Summary of Study ST002429

This data is available at the NIH Common Fund's National Metabolomics Data Repository (NMDR) website, the Metabolomics Workbench, https://www.metabolomicsworkbench.org, where it has been assigned Project ID PR001563. The data can be accessed directly via it's Project DOI: 10.21228/M8NX4M This work is supported by NIH grant, U2C- DK119886.

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This study contains a large results data set and is not available in the mwTab file. It is only available for download via FTP as data file(s) here.

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Study IDST002429
Study TitleInsights from a Multi-Omics Integration (MOI) Study in Oil Palm (Elaeis guineensis Jacq.) Response to Abiotic Stresses: Part One—Salinity
Study TypeMulti-Omics Integration (MOI) Study
Study SummaryOil 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)
DepartmentEmbrapa Agroenergy
LaboratoryGenetics and Plant Biotechnology
Last NameSouza Jr
First NameManoel Teixeira
AddressParque Estacao Biologica, Final Avenida W3 Norte - Asa Norte, Brasilia, Distrito Federal, 70770901, Brazil
Emailmanoel.souza@embrapa.br
Phone+55.61.3448.3210
Submit Date2022-09-28
Publicationshttps://doi.org/10.3390/plants11131755
Raw Data AvailableYes
Raw Data File Type(s)mzXML
Analysis Type DetailLC-MS
Release Date2023-01-20
Release Version1
Manoel Teixeira Souza Jr Manoel Teixeira Souza Jr
https://dx.doi.org/10.21228/M8NX4M
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

Select appropriate tab below to view additional metadata details:


Project:

Project ID:PR001563
Project DOI:doi: 10.21228/M8NX4M
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

Subject:

Subject ID:SU002518
Subject Type:Plant
Subject Species:Elaeis guineensis Jacq.
Taxonomy ID:NCBI:txid51953

Factors:

Subject type: Plant; Subject species: Elaeis guineensis Jacq. (Factor headings shown in green)

