{
"METABOLOMICS WORKBENCH":{"STUDY_ID":"ST002429","ANALYSIS_ID":"AN003953","VERSION":"1","CREATED_ON":"January 5, 2023, 5:02 pm"},

"PROJECT":{"PROJECT_TITLE":"Insights from a Multi-Omics Integration (MOI) Study in Oil Palm (Elaeis guineensis Jacq.) Response to Abiotic Stresses: Part One—Salinity","PROJECT_TYPE":"Multi-Omics Integration (MOI) Study","PROJECT_SUMMARY":"Oil palm (Elaeis guineensis Jacq.) is the number one source of consumed vegetable oil nowadays. It is cultivated in areas of tropical rainforest, where it meets its natural condition of high rainfall throughout the year. The palm oil industry faces criticism due to a series of practices that was considered not environmentally sustainable, and it finds itself under pressure to adopt new and innovative procedures to reverse this negative public perception. Cultivating this oilseed crop outside the rainforest zone is only possible using artificial irrigation. Close to 30% of the world’s irrigated agricultural lands also face problems due to salinity stress. Consequently, the research community must consider drought and salinity together when studying to empower breeding programs in order to develop superior genotypes adapted to those potential new areas for oil palm cultivation. Multi-Omics Integration (MOI) offers a new window of opportunity for the non-trivial challenge of unraveling the mechanisms behind multigenic traits, such as drought and salinity tolerance. The current study carried out a comprehensive, large-scale, single-omics analysis (SOA), and MOI study on the leaves of young oil palm plants submitted to very high salinity stress. Taken together, a total of 1239 proteins were positively regulated, and 1660 were negatively regulated in transcriptomics and proteomics analyses. Meanwhile, the metabolomics analysis revealed 37 metabolites that were upreg- ulated and 92 that were downregulated. After performing SOA, 436 differentially expressed (DE) full-length transcripts, 74 DE proteins, and 19 DE metabolites underwent MOI analysis, revealing sev- eral pathways affected by this stress, with at least one DE molecule in all three omics platforms used. The Cysteine and methionine metabolism (map00270) and Glycolysis/Gluconeogenesis (map00010) pathways were the most affected ones, each one with 20 DE molecules.","INSTITUTE":"The Brazilian Agricultural Research Corporation (Embrapa)","DEPARTMENT":"Embrapa Agroenergy","LABORATORY":"Genetics and Plant Biotechnology","LAST_NAME":"Souza Jr","FIRST_NAME":"Manoel Teixeira","ADDRESS":"Parque Estacao Biologica, Final Avenida W3 Norte - Asa Norte, Brasilia, Distrito Federal, 70770901, Brazil","EMAIL":"manoel.souza@embrapa.br","PHONE":"+55.61.3448.3210","FUNDING_SOURCE":"FINEP (01.13.0315.00)","PROJECT_COMMENTS":"DendêPalm Project","PUBLICATIONS":"https://doi.org/10.3390/plants11131755"},

"STUDY":{"STUDY_TITLE":"Insights from a Multi-Omics Integration (MOI) Study in Oil Palm (Elaeis guineensis Jacq.) Response to Abiotic Stresses: Part One—Salinity","STUDY_TYPE":"Multi-Omics Integration (MOI) Study","STUDY_SUMMARY":"Oil palm (Elaeis guineensis Jacq.) is the number one source of consumed vegetable oil nowadays. It is cultivated in areas of tropical rainforest, where it meets its natural condition of high rainfall throughout the year. The palm oil industry faces criticism due to a series of practices that was considered not environmentally sustainable, and it finds itself under pressure to adopt new and innovative procedures to reverse this negative public perception. Cultivating this oilseed crop outside the rainforest zone is only possible using artificial irrigation. Close to 30% of the world’s irrigated agricultural lands also face problems due to salinity stress. Consequently, the research community must consider drought and salinity together when studying to empower breeding programs in order to develop superior genotypes adapted to those potential new areas for oil palm cultivation. Multi-Omics Integration (MOI) offers a new window of opportunity for the non-trivial challenge of unraveling the mechanisms behind multigenic traits, such as drought and salinity tolerance. The current study carried out a comprehensive, large-scale, single-omics analysis (SOA), and MOI study on the leaves of young oil palm plants submitted to very high salinity stress. Taken together, a total of 1239 proteins were positively regulated, and 1660 were negatively regulated in transcriptomics and proteomics analyses. Meanwhile, the metabolomics analysis revealed 37 metabolites that were upreg- ulated and 92 that were downregulated. After performing SOA, 436 differentially expressed (DE) full-length transcripts, 74 DE proteins, and 19 DE metabolites underwent MOI analysis, revealing sev- eral pathways affected by this stress, with at least one DE molecule in all three omics platforms used. The Cysteine and methionine metabolism (map00270) and Glycolysis/Gluconeogenesis (map00010) pathways were the most affected ones, each one with 20 DE molecules.","INSTITUTE":"The Brazilian Agricultural Research Corporation (Embrapa)","DEPARTMENT":"Embrapa Agroenergy","LABORATORY":"Genetics and Plant Biotechnology","LAST_NAME":"Souza Jr","FIRST_NAME":"Manoel Teixeira","ADDRESS":"Parque Estacao Biologica, Final Avenida W3 Norte - Asa Norte, Brasilia, Distrito Federal, 70770901, Brazil","EMAIL":"manoel.souza@embrapa.br","PHONE":"+55.61.3448.3210","PUBLICATIONS":"https://doi.org/10.3390/plants11131755"},

