Summary of Study ST003958
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 PR002481. The data can be accessed directly via it's Project DOI: 10.21228/M8Z23D This work is supported by NIH grant, U2C- DK119886. See: https://www.metabolomicsworkbench.org/about/howtocite.php
| Study ID | ST003958 |
| Study Title | Comprehensive lipidomic analysis of six Hevea species and varieties related to latex biosynthesis |
| Study Summary | Latex, the raw material of natural rubber, is harvested from Hevea brasiliensis. Although there are related species within the Hevea genus, their latex is not suitable for product use due to its physicochemical properties. In this analysis, we focused on lipidomics to perform a comparative analysis aimed at identifying some of the factors underlying these differences. |
| Institute | Maebashi Institute of Technology |
| Last Name | Yuko |
| First Name | Makita |
| Address | 460-1 Kamisadori-cho, Maebashi, Gunma 371-0816 Japan |
| makita@maebashi-it.ac.jp | |
| Phone | +81-27-265-7366 |
| Submit Date | 2025-05-22 |
| Raw Data Available | Yes |
| Raw Data File Type(s) | mzML, raw(Thermo) |
| Analysis Type Detail | LC-MS |
| Release Date | 2025-06-11 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
Project:
| Project ID: | PR002481 |
| Project DOI: | doi: 10.21228/M8Z23D |
| Project Title: | Comprehensive lipidomic analysis of six Hevea species and varieties related to latex biosynthesis |
| Project Summary: | In this study, we performed lipidomic profiling of latex from Hevea brasiliensis RRIM600 and five Hevea species or varieties of similar age: H. guianensis, H. pauciflora, H. spruceana, H. collina, and H. confusa. Latex samples were analysed by LC-MS/MS, identifying 53 lipid molecules from five major categories and 16 classes. Among these, triacylglycerols (TG), phosphatidic acids (PA), and acylhexosyl sitosterols are major components. Comparative analysis revealed species-specific lipid profiles: H. guianensis and H. confusa exhibited high PA levels comparable to H. brasiliensis, whereas H. pauciflora, H. spruceana, and H. collina showed elevated TG and reduced PA content. Supervised OPLS-DA analysis separated H. brasiliensis from the other species and identified 18 differentially abundant lipid molecules, including increased diacylglycerols and phosphatidic acids, and decreased hexosylceramides. These patterns may reflect underlying metabolic divergence with potential implications for latex composition and rubber biosynthesis. The dataset provides new insights into interspecific lipidome variation in Hevea and offers a valuable resource for future studies on lipid function in latex physiology and rubber properties. |
| Institute: | Maebashi Institute of Technology |
| Department: | Faculty of Engineering |
| Laboratory: | Laboratory of Omics Science |
| Last Name: | Makita |
| First Name: | Yuko |
| Address: | 460-1 Kamisadori-cho, Maebashi, Gunma, 371-0816, Japan |
| Email: | makita@maebashi-it.ac.jp |
| Phone: | +81-27-265-7366 |
| Contributors: | Nyok-Sean Lau, miko Okubo-Kurihara, Minami Matsui |
Subject:
| Subject ID: | SU004095 |
| Subject Type: | Plant |
| Subject Species: | Hevea |
| Taxonomy ID: | 3980 (genus Hevea) |
| Species Group: | Taxonomy_id (species): 1318718 (Hevea spruceana), 3981 (Hevea brasiliensis and Hevea brasiliensis strain:RRIM 600), 882917 (Hevea guianensis var. guianensis), 882917 (Hevea guianensis var. collina), 1318717 (Hevea pauciflora), 1318717 (Hevea confusa is a synonym of Hevea pauciflora var. coriacea) |
Factors:
Subject type: Plant; Subject species: Hevea (Factor headings shown in green)
| mb_sample_id | local_sample_id | Sample source | Species |
|---|---|---|---|
| SA452731 | 11_RRIM600R2 | Latex | H. brasiliensis RRIM 600 |
| SA452732 | 12_RRIM600R3 | Latex | H. brasiliensis RRIM 600 |
| SA452733 | 10_RRIM600R1 | Latex | H. brasiliensis RRIM 600 |
| SA452734 | 07_Hcollina1 | Latex | H. collina |
| SA452735 | 08_Hcollina1 | Latex | H. collina |
| SA452736 | 09_Hcollina1 | Latex | H. collina |
| SA452737 | 05_Hconfusa2 | Latex | H. confusa |
| SA452738 | 06_Hconfusa3 | Latex | H. confusa |
| SA452739 | 04_Hconfusa1 | Latex | H. confusa |
| SA452740 | 13_HguianensisR1 | Latex | H. guianensis |
| SA452741 | 14_HguianensisR2 | Latex | H. guianensis |
| SA452742 | 15_HguianensisR3 | Latex | H. guianensis |
| SA452743 | 19_Hpauciflora1 | Latex | H. pauciflora |
| SA452744 | 20_Hpauciflora2 | Latex | H. pauciflora |
