DOI: 10.25338/b83p9q
title: 1H NMR based metabolomics from: <em>Citrus sinensis</em> leaves in response to Diaphorina citri infestation and Huanglongbing disease

description: Huanglongbing (HLB) is a fatal citrus disease currently threatening all
 commercially relevant citrus varieties worldwide. In the United States,
 the putative causative agent, Candidatus Liberibacter asiaticus (CLas), is
 transmitted by the vector Diaphorina citri, commonly known as the Asian
 citrus psyllid (ACP). Progress towards understanding CLas and its role in
 HLB has been hindered by the inability to culture the bacterium and the
 inability to confidently detect it in diseased trees during the
 asymptomatic stage. To identify early changes in citrus metabolism in
 response to inoculation of CLas using its natural psyllid vector, leaves
 from Madam Vinous sweet orange (Citrus sinensis (L.) Osbeck)
 trees were exposed to CLas-positive ACP or CLas-negative ACP and
 longitudinally analyzed using transcriptomics (RNA sequencing), proteomics
 (liquid chromatography-tandem mass spectrometry), and metabolomics (proton
 nuclear magnetic resonance). At 4 weeks post-exposure (wpe) to psyllids,
 the initial HLB plant response was primarily to the ACP and, to a lesser
 extent, the presence or absence of CLas. Additionally, analysis of 4, 8,
 12, and 16 wpe identified 17 genes that were consistently differentially
 expressed between leaves exposed to CLas-positive ACP versus CLas-negative
 ACP, one differentially abundant protein, and no differentially
 accumulated metabolites. The results of this study inform identification
 of early detection molecular targets and contribute to the broader
 understanding of vector-transmitted plant pathogen interactions. There are
 two datasets related to this research MS/MS Proteomics: 10.25338/B83H1Z 1H
 NMR based metabolomics: 10.25338/B83P9Q
description: Following <em>Citrus sinensis</em> leaf sample
 collection, the tissue was frozen until ready for NMR preparation.  The
 frozen ground leaf material was lyophilized, dried leaf material was
 transferred to 2 mL tubes. One 3.5 mm glass bead was added to each tube
 before beating and 10 mM phosphate buffer (pH 6.8) pre-heated to 90°C was
 added to the ground tissue in a 1:20 (w/v) ratio based on each
 sample's dry weight. Tubes were immediately mixed at 90 °C and then
 centrifuged at 4°C. Seven hundred fifty microliters of supernatant was
 collected, transferred to a clean tube, and centrifuged again. Sixty-five
 microliters of 4.97 mM 4,4-dimethyl-4-silapentane-1-sulfonic acid-d6
 (DSS-d6) was added as an internal standard to 585 μL of the resulting
 supernatant and vortexed. Six hundred microliters of the mixture was
 transferred to 5 mm NMR tubes and stored at 4°C until NMR data acquisition
 which took place within 24 hours of NMR sample preparation.
 <sup>1</sup>H NMR data acquisition was performed using a
 Bruker Advance 600 MHz NMR spectrometer equipped with a SampleJet using
 the Bruker “noesypr1d” (RD-90°-t-90°-tm-ACQ) acquisition
 parameters.
description: Chenomx NMR suite v8.31 (Chenomx Inc., Edmonton, Alberta, Canada)
 can be used to open these files. 
description: # Leaf Metabolomics of Citrus sinensis L. Osbeck (Sweet Orange) ##
 Description of the data and file structure In this study, proton nuclear
 magnetic resonance (1H NMR) metabolomics was carried out on leaves of
 Citrus sinensis L. Osbeck trees exposed to Diaphorina citri infestation
 and Huanglongbing disease. 1H NMR data acquisition was performed using a
 Bruker Advance 600 MHz NMR spectrometer equipped with a SampleJet using
 the Bruker `noesypr1d` (RD-90-t-90-tm-ACQ) acquisition parameters. File
 names are in the following format: `TP-` + time point of leaf sample
 collection + `_` + tree number. For example, TP-3_15 corresponds to time
 point 3, tree 15. Baseline sample collection is denoted by `BL_` + tree
 number. All of NMR data collected for each sample is can be found in a
 compressed file format (tar.gz). These files can be read using Chenomx NMR
 suite version 8.31 (Chenomx Inc., Edmonton, Alberta, Canada). These files
 include: acqu, audita.txt, format.temp, prosol_History, shimvalues,
 uxnmr.par, acqum, fid, fq1list, pulseprogram, specpar, acqus, format.ased,
 pdata, scon2, uxnmr.info. To repeat the profiling of metabolites performed
 in the manuscript associated with this data, one needs to be able to open
 the `fid` file. The remaining files provided in the list above not
 necessary to repeat the profiling of metabolites as described in the
 manuscript, but contain information pertaining to the history of the NMR
 run and collection parameters. While they are not necessary for repeating
 the profiling of metabolites carried out in Chenomx NMR suite, they are
 included as a part of NMR repository best practices. Data not included for
 the following samples: BL_1, TP-1_3, TP-3_15, and TP-3_31. ##
 Code/Software The NMR files can be opened using Chenomx NMR suite v8.31
 (Chenomx Inc., Edmonton, Alberta, Canada).