Summary of Study ST003736
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 PR002322. The data can be accessed directly via it's Project DOI: 10.21228/M8GV64 This work is supported by NIH grant, U2C- DK119886.
See: https://www.metabolomicsworkbench.org/about/howtocite.php
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.
| Study ID | ST003736 |
| Study Title | The Chromosome-Scale Assembly and Multi-Omics Analysis Reveal Adaptive Evolution and Nitrogen Utilization Mechanisms in Edible Grass (Rumex patientia L.× Rumex tianschanicus A. LOS) |
| Study Summary | Edible grass (Rumex patientia L.× Rumex tianschanicus A. LOS), a perennial herbaceous plant from the Polygonaceae family, boasts a high protein content and rapid growth rate, making it a promising solution to feed shortages as a forage protein source. In this study, we utilized the PacBio sequencing platform and integrated methods including Hi-C to achieve a chromosomal-scale assembly of the R. patientia genome. The assembled genome spans 2.19 Gb with an N50 of 18.84 Mb, and 93.61% (2.05 Gb) of the assembly has been allocated to 30 pseudochromosomes. Comparative genomic analysis has revealed significant expansion of gene families involved in nitrogen metabolism and D-glutamine and D-glutamate metabolism pathways, which are responsible for the plant's strong nitrogen utilization capabilities and high protein content. Additionally, expansions in gene families associated with the Wnt signaling pathway, ubiquitin-mediated proteolysis, Toll and Imd signaling pathways, TGF-β signaling pathway, protein processing in the endoplasmic reticulum, photosynthesis-antenna proteins, circadian rhythm, and cell cycle pathways are closely related to the rapid growth and development of R. patientia. We have also identified the rhizosphere microbiome of R. patientia and, by integrating metabolomic data from root tissues and soil, found that during rapid growth phases, the plant secretes various apigenin-like compounds into the soil, enhancing the symbiotic nitrogen-fixing capabilities and potentially providing nitrogen sources to the leaves through symbiotic nitrogen fixation. Our research provides crucial insights into the genetic basis of R. patientia 's utility as a forage protein source. |
| Institute | Hunan Agricultural University |
| Last Name | li |
| First Name | zhu |
| Address | 1 Nongda Road, Changsha City, Hunan Province, Changsha, Hunan, 410128, China |
| lizhu@stu.hunau.edu.cn | |
| Phone | 15211045071 |
| Submit Date | 2025-02-11 |
| Raw Data Available | Yes |
| Raw Data File Type(s) | wiff |
| Analysis Type Detail | LC-MS |
| Release Date | 2025-02-21 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
Project:
| Project ID: | PR002322 |
| Project DOI: | doi: 10.21228/M8GV64 |
| Project Title: | The Chromosome-Scale Assembly and Multi-Omics Analysis Reveal Adaptive Evolution and Nitrogen Utilization Mechanisms in Edible Grass (Rumex patientia L.× Rumex tianschanicus A. LOS) |
| Project Summary: | Edible grass (Rumex patientia L.× Rumex tianschanicus A. LOS), a perennial herbaceous plant from the Polygonaceae family, boasts a high protein content and rapid growth rate, making it a promising solution to feed shortages as a forage protein source. In this study, we utilized the PacBio sequencing platform and integrated methods including Hi-C to achieve a chromosomal-scale assembly of the R. patientia genome. The assembled genome spans 2.19 Gb with an N50 of 18.84 Mb, and 93.61% (2.05 Gb) of the assembly has been allocated to 30 pseudochromosomes. Comparative genomic analysis has revealed significant expansion of gene families involved in nitrogen metabolism and D-glutamine and D-glutamate metabolism pathways, which are