"SUBJECT":{"SUBJECT_TYPE":"Plant","SUBJECT_SPECIES":"Elaeis guineensis Jacq.","TAXONOMY_ID":"NCBI:txid51953"},
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"Additional sample data":{"Treatment":"2.0g NaCl","RAW_FILE_NAME":"OilPalm_Salt_20_14DAT_R4_NEG.mzXML"}
},
{
"Subject ID":"-",
"Sample ID":"OilPalm_Salt_10_14DAT_R4_NEG",
"Factors":{"Group":"14 days"},
"Additional sample data":{"Treatment":"1.0g NaCl","RAW_FILE_NAME":"OilPalm_Salt_10_14DAT_R4_NEG.mzXML"}
},
{
"Subject ID":"-",
"Sample ID":"OilPalm_Salt_05_14DAT_R4_NEG",
"Factors":{"Group":"14 days"},
"Additional sample data":{"Treatment":"0.5g NaCl","RAW_FILE_NAME":"OilPalm_Salt_05_14DAT_R4_NEG.mzXML"}
},
{
"Subject ID":"-",
"Sample ID":"OilPalm_Salt_Control_14DAT_R2_NEG",
"Factors":{"Group":"14 days"},
"Additional sample data":{"Treatment":"0.0g NaCl","RAW_FILE_NAME":"OilPalm_Salt_Control_14DAT_R2_NEG.mzXML"}
},
{
"Subject ID":"-",
"Sample ID":"OilPalm_Salt_Control_14DAT_R3_NEG",
"Factors":{"Group":"14 days"},
"Additional sample data":{"Treatment":"0.0g NaCl","RAW_FILE_NAME":"OilPalm_Salt_Control_14DAT_R3_NEG.mzXML"}
},
{
"Subject ID":"-",
"Sample ID":"OilPalm_Salt_Control_14DAT_R4_NEG",
"Factors":{"Group":"14 days"},
"Additional sample data":{"Treatment":"0.0g NaCl","RAW_FILE_NAME":"OilPalm_Salt_Control_14DAT_R4_NEG.mzXML"}
}
],
"COLLECTION":{"COLLECTION_SUMMARY":"The oil palm plants used in this study were clones regenerated out of embryogenic calluses obtained from the leaves of an adult plant—genotype AM33, a Deli x Ghana from ASD Costa Rica, as previously reported by [6]. Before starting the experiments, plants were standardized accordingly to the developmental stage, size, and number of leaves. They were in the growth stage known as bifid saplings, and the experiment was performed in March 2018 in a greenhouse at Embrapa Agroenergy in Brasília, DF, Brazil (S-15.732°, W-47.900°). The main environmental variables (temperature, humidity, and radiation) fluctuated according to the weather conditions and underwent monitoring throughout the entire experimental period using the data collected at a nearby meteorological station (S-15.789°, W-47.925°). We collected the apical leaves from control and stressed plants (0.0 and 2.0 g of NaCl per 100 g of substrate) 12 days after imposition of the treatments (DAT).","SAMPLE_TYPE":"Plant"},

"TREATMENT":{"TREATMENT_SUMMARY":"The experiment consisted of five salinity levels (0.0, 0.5, 1.0, 1.5, and 2.0 g of NaCl per 100 g of substrate (a mixture of vermiculite, soil, and the Bioplant commercial substrate (Bioplant Agrícola Ltd.a., Nova Ponte, MG, Brazil), in a 1:1:1 ratio, on a dry basis), with four replicates in a completely randomized design. The substrate mixture was fertilized using 2.5 g L−1 of the N-P2O5-K2O formula (20-20-20)."},