mb_sample_id local_sample_id Group
SA242845OilPalm_Salt_15_14DAT_R3_POS14 days
SA242846OilPalm_Salt_15_14DAT_R4_POS14 days
SA242847OilPalm_Salt_10_14DAT_R2_POS14 days
SA242848OilPalm_Salt_10_14DAT_R1_POS14 days
SA242849OilPalm_Salt_05_14DAT_R3_POS14 days
SA242850OilPalm_Salt_15_14DAT_R2_POS14 days
SA242851OilPalm_Salt_20_14DAT_R2_POS14 days
SA242852OilPalm_Salt_15_14DAT_R1_POS14 days
SA242853OilPalm_Salt_05_14DAT_R2_POS14 days
SA242854OilPalm_Salt_10_14DAT_R3_POS14 days
SA242855OilPalm_Salt_20_14DAT_R3_POS14 days
SA242856OilPalm_Salt_Control_14DAT_R4_POS14 days
SA242857OilPalm_Salt_20_14DAT_R1_NEG14 days
SA242858OilPalm_Salt_Control_14DAT_R1_NEG14 days
SA242859OilPalm_Salt_Control_14DAT_R3_POS14 days
SA242860OilPalm_Salt_Control_14DAT_R2_POS14 days
SA242861OilPalm_Salt_20_14DAT_R4_POS14 days
SA242862OilPalm_Salt_10_14DAT_R4_POS14 days
SA242863OilPalm_Salt_05_14DAT_R4_POS14 days
SA242864OilPalm_Salt_20_14DAT_R1_POS14 days
SA242865OilPalm_Salt_05_14DAT_R1_POS14 days
SA242866OilPalm_Salt_20_14DAT_R4_NEG14 days
SA242867OilPalm_Salt_Control_14DAT_R1_POS14 days
SA242868OilPalm_Salt_10_14DAT_R3_NEG14 days
SA242869OilPalm_Salt_10_14DAT_R2_NEG14 days
SA242870OilPalm_Salt_10_14DAT_R4_NEG14 days
SA242871OilPalm_Salt_05_14DAT_R4_NEG14 days
SA242872OilPalm_Salt_Control_14DAT_R4_NEG14 days
SA242873OilPalm_Salt_Control_14DAT_R3_NEG14 days
SA242874OilPalm_Salt_Control_14DAT_R2_NEG14 days
SA242875OilPalm_Salt_05_14DAT_R3_NEG14 days
SA242876OilPalm_Salt_20_14DAT_R3_NEG14 days
SA242877OilPalm_Salt_05_14DAT_R1_NEG14 days
SA242878OilPalm_Salt_15_14DAT_R1_NEG14 days
SA242879OilPalm_Salt_15_14DAT_R4_NEG14 days
SA242880OilPalm_Salt_05_14DAT_R2_NEG14 days
SA242881OilPalm_Salt_20_14DAT_R2_NEG14 days
SA242882OilPalm_Salt_15_14DAT_R2_NEG14 days
SA242883OilPalm_Salt_15_14DAT_R3_NEG14 days
SA242884OilPalm_Salt_10_14DAT_R1_NEG14 days
SA242885OilPalm_Salt_20_07DAT_R4_NEG7 days
SA242886OilPalm_Salt_20_07DAT_R3_NEG7 days
SA242887OilPalm_Salt_10_07DAT_R4_NEG7 days
SA242888OilPalm_Salt_10_07DAT_R3_NEG7 days
SA242889OilPalm_Salt_Control_07DAT_R3_NEG7 days
SA242890OilPalm_Salt_10_07DAT_R2_NEG7 days
SA242891OilPalm_Salt_Control_07DAT_R4_NEG7 days
SA242892OilPalm_Salt_Control_07DAT_R2_NEG7 days
SA242893OilPalm_Salt_05_07DAT_R4_NEG7 days
SA242894OilPalm_Salt_Control_07DAT_R1_NEG7 days
SA242895OilPalm_Salt_05_07DAT_R3_POS7 days
SA242896OilPalm_Salt_15_07DAT_R4_POS7 days
SA242897OilPalm_Salt_10_07DAT_R2_POS7 days
SA242898OilPalm_Salt_10_07DAT_R3_POS7 days
SA242899OilPalm_Salt_20_07DAT_R4_POS7 days
SA242900OilPalm_Salt_20_07DAT_R3_POS7 days
SA242901OilPalm_Salt_15_07DAT_R3_POS7 days
SA242902OilPalm_Salt_10_07DAT_R1_POS7 days
SA242903OilPalm_Salt_20_07DAT_R2_POS7 days
SA242904OilPalm_Salt_20_07DAT_R1_POS7 days
SA242905OilPalm_Salt_15_07DAT_R1_POS7 days
SA242906OilPalm_Salt_05_07DAT_R1_POS7 days
SA242907OilPalm_Salt_15_07DAT_R2_POS7 days
SA242908OilPalm_Salt_05_07DAT_R2_POS7 days
SA242909OilPalm_Salt_10_07DAT_R4_POS7 days
SA242910OilPalm_Salt_05_07DAT_R4_POS7 days
SA242911OilPalm_Salt_05_07DAT_R2_NEG7 days
SA242912OilPalm_Salt_05_07DAT_R1_NEG7 days
SA242913OilPalm_Salt_15_07DAT_R2_NEG7 days
SA242914OilPalm_Salt_10_07DAT_R1_NEG7 days
SA242915OilPalm_Salt_15_07DAT_R4_NEG7 days
SA242916OilPalm_Salt_15_07DAT_R3_NEG7 days
SA242917OilPalm_Salt_15_07DAT_R1_NEG7 days
SA242918OilPalm_Salt_20_07DAT_R2_NEG7 days
SA242919OilPalm_Salt_Control_07DAT_R3_POS7 days
SA242920OilPalm_Salt_Control_07DAT_R2_POS7 days
SA242921OilPalm_Salt_Control_07DAT_R4_POS7 days
SA242922OilPalm_Salt_Control_07DAT_R1_POS7 days
SA242923OilPalm_Salt_20_07DAT_R1_NEG7 days
SA242924OilPalm_Salt_05_07DAT_R3_NEG7 days
Showing results 1 to 80 of 80

Collection:

Collection ID:CO002511
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 ID:TR002530
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).

Sample Preparation:

Sampleprep ID:SP002524
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.

Combined analysis:

Analysis ID AN003953 AN003954
Analysis type MS MS
Chromatography type Reversed phase Reversed phase
Chromatography system Shimadzu Nexera X2 Shimadzu Nexera X2
Column Waters Acquity BEH HSS T3 (100 x 2.1mm, 1.8um) Waters Acquity BEH HSS T3 (100 x 2.1mm, 1.8um)
MS Type ESI ESI
MS instrument type QTOF QTOF
MS instrument name Bruker maXis Impact qTOF Bruker maXis Impact qTOF
Ion Mode POSITIVE NEGATIVE
Units Peak intensity Peak intensity

Chromatography:

Chromatography ID:CH002926
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.
Instrument Name:Shimadzu Nexera X2
Column Name:Waters Acquity BEH HSS T3 (100 x 2.1mm, 1.8um)
Column Temperature:-
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
Solvent A:100% water; 0.1% formic acid
Solvent B:70% acetonitrile/30% methanol; 0.1% formic acid
Chromatography Type:Reversed phase

MS:

MS ID:MS003688
Analysis ID:AN003953
Instrument Name:Bruker maXis Impact qTOF
Instrument Type:QTOF
MS Type:ESI
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.
Ion Mode:POSITIVE
  
MS ID:MS003689
Analysis ID:AN003954
Instrument Name:Bruker maXis Impact qTOF
Instrument Type:QTOF
MS Type:ESI
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.
Ion Mode:NEGATIVE
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