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Alternative splicing in the obligate biotrophic oomycete pathogen, Pseudoperonospora cubensis

Creator:: Cumbie, Jason S.
Abstract:: Oomycetes are some of the most devastating pathogens, causing upwards of billions of dollars of damage each year to plants. They also diminish ecological diversity and health through the destruction of trees and shrubs. The genome sequence of Pseudoperonospora cubensis, an obligate plant pathogen and causative agent of downy mildew...
Resource Type:: Dissertation
Full Text:: AN ABSTRACT OF THE DISSERTATION OF Jason S. Cumbie for the degree of Doctor of Philosophy in

Improved DNase‑seq protocol facilitates high resolution mapping of DNase I hypersensitive sites in roots in Arabidopsis thaliana

Creator:: Cumbie, Jason S., Filichkin, Sergei A., and Megraw, Molly
Abstract:: Background: Identifying cis-regulatory elements is critical in understanding the direct and indirect regulatory mechanisms of gene expression. Current approaches include DNase-seq, a technique that combines sensitivity to the nonspecific endonuclease DNase I with high throughput sequencing to identify regions of regulatory DNA on a genome-wide scale. While this method was...
Resource Type:: Article
Full Text:: facilitates high resolution mapping of DNase I hypersensitive sites in roots in Arabidopsis thaliana Jason S

Updates_supplementalTable.csv

Creator:: Burkhardt, Alyssa, Buchanan, Alex, Cumbie, Jason S., Savory, Elizabeth, A., Chang, Jeff H., and Day, Brad
Abstract:: We re-sequenced the Pseudoperonospora cubensis transcriptome to provide the first extensive transcriptome-wide survey of alternative splicing in an obligate biotrophic pathogen during host infection. The libraries from biological replicates of cucumber leaves infected with Ps. cubensis for 2, 3, 4, and 8 days post inoculation (dpi) were re-sequenced using 100-mer...

rename_map.csv

Creator:: Burkhardt, Alyssa, Buchanan, Alex, Cumbie, Jason S., Savory, Elizabeth, A., Chang, Jeff H., and Day, Brad
Abstract:: We re-sequenced the Pseudoperonospora cubensis transcriptome to provide the first extensive transcriptome-wide survey of alternative splicing in an obligate biotrophic pathogen during host infection. The libraries from biological replicates of cucumber leaves infected with Ps. cubensis for 2, 3, 4, and 8 days post inoculation (dpi) were re-sequenced using 100-mer...

PCU_annotation.gff

Creator:: Burkhardt, Alyssa, Buchanan, Alex, Cumbie, Jason S., Savory, Elizabeth, A., Chang, Jeff H., and Day, Brad
Abstract:: We re-sequenced the Pseudoperonospora cubensis transcriptome to provide the first extensive transcriptome-wide survey of alternative splicing in an obligate biotrophic pathogen during host infection. The libraries from biological replicates of cucumber leaves infected with Ps. cubensis for 2, 3, 4, and 8 days post inoculation (dpi) were re-sequenced using 100-mer...

Alternative Splicing in the Obligate Biotrophic Oomycete Pathogen Pseudoperonospora cubensis

Creator:: Burkhardt, Alyssa, Buchanan, Alex, Cumbie, Jason S., Savory, Elizabeth A., Chang, Jeff H., and Day, Brad
Abstract:: Pseudoperonospora cubensis is an obligate pathogen and causative agent of cucurbit downy mildew. To help advance our understanding of the pathogenicity of P. cubensis, we used RNA-Seq to improve the quality of its reference genome sequence. We also characterized the RNA-Seq dataset to inventory transcript isoforms and infer alternative splicing...
Resource Type:: Article
Full Text:: Oomycete Pathogen Pseudoperonospora cubensis Alyssa Burkhardt,1 Alex Buchanan,2 Jason S. Cumbie,2,3

Alternative splicing in the obligate biotrophic oomycete pathogen, Pseudoperonospora cubensis

