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Data from: Plasmopara echinaceae, a new species of downy mildew affecting cone flowers (Echinacea purpurea) in the United States

A new species of downy mildew (Oomycota, Peronosporales) is reported. This dataset contains alignments of DNA sequences (cox2 and LSU) markers, alignment of cox2 marker to be used in species identification and resulting phylogenetic trees.

Resources in this dataset:

  • Resource Title: Alignment Cox2 dataset
    File Name: Cox2_EchDM_final_alignment.fasta
    Resource Description: Alignment of Cox2 DNA sequences.

  • Resource Title: Alignment LSU dataset
    File Name: LSU_EchDM_final_alignment.fasta
    Resource Description: Alignment of LSU DNA sequences.

  • Resource Title: Alignment Cox2 dataset Barcoding
    File Name: Cox2_EchDM_Genetic_differences_alignment.fasta
    Resource Description: Alignment of cox2 marker to be used in species identification and resulting phylogenetic trees.

See all >>
FieldValue
Tags
downy mildew
Plasmopara
oomycete pathogen
Peronosporales
Alignments
cox2
LSU
new species
phylogenetic analysis
phylogenetic trees
NP303
Modified
2023-08-07
Release Date
2023-07-07
Identifier
0e5c3712-dad6-46fd-8bc6-6fd42349a617
Spatial / Geographical Coverage Area
POINT (-89.329284676351 43.218237471232)
Publisher
Ag Data Commons
Spatial / Geographical Coverage Location
New species of downy mildew was originally collected in Jefferson County, WI
Temporal Coverage
August 22, 2022
License
Creative Commons CCZero
Contact Name
Salgado-Salazar, Catalina
Contact Email
catalina.salgado@usda.gov
Public Access Level
Public
Program Code
005:040 - Department of Agriculture - National Research
Bureau Code
005:18 - Agricultural Research Service
Extended Metadata: 
FieldValue
Authors
Romberg, Megan K. (ORCID)
Hudelson, Brian (Scopus Author ID)
Salgado-Salazar, Catalina (ORCID)
Peer Reviewed
No
Intended Use
This dataset will allow the repeatability of methods used to identify this new species of downy mildew. Alignments can be downloaded and new sequences can be added to perform phylogenetic analyses. An additional cox2 alignment is provided to help in the identification of this species based on species-specific single nucleotide polymorphisms.
Use Limitations
Users have to consult the publication to obtain more important information, such as accession numbers at other data repositories.
Equipment or Software Used
RAxML GUI v 2.0
Mafft Online Alignment Tool
Tree Figure Drawing Tool
Funding Sources
Agricultural Research Service
8042-22000-298-00-D
Dataset DOI (digital object identifier)
10.15482/USDA.ADC/1529170
Product Type
Dataset
FieldValue
OSTI Identifier
ISO Topic(s)
biota
State or Territory
Maryland
Wisconsin
National Agricultural Library Thesaurus Term
Plasmopara
new species
downy mildew
flowers
Echinacea purpurea
data collection
nucleotide sequences
ribosomal DNA
species identification
phylogeny
pathogens
single nucleotide polymorphism
Wisconsin
United States
Ag Data Commons Keywords
  • Agroecosystems & Environment
  • Agroecosystems & Environment
  • Agricultural pests
  • Plants & Crops
  • Plants & Crops
  • Plant health
  • Genomics & Genetics
  • Genomics & Genetics
  • Sequence Assembly
Program
AgBioData

Suggested Citation:

(dataset) Romberg, Megan K.; Hudelson, Brian; Salgado-Salazar, Catalina (2023). Data from: Plasmopara echinaceae, a new species of downy mildew affecting cone flowers (Echinacea purpurea) in the United States. Ag Data Commons. https://doi.org/10.15482/USDA.ADC/1529170. Accessed 2023-09-28.