuclear haplotype from each sample assorted independently, indicating an independent ancestry. We found no support for emergence of any other of the U.S. lineages from a common ancestor shared with the other U.S. lineages. Each of the U.S. 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.
authors.affiliation: First and fifth authors: Horticultural Crop Research Unit, United States Department of Agriculture-Agricultural Research Service, Corvallis, OR 97330; second and fifth authors: Department of Botany and Plant Pathology, Oregon State University, Corvallis 97331; and third and fourth authors: Department of Plant Pathology, University of California, Riverside 92521.
authors.forename: B J
authors.initials: BJ
authors.lastname: Knaus
authors.affiliation: First and fifth authors: Horticultural Crop Research Unit, United States Department of Agriculture-Agricultural Research Service, Corvallis, OR 97330; second and fifth authors: Department of Botany and Plant Pathology, Oregon State University, Corvallis 97331; and third and fourth authors: Department of Plant Pathology, University of California, Riverside 92521.
authors.forename: J F
authors.initials: JF
authors.lastname: Tabima
authors.affiliation: First and fifth authors: Horticultural Crop Research Unit, United States Department of Agriculture-Agricultural Research Service, Corvallis, OR 97330; second and fifth authors: Department of Botany and Plant Pathology, Oregon State University, Corvallis 97331; and third and fourth authors: Department of Plant Pathology, University of California, Riverside 92521.
authors.forename: C E
authors.initials: CE
authors.lastname: Davis
authors.affiliation: First and fifth authors: Horticultural Crop Research Unit, United States Department of Agriculture-Agricultural Research Service, Corvallis, OR 97330; second and fifth authors: Department of Botany and Plant Pathology, Oregon State University, Corvallis 97331; and third and fourth authors: Department of Plant Pathology, University of California, Riverside 92521.
authors.forename: H S
authors.initials: HS
authors.lastname: Judelson
authors.affiliation: First and fifth authors: Horticultural Crop Research Unit, United States Department of Agriculture-Agricultural Research Service, Corvallis, OR 97330; second and fifth authors: Department of Botany and Plant Pathology, Oregon State University, Corvallis 97331; and third and fourth authors: Department of Plant Pathology, University of California, Riverside 92521.
authors.forename: N J
authors.identifier: 0000-0003-1656-7602
authors.initials: NJ
authors.lastname: Grünwald
mesh_terms: D005075:Biological Evolution; D004272:DNA, Mitochondrial / Q000737:chemistry / Q000235:genetics; D054629:Genome, Mitochondrial / Q000235:genetics*; D023281:Genomics; D006239:Haplotypes; D059014:High-Throughput Nucleotide Sequencing; D018551:Solanum lycopersicum / Q000469:parasitology*; D016366:Open Reading Frames / Q000235:genetics; D010802:Phylogeny; D055750:Phytophthora infestans / Q000235:genetics* / Q000302:isolation & purification; D010935:Plant Diseases / Q000469:parasitology*; D017422:Sequence Analysis, DNA; D011198:Solanum tuberosum / Q000469:parasitology*
chemical_list: D004272:DNA, Mitochondrial