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. |
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| Format: | info dataset Journal |
| Terbitan: |
, 2017
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| Subjects: | |
| Online Access: |
https://zenodo.org/record/4965239 |
Daftar Isi:
- 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