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.

• Resource Title: Phytophthora infestans supercontig_1.1 variants.

  File Name: sc1_corephased.vcf.gz

  Resource Description: Phytophthora infestans supercontig_1.1 variants: Sequence data for superconti_1.1 from the Phytophthora infestans reference genome of strain T30-4.

  Resource Software Recommended: GATK,url: https://www.broadinstitute.org/gatk/




• Resource Title: Phytophthora infestans supercontig_1.5 variants.

  File Name: sc5_corephased.vcf.gz

  Resource Description: Phytophthora infestans supercontig_1.5 variants: Sequence data for superconti_1.5 from the Phytophthora infestans reference genome of strain T30-4.

  Resource Software Recommended: GATK,url: https://www.broadinstitute.org/gatk/




• Resource Title: Phytophthora infestans SSR data.

  File Name: pinf_ssrs.csv

  Resource Description: Phytophthora infestans SSR data: Microsatellite data for a population of strains.

  Resource Software Recommended: poppr R package,url: https://cran.r-project.org/web/packages/poppr/index.html




• Resource Title: PITG_Supercontig_1.MT_noindels.fasta.

  File Name: PITG_Supercontig_1.MT_noindels.fasta

  Resource Description: PITG_Supercontig_1.MT_noindels.fasta: Whole genome mitochondrial for a population of strains.

  Phytophthora infestans mitochondrial DNA sequences for US clonal lineages




• Resource Title: PITG_00142.fasta.

  File Name: PITG_00142.fasta

  Resource Description: Phytophthora infestans alignment for predicted gene NEP1 (PITG_00142).

  More information on gene PITG_00142 can be found on UniProt: http://www.uniprot.org/uniprot/D0MSZ9




• Resource Title: PITG_00156.fasta.

  File Name: PITG_00156.fasta

  Resource Description: Phytophthora infestans alignment for the gene Beta-tubulin (PITG_00156).

  More information on gene PITG_00156 can be found on UniProt: http://www.uniprot.org/uniprot/D0MT13




• Resource Title: PITG_00953.fasta.

  File Name: PITG_00953.fasta

  Resource Description: Phytophthora infestans alignment for predicted gene trafficking protein particle complex subunit 6B (PITG_00953).

  More information on gene PITG_00953 is available on UniProt: http://www.uniprot.org/uniprot/D0MS35




• Resource Title: PITG_04066.fasta.

  File Name: PITG_04066.fasta

  Resource Description: Phytophthora infestans alignment for predicted gene serin S09X (PITG_04066).

  More information on gene PITG_04066 can be found on UniProt: http://www.uniprot.org/uniprot/D0N0G9




• Resource Title: PITG_04424.fasta.

  File Name: PITG_04424.fasta

  Resource Description: Phytophthora infestans alignment for predicted gene SNARE (PITG_04424).

  More information on gene PITG_04424 is available on UniProt: http://www.uniprot.org/uniprot/D0N182




• Resource Title: PITG_11126.fasta.

  File Name: PITG_11126.fasta

  Resource Description: Phytophthora infestans alignment for a conserved hypothetical protein (PITG_11126).

  More information on gene PITG_11126 can be found on UniProt: http://www.uniprot.org/uniprot/D0NG88