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Data from: Characterization of Pythium spp. associated with asymptomatic soybeans in southeastern Pennsylvania

Main Authors: Coffua, Lauren S., Veterano, S. Tyler, Clipman, Steven J., Mena-Ali, Jorge I., Blair, Jaime E.
Format: info dataset Journal
Terbitan: , 2017
Subjects:
Soybean
Pythium
oomycetes
pyrosequencing
Online Access: https://zenodo.org/record/4965239
ctrlnum 4965239
fullrecord <?xml version="1.0"?> <dc schemaLocation="http://www.openarchives.org/OAI/2.0/oai_dc/ http://www.openarchives.org/OAI/2.0/oai_dc.xsd"><creator>Coffua, Lauren S.</creator><creator>Veterano, S. Tyler</creator><creator>Clipman, Steven J.</creator><creator>Mena-Ali, Jorge I.</creator><creator>Blair, Jaime E.</creator><date>2017-01-28</date><description>Soybean production in Pennsylvania has increased substantially over the past twenty years and is a highly valued field crop together with corn. Soilborne pathogens such as Pythium spp. can contribute to soybean stand establishment issues, particularly under the conservation tillage practices that are common in the state. In this study, we collected soil samples from eight asymptomatic soybean-corn rotation fields across six counties in southeastern Pennsylvania between May and June, 2012. Pythium species were isolated via baiting, and tested for aggressiveness on both soybean and corn using laboratory pathogenicity assays. In addition to our culture-based survey, we also assessed the use of cytochrome oxidase subunit 1 (COI) pyrosequencing as a culture-independent method for measuring Pythium species diversity from environmental samples. Diversity estimates were consistent between the culture-based and pyrosequencing datasets; however, important methodological biases inherent to culture-independent methods may have led to some differences. Our results show that several Pythium species previously characterized as soybean and/or corn pathogens are present in southeastern Pennsylvania, including P. irregulare, P. sylvaticum, and P. ultimum var. sporangiiferum, with isolates showing aggressive phenotypes in lab assays.</description><description>COI alignmentCOI alignment file in Nexus format. NCBI block included after data block, which gives organism and isolation information for each sequence (as submitted to GenBank).C12Cox1_Data.nexusCOI alignment MEGA formatCOI alignment formatted for analysis in MEGA. Missing data coded as '?'C12Cox1_Data.megCOI Neighbor-joining TreeNewick format tree file from neighbor-joining analysis in MEGA (Kimura 2-Parameter model, pairwise deletion of gaps/missing data).C12_NJ_K2P_pairwisedeletion.nwkCOI Neighbor-joining Tree with Species LabelsPDF file of tree from neighbor-joining analysis with species (or aff) designations labeled.SpeciesLabeled.pdfCOI alignment with Reference Sequences in MEGA formatPythium (and select other oomycetes) included with COI sequences generated here. Sequences were obtained from NCBI.Cox1_C12plusRefs.megCOI Neighbor-joining Tree with Reference SequencesPDF of neighbor-joining tree from alignment with Pythium and other oomycete reference sequences included.Cox1NJtree_C12plusRefs.pdf</description><identifier>https://zenodo.org/record/4965239</identifier><identifier>10.5061/dryad.3s4d3</identifier><identifier>oai:zenodo.org:4965239</identifier><relation>doi:10.1094/PDIS-11-15-1355-RE</relation><relation>url:https://zenodo.org/communities/dryad</relation><rights>info:eu-repo/semantics/openAccess</rights><rights>https://creativecommons.org/publicdomain/zero/1.0/legalcode</rights><subject>Soybean</subject><subject>Pythium</subject><subject>oomycetes</subject><subject>pyrosequencing</subject><title>Data from: Characterization of Pythium spp. associated with asymptomatic soybeans in southeastern Pennsylvania</title><type>Other:info:eu-repo/semantics/other</type><type>Other:dataset</type><recordID>4965239</recordID></dc>
format Other:info:eu-repo/semantics/other
Other
Other:dataset
Journal:Journal
Journal
author Coffua, Lauren S.
Veterano, S. Tyler
Clipman, Steven J.
Mena-Ali, Jorge I.
Blair, Jaime E.
title Data from: Characterization of Pythium spp. associated with asymptomatic soybeans in southeastern Pennsylvania
publishDate 2017
topic Soybean
Pythium
oomycetes
pyrosequencing
url https://zenodo.org/record/4965239
contents Soybean production in Pennsylvania has increased substantially over the past twenty years and is a highly valued field crop together with corn. Soilborne pathogens such as Pythium spp. can contribute to soybean stand establishment issues, particularly under the conservation tillage practices that are common in the state. In this study, we collected soil samples from eight asymptomatic soybean-corn rotation fields across six counties in southeastern Pennsylvania between May and June, 2012. Pythium species were isolated via baiting, and tested for aggressiveness on both soybean and corn using laboratory pathogenicity assays. In addition to our culture-based survey, we also assessed the use of cytochrome oxidase subunit 1 (COI) pyrosequencing as a culture-independent method for measuring Pythium species diversity from environmental samples. Diversity estimates were consistent between the culture-based and pyrosequencing datasets; however, important methodological biases inherent to culture-independent methods may have led to some differences. Our results show that several Pythium species previously characterized as soybean and/or corn pathogens are present in southeastern Pennsylvania, including P. irregulare, P. sylvaticum, and P. ultimum var. sporangiiferum, with isolates showing aggressive phenotypes in lab assays.
COI alignmentCOI alignment file in Nexus format. NCBI block included after data block, which gives organism and isolation information for each sequence (as submitted to GenBank).C12Cox1_Data.nexusCOI alignment MEGA formatCOI alignment formatted for analysis in MEGA. Missing data coded as '?'C12Cox1_Data.megCOI Neighbor-joining TreeNewick format tree file from neighbor-joining analysis in MEGA (Kimura 2-Parameter model, pairwise deletion of gaps/missing data).C12_NJ_K2P_pairwisedeletion.nwkCOI Neighbor-joining Tree with Species LabelsPDF file of tree from neighbor-joining analysis with species (or aff) designations labeled.SpeciesLabeled.pdfCOI alignment with Reference Sequences in MEGA formatPythium (and select other oomycetes) included with COI sequences generated here. Sequences were obtained from NCBI.Cox1_C12plusRefs.megCOI Neighbor-joining Tree with Reference SequencesPDF of neighbor-joining tree from alignment with Pythium and other oomycete reference sequences included.Cox1NJtree_C12plusRefs.pdf
id IOS16997.4965239
institution ZAIN Publications
institution_id 7213
institution_type library:special
library
library Cognizance Journal of Multidisciplinary Studies
library_id 5267
collection Cognizance Journal of Multidisciplinary Studies
repository_id 16997
subject_area Multidisciplinary
city Stockholm
province INTERNASIONAL
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repoId IOS16997
first_indexed 2022-06-06T05:24:29Z
last_indexed 2022-06-06T05:24:29Z
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