E counted using Image J. This was repeated twice.Salicylic acid measurementsAcknowledgements We thank ABRC for T-DNA mutant seeds, GCAT-SEEK for preliminary training on building RNA-seq RIP-seq libraries, Timothy Miguel for SEM training and the use of EM facility at Univ. of Maryland, College Park, Thomas W. Leary from DNASTAR for troubleshooting with Lasergene, and Dr. A.S.N. Reddy’s lab for the GFP Col-0 AZD-8055 supplier control seeds. Funding This work was supported by National Science Foundation (DBI-1146300 to X. Zhang, IOS-1456140 to H. Lu, and DBI-1564785 to S. M. Mount), research fund in Department of Biology at St. Bonaventure University, and The Fulbright Scholar Program and The Council for International Exchange of Scholars to H. M. M. Ibrahim. Availability of data and material All Arabidopsis wild type and mutant plants, sr45? (SALK_004132), upf3? (SALK_025175) and pad4? (CS3806) were originally from Arabidopsis Biological Resource Center (ABRC). All SR45 overexpression lines were published previously [3]. The sequence of all primers used in this study is listed in Supplemental Data Set 6. All RNA-seq and RIP-seq reads are stored as a BioProject (PRJNA382852) at NCBI Sequence Read Archive (SRA). Authors’ contributions All authors have read and approved the final version of this manuscript. XZ, HL, and SMM designed experiments, analyzed data, and PubMed ID:https://www.ncbi.nlm.nih.gov/pubmed/28494239 wrote the paper. XZ and JJP performed research, confirmed bioinformatics data, performed plant defense assays, and subsequent data analysis. XZ, YS, NBG, HMMI, HBB SLC: bioinformatics analyses. CZ: performed plant defense assays and subsequent data analysis. Ethics approval and consent to participate Arabidopsis thaliana is a publically available model organism that is commonly used in plant biology labs worldwide. No specific permits were requires for studies with A. thaliana. For pathogen assays, both P. syringae DG3 and oomycete Hpa Noco2 were both housed in Dr. Hua Lu’s lab with USDA permits. Consent for publication Not applicable. Competing interests The authors declare no competing interests.Rosette leaves from 28-day old plants were ground in liquid nitrogen, and salicylic acid was extracted and analysed by HPLC as described previously [54]. It was repeated at least twice.Large datasetsAll RNA-seq and RIP-seq reads are stored as a BioProject (PRJNA382852) at NCBI Sequence Read Archive (SRA).Additional filesAdditional file 1: Figure S1. An illustration of the experimental design. (TIFF 38 kb) Additional file 2: Figure S2. Flowcharts illustrating all three (TOPHAT, STAR and LG12) pipelines used in RNA-seq data analysis. (TIFF 247 kb) Additional file 3: Table S1. A summary of assembly results. (XLSX 35 kb) Additional file 4: Figure S3. A heat map showing a pair-wise comparison of all 24 RNA-seq and RIP-seq libraries by ranking of R2 values. (TIFF 201 kb) Additional file 5: Table S2. Summary lists of SR45 differentially regulated (SDR) genes identified by three different pipelines. (XLSX 891 kb) Additional file 6: Table S3. GO enrichment comparison for SR45downregulated genes among three different pipelines. (XLSX 22 kb) Additional file 7: Figure S4. A flowchart showing the pipeline used to identify alternative splicing events based on AtRTD2. (TIFF 258 kb) Additional file 8: Table S4. SR45-dependent alternative splicing (SAS) events. (XLSX 210 kb) Additional file 9: Figure S6. Flowcharts illustrating the two (Salmon LG12) pipelines used in RIP-seq data analysis. (TIFF 250 kb) Additional fil.