Data From: Two Novel Species of Pestalotiopsis Fungi on Picea and Tsuga from Temperate Forests in the United States
In a 2023 survey evaluating conifers with Rosellinia infections, five Pestalotiopsis-like fungal endophytes were isolated from plant samples obtained from Maine, New Hampshire, and Ohio by The Mycology & Nematology Genetic Diversity & Biology Laboratory at the United States Department of Agriculture. The two data sets provided herein contain species-specific base pair substitutions for the partial translation elongation factor 1-alpha gene (TEF). In the alignments, the novel Pestalotiopsis fungi are compared to their most closely related species. The data set can be used as a diagnostic tool to differentiate between the closely related species.
DNA was extracted from fungal samples using the E.Z.N.A HP Plant & Fungal DNA Kit (OMEGA® Bio-Tek, Norcross, GA, USA) following manufacturer’s protocol. The TEF locus was amplified, and reactions were conducted in 25 μL volumes with 12.5 μL of KAPA2G Robust Hotstart® (Kapa Biosystems, Inc., Wilmington, MA, USA), 1.25 μL of the forward and reverse primers at 10 μM, 1-1.75 μL of DNA at 10-20 ng, and 8 μL of molecular grade H2O. Amplifications were performed following the protocol described by Maharachchikumbura et al. (2014) in a C1000 Touch PCR Thermal Cycler (Bio-Rad, Hercules, CA). PCR products were analyzed through capillary electrophoresis with the QIAxcel Advanced System instrument and the QIAxcel ScreenGel software (Qiagen, Hilden, Germany). PCR products were then purified using ExoSAP-IT Cleanup (Affymetrix, Santa Clara, CA) following the manufacturer’s protocol. The BigDye™ 3.1 Terminator Cycle sequencing kit was used to sequence amplicons bi-directionally with the Applied Biosystems SeqStudio Genetic Analyzer (Thermo Fisher Scientific, Waltham, MA, USA).
Resources in this dataset:
- Resource Title: TEF P. neohantoniensis alignment, File Name: TEF_P. neohantoniensis alignment, Resource Description: Alignment of TEF DNA sequences for species closely related to Pestalotiopsis neohantoniensis.
- Resource Title: TEF P. maineana alignment, File Name: TEF_P. maineana alignment, Resource Description: Alignment of TEF DNA sequences for species closely related to Pestalotiopsis maineana.
Funding
USDA-ARS: 8042-22000-323-000-D
History
Data contact name
Miller, Stephan, T.Data contact email
stephantomasmi@gmail.comPublisher
Ag Data CommonsIntended use
This dataset will allow the repeatability of methods used to identify this new species of Pestalotiopsis which are closely related to the novel species described herein. Alignments can be downloaded, and new sequences can be added to compare species-specific base pare substitutions.Use limitations
Users have to consult the publication to obtain more important information, such as accession numbers at other data repositories.Temporal Extent Start Date
2024-01-01Theme
- Not specified
Geographic location - description
New species were collected from Maine and New Hampshire. Refer to publications for detailed collection information.ISO Topic Category
- biota
National Agricultural Library Thesaurus terms
Pestalotiopsis; fungi; Picea; Tsuga; temperate forests; United States; new species; data collection; DNA; nucleotide sequences; diagnostic techniquesOMB Bureau Code
- 005:18 - Agricultural Research Service
OMB Program Code
- 005:040 - National Research
ARS National Program Number
- 303
ARIS Log Number
424468Pending citation
- Yes
Public Access Level
- Public