Creator:: Burkhardt, Alyssa, Buchanan, Alex, Cumbie, Jason S., Savory, Elizabeth A., Chang, Jeff H., and Day, Brad
Abstract:: We re-sequenced the Pseudoperonospora cubensis transcriptome to provide the first extensive transcriptome-wide survey of alternative splicing in an obligate biotrophic pathogen during host infection. The libraries from biological replicates of cucumber leaves infected with Ps. cubensis for 2, 3, 4, and 8 days post inoculation (dpi) were re-sequenced using 100-mer...
Resource Type:: Dataset

Length Bias Correction in Gene Ontology Enrichment Analysis Using Logistic Regression

Creator:: Mi, Gu, Di, Yanming, Emerson, Sarah, Cumbie, Jason S., and Chang, Jeff H.
Abstract:: When assessing differential gene expression from RNA sequencing data, commonly used statistical tests tend to have greater power to detect differential expression of genes encoding longer transcripts. This phenomenon, called "length bias", will influence subsequent analyses such as Gene Ontology enrichment analysis. In the presence of length bias, Gene Ontology...
Resource Type:: Article
Full Text:: Enrichment Analysis Using Logistic Regression Gu Mi1*, Yanming Di1,2, Sarah Emerson1, Jason S. Cumbie2,3

Genome-Wide Profiling and Analysis of Arabidopsis siRNAs

Creator:: Kasschau, Kristin D., Fahlgren, Noah, Chapman, Elisabeth J., Sullivan, Christopher M., Cumbie, Jason S., Givan, Scott A., and Carrington, James C.
Abstract:: Eukaryotes contain a diversified set of small RNA-guided pathways that control genes, repeated sequences, and viruses at the transcriptional and posttranscriptional levels. Genome-wide profiles and analyses of small RNAs, particularly the large class of 24-nucleotide (nt) short interfering RNAs (siRNAs), were done for wild-type Arabidopsis thaliana and silencing pathway mutants...
Resource Type:: Article
Full Text:: . Sullivan 1,2 , Jason S. Cumbie 1,2 , Scott A. Givan 1,2 , James C. Carrington 1,2* 1 Center for Genome

CumbieJasonBotanyPlantPathologyVariableSuitesNon-Effector.pdf

Creator:: Mucyn, Tatiana S., Yourstone, Scott, Lind, Abigail L., Biswas, Surojit, Nishimura, Marc T., Baltrus, David A., Cumbie, Jason S., Chang, Jeff H., Jones, Corbin D., Dangl, Jeffery L., and Grant, Sarah R.
Abstract:: Pseudomonas syringae is a phylogenetically diverse species of Gram-negative bacterial plant pathogens responsible for crop diseases around the world. The HrpL sigma factor drives expression of the major P. syringae virulence regulon. HrpL controls expression of the genes encoding the structural and functional components of the type III secretion system...
Full Text:: . Baltrus3, Jason S. Cumbie4,5, Jeff H. Chang4,5,6, Corbin D. Jones1,2,7,8,9, Jeffery L. Dangl1,2,7,9,10,11

ScholarsArchive@OSU

Alternative splicing in the obligate biotrophic oomycete pathogen, Pseudoperonospora cubensis

Improved DNase‑seq protocol facilitates high resolution mapping of DNase I hypersensitive sites in roots in Arabidopsis thaliana

Updates_supplementalTable.csv

rename_map.csv

PCU_annotation.gff

Alternative Splicing in the Obligate Biotrophic Oomycete Pathogen Pseudoperonospora cubensis

Alternative splicing in the obligate biotrophic oomycete pathogen, Pseudoperonospora cubensis

Length Bias Correction in Gene Ontology Enrichment Analysis Using Logistic Regression

Genome-Wide Profiling and Analysis of Arabidopsis siRNAs

CumbieJasonBotanyPlantPathologyVariableSuitesNon-Effector.pdf

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