responsible for the plant's strong nitrogen utilization capabilities and high protein content. Additionally, expansions in gene families associated with the Wnt signaling pathway, ubiquitin-mediated proteolysis, Toll and Imd signaling pathways, TGF-β signaling pathway, protein processing in the endoplasmic reticulum, photosynthesis-antenna proteins, circadian rhythm, and cell cycle pathways are closely related to the rapid growth and development of R. patientia. We have also identified the rhizosphere microbiome of R. patientia and, by integrating metabolomic data from root tissues and soil, found that during rapid growth phases, the plant secretes various apigenin-like compounds into the soil, enhancing the symbiotic nitrogen-fixing capabilities and potentially providing nitrogen sources to the leaves through symbiotic nitrogen fixation. Our research provides crucial insights into the genetic basis of R. patientia 's utility as a forage protein source. |
| Institute: | Hunan Agricultural University |
| Last Name: | li |
| First Name: | zhu |
| Address: | 1 Nongda Road, Changsha City, Hunan Province, Changsha, Hunan, 410128, China |
| Email: | lizhu@stu.hunau.edu.cn |
| Phone: | 15211045071 |
Subject:
| Subject ID: | SU003868 |
| Subject Type: | Plant |
| Subject Species: | Rumex patientia L.× Rumex tianschanicus A. LOS |
| Taxonomy ID: | 3143261 |
Factors:
Subject type: Plant; Subject species: Rumex patientia L.× Rumex tianschanicus A. LOS (Factor headings shown in green)
| mb_sample_id | local_sample_id | Sample date | Sample source | Group |
|---|---|---|---|---|
| SA407784 | T-G3-1 | 3 day | Rhizosphere soil | T-G3 |
| SA407785 | T-G3-2 | 3 day | Rhizosphere soil | T-G3 |
| SA407786 | T-G3-3 | 3 day | Rhizosphere soil | T-G3 |
| SA407787 | T-G3-4 | 3 day | Rhizosphere soil | T-G3 |
| SA407788 | T-G3-5 | 3 day | Rhizosphere soil | T-G3 |
| SA407789 | T-G3-6 | 3 day | Rhizosphere soil | T-G3 |
| SA407790 | T-G9-1 | 9 day | Rhizosphere soil | T-G9 |
| SA407791 | T-G9-2 | 9 day | Rhizosphere soil | T-G9 |
| SA407792 | T-G9-3 | 9 day | Rhizosphere soil | T-G9 |
| SA407793 | T-G9-4 | 9 day | Rhizosphere soil | T-G9 |
| SA407794 | T-G9-5 | 9 day | Rhizosphere soil | T-G9 |
| SA407795 | T-G9-6 | 9 day | Rhizosphere soil | T-G9 |
| Showing results 1 to 12 of 12 |
Collection:
| Collection ID: | CO003861 |
| Collection Summary: | All plant materials used in this study were collected and utilized in accordance with local, national, and international guidelines and regulations. Necessary permissions for sample collection were obtained from relevant authorities, and no protected or endangered species were involved in this research. R. patientia was cultivated at Hunan Agricultural University, located in Changsha City, Hunan Province, for comprehensive molecular profiling. We collected fresh, healthy roots and leaves from plants at two distinct growth stages, specifically on the 3rd and 9th days after planting, with six biological replicates at each time point to ensure statistical robustness. |
| Sample Type: | Rhizosphere soil |
Treatment:
| Treatment ID: | TR003877 |
| Treatment Summary: | Immediately post-collection, samples were submerged in liquid nitrogen to halt metabolic activities and maintain biochemical integrity. Each sample was subsequently finely ground in liquid nitrogen, and the resulting homogenized tissue was divided into aliquots: one for RNA extraction, another for protein isolation, and additional portions for Untargeted metabolomics analysis. This meticulous division guarantees consistent and comparative datasets across transcriptomic, proteomic, and metabolomic analyses. |
Sample Preparation:
| Sampleprep ID: | SP003874 |