| SA452745 | 21_Hpauciflora3 | Latex | H. pauciflora |
| SA452746 | 02_Hspruceana2 | Latex | H. spruceana |
| SA452747 | 03_Hspruceana3 | Latex | H. spruceana |
| SA452748 | 01_Hspruceana1 | Latex | H. spruceana |
| Showing results 1 to 18 of 18 |
Collection:
| Collection ID: | CO004088 |
| Collection Summary: | All samples used in this study were obtained from mature, seven-year-old H. brasiliensis and other Hevea species grown at the same location within the plantation of the Rubber Research Institute of Indonesia. Latex samples were harvested for lipidomic analyses. To standardize latex sampling, each tree was tapped once on the same morning, and 2 mL of latex was collected immediately after tapping. The trees are maintained as a species collection for research purposes; they were not part of a commercial plantation and thus were not regularly tapped. |
| Sample Type: | Latex |
| Collection Method: | Tapping |
| Collection Location: | Sembawa, Indonesia |
Treatment:
| Treatment ID: | TR004104 |
| Treatment Summary: | No special treatment was applied other than sample preparation. |
| Plant Growth Support: | seven-year-old |
| Plant Growth Location: | Sembawa, Indonesia |
Sample Preparation:
| Sampleprep ID: | SP004101 |
| Sampleprep Summary: | 100 µL of chloroform was added to 1 mg of latex samples, followed by shaking, sonication, and centrifugation. Methanol was then added to 50 µL of the supernatant, stirred, and centrifuged again, and the supernatant was collected. Lysophosphatidylcholine (18:1-d7) was added as an internal standard at a final concentration of 500 ng/mL, and the sample was analysed using LC-MS/MS. |
Combined analysis:
| Analysis ID | AN006505 | AN006506 |
|---|---|---|
| Chromatography ID | CH004941 | CH004941 |
| MS ID | MS006204 | MS006205 |
| Analysis type | MS | MS |
| Chromatography type | Reversed phase | Reversed phase |
| Chromatography system | Thermo Dionex Ultimate 3000 RS | Thermo Dionex Ultimate 3000 RS |
| Column | CERI L-column3 C18 Metal-Free column (100 x 2mm, 2µm) | CERI L-column3 C18 Metal-Free column (100 x 2mm, 2µm) |
| MS Type | ESI | ESI |
| MS instrument type | Orbitrap | Orbitrap |
| MS instrument name | Thermo LTQ XL | Thermo LTQ XL |
| Ion Mode | POSITIVE | NEGATIVE |
| Units | peak area | peak area |
Chromatography:
| Chromatography ID: | CH004941 |
| Chromatography Summary: | Chromatographic separation was achieved using an L-column3 C18 metal-free column (2.0 mm I.D. × 100 mm, 2 µm particle size; CERI). Solvent A: 59% ultrapure water; 40% acetonitrile; 1% 1 M ammonium formate solution; 0.1% formic acid. Solvent B: 90% 2-propanol; 9% acetonitrile; 1% 1 M ammonium formate solution;0.1% formic acid. |
| Instrument Name: | Thermo Dionex Ultimate 3000 RS |
| Column Name: | CERI L-column3 C18 Metal-Free column (100 x 2mm, 2µm) |
| Column Temperature: | 55℃ |
| Flow Gradient: | Time (min):%B: 0.0:25, 0.5:25, 6.5:60, 21.5:90, 22.0:99, 26.0:99, 26.1:25, 35.0:25 |
| Flow Rate: | 0.2 mL/min |
| Solvent A: | 60% water/40% acetonitrile; 10 mM ammonium formate solution; 0.1% formic acid |
| Solvent B: | 90% Isopropanol/10% acetonitrile; 10mM ammonium formate;0.1% formic acid |
| Chromatography Type: | Reversed phase |
MS:
| MS ID: | MS006204 |
| Analysis ID: | AN006505 |
| Instrument Name: | Thermo LTQ XL |
| Instrument Type: | Orbitrap |
| MS Type: | ESI |
| MS Comments: | Data analysis, including peak detection, lipid species estimation within each class, and sample alignment, was conducted using MS-DIAL (v4.80). Lipid peaks were considered detected if they met the following criteria: peak height in QC samples ≥10,000; peak area at least twice that of the operational blank; average signal-to-noise ratio ≥3; and consistent detection across all QC measurements with a coefficient of variation <20%. The lipid content was determined relative to an internal standard by comparing the analyte peak area. OPLS-DA was performed using the R package ropls (v1.39.0) to estimate lipid differences between H. brasiliensis and other Hevea species. Lipid abundances were log-transformed prior to analysis. Variable importance in projection values were obtained from ropls, and p-values were calculated using a two-sample t-test. |
| Ion Mode: | POSITIVE |
| MS ID: | MS006205 |
| Analysis ID: | AN006506 |
| Instrument Name: | Thermo LTQ XL |
| Instrument Type: | Orbitrap |
| MS Type: | ESI |
| MS Comments: | - |
| Ion Mode: | NEGATIVE |
