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.

See: https://www.metabolomicsworkbench.org/about/howtocite.php

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Study ID	ST002429
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
Submit Date	2022-09-28
Publications	https://doi.org/10.3390/plants11131755
Raw Data Available	Yes
Raw Data File Type(s)	mzXML
Analysis Type Detail	LC-MS
Release Date	2023-01-20
Release Version	1

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
Species Group:	Plants

Factors:

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

mb_sample_id	local_sample_id	Group
SA242845	OilPalm_Salt_15_14DAT_R3_POS	14 days
SA242846	OilPalm_Salt_15_14DAT_R4_POS	14 days
SA242847	OilPalm_Salt_10_14DAT_R2_POS	14 days
SA242848	OilPalm_Salt_10_14DAT_R1_POS	14 days
SA242849	OilPalm_Salt_05_14DAT_R3_POS	14 days
SA242850	OilPalm_Salt_15_14DAT_R2_POS	14 days
SA242851	OilPalm_Salt_20_14DAT_R2_POS	14 days
SA242852	OilPalm_Salt_15_14DAT_R1_POS	14 days
SA242853	OilPalm_Salt_05_14DAT_R2_POS	14 days
SA242854	OilPalm_Salt_10_14DAT_R3_POS	14 days
SA242855	OilPalm_Salt_20_14DAT_R3_POS	14 days
SA242856	OilPalm_Salt_Control_14DAT_R4_POS	14 days
SA242857	OilPalm_Salt_20_14DAT_R1_NEG	14 days
SA242858	OilPalm_Salt_Control_14DAT_R1_NEG	14 days
SA242859	OilPalm_Salt_Control_14DAT_R3_POS	14 days
SA242860	OilPalm_Salt_Control_14DAT_R2_POS	14 days
SA242861	OilPalm_Salt_20_14DAT_R4_POS	14 days
SA242862	OilPalm_Salt_10_14DAT_R4_POS	14 days
SA242863	OilPalm_Salt_05_14DAT_R4_POS	14 days
SA242864	OilPalm_Salt_20_14DAT_R1_POS	14 days
SA242865	OilPalm_Salt_05_14DAT_R1_POS	14 days
SA242866	OilPalm_Salt_20_14DAT_R4_NEG	14 days
SA242867	OilPalm_Salt_Control_14DAT_R1_POS	14 days
SA242868	OilPalm_Salt_10_14DAT_R3_NEG	14 days
SA242869	OilPalm_Salt_10_14DAT_R2_NEG	14 days
SA242870	OilPalm_Salt_10_14DAT_R4_NEG	14 days
SA242871	OilPalm_Salt_05_14DAT_R4_NEG	14 days
SA242872	OilPalm_Salt_Control_14DAT_R4_NEG	14 days
SA242873	OilPalm_Salt_Control_14DAT_R3_NEG	14 days
SA242874	OilPalm_Salt_Control_14DAT_R2_NEG	14 days
SA242875	OilPalm_Salt_05_14DAT_R3_NEG	14 days
SA242876	OilPalm_Salt_20_14DAT_R3_NEG	14 days
SA242877	OilPalm_Salt_05_14DAT_R1_NEG	14 days
SA242878	OilPalm_Salt_15_14DAT_R1_NEG	14 days
SA242879	OilPalm_Salt_15_14DAT_R4_NEG	14 days
SA242880	OilPalm_Salt_05_14DAT_R2_NEG	14 days
SA242881	OilPalm_Salt_20_14DAT_R2_NEG	14 days
SA242882	OilPalm_Salt_15_14DAT_R2_NEG	14 days
SA242883	OilPalm_Salt_15_14DAT_R3_NEG	14 days
SA242884	OilPalm_Salt_10_14DAT_R1_NEG	14 days
SA242885	OilPalm_Salt_20_07DAT_R4_NEG	7 days
SA242886	OilPalm_Salt_20_07DAT_R3_NEG	7 days
SA242887	OilPalm_Salt_10_07DAT_R4_NEG	7 days
SA242888	OilPalm_Salt_10_07DAT_R3_NEG	7 days
SA242889	OilPalm_Salt_Control_07DAT_R3_NEG	7 days
SA242890	OilPalm_Salt_10_07DAT_R2_NEG	7 days
SA242891	OilPalm_Salt_Control_07DAT_R4_NEG	7 days
SA242892	OilPalm_Salt_Control_07DAT_R2_NEG	7 days
SA242893	OilPalm_Salt_05_07DAT_R4_NEG	7 days
SA242894	OilPalm_Salt_Control_07DAT_R1_NEG	7 days
SA242895	OilPalm_Salt_05_07DAT_R3_POS	7 days
SA242896	OilPalm_Salt_15_07DAT_R4_POS	7 days
SA242897	OilPalm_Salt_10_07DAT_R2_POS	7 days
SA242898	OilPalm_Salt_10_07DAT_R3_POS	7 days
SA242899	OilPalm_Salt_20_07DAT_R4_POS	7 days
SA242900	OilPalm_Salt_20_07DAT_R3_POS	7 days
SA242901	OilPalm_Salt_15_07DAT_R3_POS	7 days
SA242902	OilPalm_Salt_10_07DAT_R1_POS	7 days
SA242903	OilPalm_Salt_20_07DAT_R2_POS	7 days
SA242904	OilPalm_Salt_20_07DAT_R1_POS	7 days
SA242905	OilPalm_Salt_15_07DAT_R1_POS	7 days
SA242906	OilPalm_Salt_05_07DAT_R1_POS	7 days
SA242907	OilPalm_Salt_15_07DAT_R2_POS	7 days
SA242908	OilPalm_Salt_05_07DAT_R2_POS	7 days
SA242909	OilPalm_Salt_10_07DAT_R4_POS	7 days
SA242910	OilPalm_Salt_05_07DAT_R4_POS	7 days
SA242911	OilPalm_Salt_05_07DAT_R2_NEG	7 days
SA242912	OilPalm_Salt_05_07DAT_R1_NEG	7 days
SA242913	OilPalm_Salt_15_07DAT_R2_NEG	7 days
SA242914	OilPalm_Salt_10_07DAT_R1_NEG	7 days
SA242915	OilPalm_Salt_15_07DAT_R4_NEG	7 days
SA242916	OilPalm_Salt_15_07DAT_R3_NEG	7 days
SA242917	OilPalm_Salt_15_07DAT_R1_NEG	7 days
SA242918	OilPalm_Salt_20_07DAT_R2_NEG	7 days
SA242919	OilPalm_Salt_Control_07DAT_R3_POS	7 days
SA242920	OilPalm_Salt_Control_07DAT_R2_POS	7 days
SA242921	OilPalm_Salt_Control_07DAT_R4_POS	7 days
SA242922	OilPalm_Salt_Control_07DAT_R1_POS	7 days
SA242923	OilPalm_Salt_20_07DAT_R1_NEG	7 days
SA242924	OilPalm_Salt_05_07DAT_R3_NEG	7 days

Showing results 1 to 80 of 80

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).

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.

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