Data From: Two Novel Species of <i>Pestalotiopsis</i> Fungi on <i>Picea</i> and <i>Tsuga </i>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.
Resources
2 resources available
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TEF_P. neohantoniensis alignment.txt
TXT -
TEF_P. maineana alignment.txt
TXT
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Complete Metadata
| @type | dcat:Dataset |
|---|---|
| accessLevel | public |
| bureauCode |
[ "005:18" ] |
| contactPoint |
{ "fn": "Miller, Stephan, T.", "hasEmail": "mailto:stephantomasmi@gmail.com" } |
| description | <p dir="ltr">In a 2023 survey evaluating conifers with <i>Rosellinia </i>infections, five <i>Pestalotiopsis</i>-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 (<i>TEF)</i>. In the alignments, the novel <i>Pestalotiopsis</i> 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. </p><p dir="ltr">DNA was extracted from fungal samples using the E.Z.N.A HP Plant & Fungal DNA Kit (OMEGA<sup>® </sup>Bio-Tek, Norcross, GA, USA) following manufacturer’s protocol. The <i>TEF </i>locus was amplified, and reactions were conducted in 25 μL volumes with 12.5 μL of KAPA2G Robust Hotstart<sup>® </sup>(Kapa Biosystems, Inc., Wilmington, MA, USA), 1.25<sup> </sup>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 H<sub>2</sub>O. Amplifications were performed following the protocol described by Maharachchikumbura <i>et al.</i> (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).</p><p dir="ltr">Resources in this dataset:</p><ul><li>Resource Title: TEF <i>P. neohantoniensis</i> alignment, File Name: TEF_<i>P. neohantoniensis</i> alignment, Resource Description: Alignment of <i>TEF</i> DNA sequences for species closely related to <i>Pestalotiopsis neohantoniensis</i>.</li><li>Resource Title: TEF <i>P</i><i>. maineana</i> alignment, File Name: TEF_<i>P. maineana</i> alignment, Resource Description: Alignment of <i>TEF</i> DNA sequences for species closely related to <i>Pestalotiopsis maineana.</i></li></ul><p dir="ltr"><br></p><p dir="ltr"><br></p> |
| distribution |
[ { "@type": "dcat:Distribution", "title": "TEF_P. neohantoniensis alignment.txt", "format": "txt", "mediaType": "text/plain", "downloadURL": "https://ndownloader.figshare.com/files/53127404" }, { "@type": "dcat:Distribution", "title": "TEF_P. maineana alignment.txt", "format": "txt", "mediaType": "text/plain", "downloadURL": "https://ndownloader.figshare.com/files/53127407" } ] |
| identifier | 10.15482/USDA.ADC/28263920.v1 |
| keyword |
[ "Ascomycota", "Endophyte", "Pestalotiopsis", "Sporocadaceae" ] |
| license | https://www.usa.gov/publicdomain/label/1.0/ |
| modified | 2025-08-15 |
| programCode |
[ "005:040" ] |
| publisher |
{ "name": "Agricultural Research Service", "@type": "org:Organization" } |
| temporal | 2024-01-01/2024-01-01 |
| title | Data From: Two Novel Species of <i>Pestalotiopsis</i> Fungi on <i>Picea</i> and <i>Tsuga </i>from Temperate Forests in the United States |