"SAMPLEPREP":{"SAMPLEPREP_SUMMARY":"Leaves harvested from control and stressed plants were immediately immersed in liquid nitrogen and stored at −80 °C until metabolite extraction: four plants for treatments. Before solvent extraction, all samples underwent grounding in liquid nitrogen. The solvents used were methanol grade UHPLC, acetonitrile grade LC-MS, formic acid grade LC-MS, sodium hydroxide ACS grade LC-MS, all from Sigma-Aldrich, and water treated in a Milli-Q system from Millipore. We employed a protocol to extract the metabolites in three phases (polar, non-polar, and protein pellet). Aliquots of 50 mg of ground sample were transferred to 2 mL microtubes, and then 1 mL of a mixture of 1:3 (v:v) methanol/methyl tert-butyl ether (MTBE) at −20 °C was added. Homogenization on an orbital shaker at 4.0 °C and ultrasound treatment in an ice bath were each performed for 10 min. As the next step, we added 500 μL of a mixture of 1:3 (v:v) methanol/water to each microtube. After centrifugation (15,300× g at 4.0 °C for 5 min), an upper non-polar (green) and a lower polar (brown) phase and a protein pellet remained in each microtube. After transferring both fractions separately to 1.5 mL microtubes, they were submitted to a Speed vac system (Centrivap, Labconco) to be vacuum dried. Finally, the dry-fraction, resuspended in 500 μL of 1:3 (v:v) methanol and water mixture and transferred to vials, were now ready for analysis."},

"CHROMATOGRAPHY":{"CHROMATOGRAPHY_SUMMARY":"Solvent A was 0.1% (v:v) formic acid in water and solvent B was 0.1% (v:v) formic acid in acetonitrile/methanol (70:30, v:v). The gradient elution used, with a flow rate of 0.4 mL min–1, was as follows: 0–1 min isocratic, 0% B; 1–3 min, 5% B; 3–10 min, 50% B; 10–13 min, 100% B; 13–15 min isocratic, 100% B; then, 5 min rebalancing was conducted to the initial conditions.","CHROMATOGRAPHY_TYPE":"Reversed phase","INSTRUMENT_NAME":"Shimadzu Nexera X2","COLUMN_NAME":"Waters Acquity BEH HSS T3 (100 x 2.1mm, 1.8um)","SOLVENT_A":"100% water; 0.1% formic acid","SOLVENT_B":"70% acetonitrile/30% methanol; 0.1% formic acid","FLOW_GRADIENT":"0–1 min isocratic, 0% B; 1–3 min, 5% B; 3–10 min, 50% B; 10–13 min, 100% B; 13–15 min isocratic, 100% B; then, 5 min rebalancing was conducted to the initial conditions.","FLOW_RATE":"0.4 mL/min","COLUMN_TEMPERATURE":"-"},

"ANALYSIS":{"ANALYSIS_TYPE":"MS"},

"MS":{"INSTRUMENT_NAME":"Bruker maXis Impact qTOF","INSTRUMENT_TYPE":"QTOF","MS_TYPE":"ESI","ION_MODE":"POSITIVE","MS_COMMENTS":"The rate of acquisition spectra was 3.00 Hz, mass range m/z 70–1200 for the polar fraction analysis and m/z 300–1600 for the lipidic fraction. High-resolution mass spectrometry was used for detection (MaXis 4G Q-TOF MS, Bruker Daltonics) equipped with an electrospray source in positive (ESI-(+)-MS) and negative (ESI-(−)-MS) modes. The settings of the mass spectrometer were as follows: capillary voltage, 3800 V; dry gas flow, 9 L min−1; dry temperature, 200 °C; nebulizer pressure, 4 bar; final plate offset, 500 V. For the external calibration of the equipment, we used a sodium formate solution (10 mM HCOONa solution in 50:50 v:v isopropanol and water containing 0.2% formic acid) injected through a six-way valve at the beginning of each chromatographic run. Ampicillin ([M+H] + m/z 350.1186729 and [M-H]- m/z 348.1028826) was the internal standard for later peak normalization on data analysis.","MS_RESULTS_FILE":"ST002429_AN003953_Results.txt UNITS:Peak intensity Has m/z:Yes Has RT:No RT units:No RT data"}

}