Citrus Metabolomics

The purpose of metabolomics analysis is to identify and quantify the metabolites in a biological sample. The metabolome of the host citrus represents the complete set of metabolites, which are the end products of cellular processes, in a cell or tissue such as a leaf. When used in conjunction with transcriptomics and proteomics, metabolomics offers an insight into the physiology of the plant host under healthy and HLB-positive conditions. (adapted from Wikipedia)


Longitudinal transcriptomic, proteomic, and metabolomic analyses of Navel orange

Longitudinal transcriptomic, proteomic, and metabolomic analyses of Citrus sinensis (L.) Osbeck graft-inoculated with Candidatus Liberibacter asiaticus

Transcriptomic, proteomic, and metabolomic data were collected from leaf samples obtained from greenhouse grown Parent Washington Navel orange (Citrus sinensis (L.) Osbeck) plants. Plants were grafted with pieces of budwood originating from CLas-infected orange plants or from healthy, uninfected orange plants. The purpose of the data collection was to analyze longitudinal changes between infected and uninfected plants. Transcriptomic data were collected from leaf RNA samples using Illumina HiSeq4000 PE100 sequencing and data were mapped to the C. sinensis genome and differential expression analysis was subsequently performed. Raw reads are available at NCBI SRA using the BioProject ID PRJNA417324. Proteomics data was collected from navel leaf samples using liquid chromatography/tandem mass spectrometry (MS), and proteins were identified from a manually curated database containing proteins from C. sinensis and C. clementina. MS proteomic data has been deposited to the ProteomeXchange Consortium via the PRIDE partner repository with the identifier PDX006316. Metabolomic data were collected from leaf samples using 1H NMR. NMR spectral analysis and metabolite identification and quantification was performed using Chenomx NMR Suite. 1H NMR data files are available through the link below.

Data Overview

Data Type 1H NMR-based metabolomics
Spectrometer Bruker AVANCE 600 MHz
Species Citrus sinensis (L.) Osbeck
Common name Parent Washington Navel Orange
Tissue Mature leaves
Treatments Control (uninfected, n = 6); Infected (CLas grafted, n = 6; of those 6 qPCR confirmed CLas positive, n = 4)


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, 24, 26, 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).

The linked data (coming soon!!) will contain directories, each corresponding to a sample collection time point. Each sub-directory will contain all Bruker NMR output files for a single tree.

Citation

Chin EL, Ramsey JS, Mishchuk DO, Saha S, Mitrovic E, Chavez JD, Howe K, Zhong X, Polek M, Godfrey KE, Mueller LA, Bruce JE, Heck M and Slupsky CM. Longitudinal transcriptomic, proteomic, and metabolomic analyses of Citrus sinensis (L.) Osbeck graft-inoculated with Candidatus Liberibacter asiaticus (CLas). submitted


Longitudinal transcriptomic, proteomic, and metabolomic analyses of Lisbon lemon

Longitudinal transcriptomic, proteomic, and metabolomic analysis of Citrus limon response to graft inoculation by Candidatus Liberibacter asiaticus

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. Raw reads are available at NCBI SRA using the BioProject ID PRJNA348468. 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. The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE partner repository with the dataset identifiers PXD005905, PXD006010, and PXD006011. 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. 1H NMR data files are available through the link below.

Data Overview

Data Type 1H NMR-based metabolomics
Spectrometer Bruker AVANCE 600 MHz
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).

The linked data (coming soon!!) will contain directories, each corresponding to a sample collection time point. Each sub-directory will contain all Bruker NMR output files for a single tree.

Citation

Ramsey JS, Chin EL, Chavez JD, Saha S, Mischuk DO, Mahoney J, Mohr J, Robison FM, Foster E, Xu Y, Strickler S, Fernandez N, Zhong X, Polek M, Godfrey KE, Giovannoni JG, Mueller LA, Slupsky CM, Bruce JE and Heck M. Longitudinal transcriptomic, proteomic, and metabolomic analysis of Citrus limon response to graft inoculation by Candidatus Liberibacter asiaticus. submitted