------------------------------------------------------------------------- Project ------------------------------------------------------------------------- Manuscript Title Title: Longitudinal transcriptomic, proteomic, and metabolomic analysis of Citrus limon response to graft inoculation by ‘Candidatus Liberibacter asiaticus' Abstract Transcriptomic, proteomic, and metabolomic data were collected from samples prepared from leaf tissue of lemon (Citrus limon) plants reared in controlled environment greenhouses. The purpose of the data collection was to analyze the differences over time between lemon plants which were graft-inoculated with budwood originating from trees infected with the citrus greening bacterium (‘Candidatus Liberibacter asiaticus’) and lemon plants which were graft-inoculated with disease-free budwood. Transcriptome data were collected from lemon leaf RNA samples using Illumina sequencing. Raw RNAseq data were curated at the Boyce Thompson Institute, and deposited in Genbank for public access. RNAseq data quality control analysis and filtering, mapping, assembly, and differential expression analysis was performed using bioinformatics pipelines established by the Solanaceae Genomics Network and installed on Boyce Thompson Institute servers. Proteomics data were collected from lemon leaf samples using liquid chromatography/tandem mass spectrometry. Raw mass spectrometry data were curated on Cornell University and University of Washington servers, and deposited along in ProteomeXchange for public access. Proteome data quality control analysis included the use of a decoy reverse sequence database to enable false discovery rate calculation during Mascot and Scaffold analysis. Metabolomics data were collected from lemon leaf samples using 1H NMR. NMR spectra were processed, and metabolites were identified and quantified using Chenomx NMR Suite. ------------------------------------------------------------------------- Data Overview ------------------------------------------------------------------------- Data Type 1H NMR-based metabolomics Spectrometer Bruker Advance 600 MHz Experiment Bruker 1D noesypr1d Acquisition Overview 12 ppm sweep width; 2.5 s acquisition time with 2.5 s relaxation delay; 100 ms mixing time with water saturation applied during the relaxation delay and mixing time; n scans = 32; spectra zero-filled with 128000 data points; exponential apodization function corresponding to line broadening of 0.5 Hz applied Species Citrus limon Common name Lisbon lemon Tissue Mature leaves Treatments Control (uninfected, n = 11); Infected (CLas-grafted, n = 11; of those 11 qPCR confirmed CLas(+), n = 6) Sample Collection Overview 6-8 leaves were collected per tree and pooled into a single sample. Samples were transported on dry ice and stored at -80C until metabolite extraction. Samples were collected at baseline, 2, 8, 10, 12, 14, 16, 18, 20, 22, and 46 weeks post-grafting. Sample Preparation Overview Polar metabolites extracted from leaf disks obtained from the mesophyllic tissue, midrib, and petiole taken from each leaf. Disks were pooled and dried for 24 h. 75 mg of dried leaf material was ground. Phosphate buffer (10mM, pH 6.8) heated to 90C was added to ground leaf material (1:20 (w:v)), mixed for 15 min at 90C at 1000 rpm (Eppendorf ThermoMixer C). Sample centrifuged for 15 min, 4C, 14000 x g. 750 uL of supernatant collected and centrifuged at 4C, 15 min, 14000 x g. 65uL of internal standard containing 5 mM 3-(trimethylsilyl)-1-propanesulfonic acid-d6 (DSS-d6) was added to 585 uL of the resulting supernatant, and 600 uL of the subsequent mixture was transferred to 5 mm NMR tubes and stored at 4C until NMR data acquisition (within 24 h of sample preparation). ------------------------------------------------------------------------- File Organization & Description ------------------------------------------------------------------------- Each directory corresponds to a sample collection time point. Each sub-directory contains all Bruker NMR output files for a single tree. File/Directory name Description ------------------- ---------------- week0 directory for all files for baseline (0 weeks post-grafting) week2 directory for all files for 2 weeks post-grafting week8 directory for all files for 8 weeks post-grafting week10 directory for all files for 10 weeks post-grafting week12 directory for all files for 12 weeks post-grafting week14 directory for all files for 14 weeks post-grafting week16 directory for all files for 16 weeks post-grafting week18 directory for all files for 18 weeks post-grafting week20 directory for all files for 20 weeks post-grafting week22 directory for all files for 22 weeks post-grafting week46 directory for all files for 46 weeks post-grafting