| Sampleprep Summary: | Take out the sample from the -80°C refrigerator and thaw it on ice. Mix 500 mg of the sample and 1000 µL of 70% methanol water internal standard extractant, vortex for 3 minutes, then sonicate for 10 minutes in ice water bath, and stand still at -20°C for 30 minutes. Centrifuge (12000 rpm, 4°C) for 10 min, and transfer 300 µL of the supernatant to a new centrifugal tube. Finally centrifuge (12000 rpm, 4°C) for 3 min and take the supernatant for analysis. All samples were acquired by the LC-MS system followed machine orders. The analytical conditions were as follows, UPLC: column, Waters ACQUITY UPLC HSS T3 C18 (1.8 µm, 2.1 mm*100 mm); column temperature, 40℃; flow rate, 0.4 mL/min; injection volume, 2 μL; solvent system, water (0.1% formic acid): acetonitrile (0.1% formic acid); The column was eluted with 5% mobile phase B (0.1% formic acid in acetonitrile) at 0 minute followed by a linear gradient to 90% mobile phase B (0.1% formic acid in acetonitrile) over 11 minutes, held for 1 minute, and then come back to 5% mobile phase B within 0.1 minute, held for 1.9 minutes. |
Combined analysis:
| Analysis ID | AN006130 | AN006131 |
|---|---|---|
| Analysis type | MS | MS |
| Chromatography type | HILIC | HILIC |
| Chromatography system | Shimadzu 20AD | Shimadzu 20AD |
| Column | Waters ACQUITY UPLC HSS C18 (100 x 2.1 mm, 1.8 µm) | Waters ACQUITY UPLC HSS C18 (100 x 2.1 mm, 1.8 µm) |
| MS Type | ESI | ESI |
| MS instrument type | Triple TOF | Triple TOF |
| MS instrument name | ABI Sciex 6600 TripleTOF | ABI Sciex 6600 TripleTOF |
| Ion Mode | POSITIVE | NEGATIVE |
| Units | µg/g | µg/g |
Chromatography:
| Chromatography ID: | CH004655 |
| Instrument Name: | Shimadzu 20AD |
| Column Name: | Waters ACQUITY UPLC HSS C18 (100 x 2.1 mm, 1.8 µm) |
| Column Temperature: | 40℃ |
| Flow Gradient: | 0 - 11 min 95% A (5% B) to 10% A (90% B); 11.0 - 12.0 10% A; at 12.1 min quickly adjusted to 95% A (5% B); 12.1 - 14.0 min 95% A (5% B) |
| Flow Rate: | 0.40 mL/min |
| Solvent A: | 100% Ultrapure water; 0.1% formic acid |
| Solvent B: | 100% Acetonitrile; 0.1% formic acid |
| Chromatography Type: | HILIC |
MS:
| MS ID: | MS005836 |
| Analysis ID: | AN006130 |
| Instrument Name: | ABI Sciex 6600 TripleTOF |
| Instrument Type: | Triple TOF |
| MS Type: | ESI |
| MS Comments: | All samples were acquired by the LC-MS system followed machine orders. The analytical conditions were as follows, UPLC: column, Waters ACQUITY UPLC HSS T3 C18 (1.8 µm, 2.1 mm*100 mm); column temperature, 40℃; flow rate, 0.4 mL/min; injection volume, 2 μL; solvent system, water (0.1% formic acid): acetonitrile (0.1% formic acid); The column was eluted with 5% mobile phase B (0.1% formic acid in acetonitrile) at 0 minute followed by a linear gradient to 90% mobile phase B (0.1% formic acid in acetonitrile) over 11 minutes, held for 1 minute, and then come back to 5% mobile phase B within 0.1 minute, held for 1.9 minutes. |
| Ion Mode: | POSITIVE |
| MS ID: | MS005837 |
| Analysis ID: | AN006131 |
| Instrument Name: | ABI Sciex 6600 TripleTOF |
| Instrument Type: | Triple TOF |
| MS Type: | ESI |
| MS Comments: | All samples were acquired by the LC-MS system followed machine orders. The analytical conditions were as follows, UPLC: column, Waters ACQUITY UPLC HSS T3 C18 (1.8 µm, 2.1 mm*100 mm); column temperature, 40℃; flow rate, 0.4 mL/min; injection volume, 2 μL; solvent system, water (0.1% formic acid): acetonitrile (0.1% formic acid); The column was eluted with 5% mobile phase B (0.1% formic acid in acetonitrile) at 0 minute followed by a linear gradient to 90% mobile phase B (0.1% formic acid in acetonitrile) over 11 minutes, held for 1 minute, and then come back to 5% mobile phase B within 0.1 minute, held for 1.9 minutes. |
| Ion Mode: | NEGATIVE |
