Summary of Study ST003768
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 | ST003768 |
| Study Title | The Chromosome-Scale Assembly and Multi-Omics Analysis Reveal Adaptive Evolution and Nitrogen Utilization Mechanisms in Edible Grass |
| Study Summary | Edible grass, 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 |
| lizhu@stu.hunau.edu.cn | |
| Phone | 15211045071 |
| Submit Date | 2025-02-12 |
| Raw Data Available | Yes |
| Raw Data File Type(s) | wiff |
| Analysis Type Detail | LC-MS |
| Release Date | 2025-03-05 |
| 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: | SU003901 |
| 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 | data | Sample source |
|---|---|---|---|
| SA409586 | Y-3d-2 | 3 day | leaf |
| SA409587 | Y-3d-6 | 3 day | leaf |
| SA409588 | Y-3d-5 | 3 day | leaf |
| SA409589 | Y-3d-4 | 3 day | leaf |
| SA409590 | Y-3d-3 | 3 day | leaf |
| SA409591 | Y-3d-1 | 3 day | leaf |
| SA409592 | G-3d-1 | 3 day | root |
| SA409593 | G-3d-6 | 3 day | root |
| SA409594 | G-3d-3 | 3 day | root |
| SA409595 | G-3d-5 | 3 day | root |
| SA409596 | G-3d-4 | 3 day | root |
| SA409597 | G-3d-2 | 3 day | root |
| SA409598 | Y-9d-1 | 9 day | leaf |
| SA409599 | Y-9d-2 | 9 day | leaf |
| SA409600 | Y-9d-3 | 9 day | leaf |
| SA409601 | Y-9d-4 | 9 day | leaf |
| SA409602 | Y-9d-5 | 9 day | leaf |
| SA409603 | Y-9d-6 | 9 day | leaf |
| SA409604 | G-9d-1 | 9 day | root |
| SA409605 | G-9d-6 | 9 day | root |
| SA409606 | G-9d-5 | 9 day | root |
| SA409607 | G-9d-3 | 9 day | root |
| SA409608 | G-9d-4 | 9 day | root |
| SA409609 | G-9d-2 | 9 day | root |
| Showing results 1 to 24 of 24 |
Collection:
| Collection ID: | CO003894 |
| 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: | Root; Leaf |
Treatment:
| Treatment ID: | TR003910 |
| Treatment Summary: | Immediately post-collection, samples were submerged in liquid nitrogen to halt metabolic activities and maintain biochemical integrity. |
Sample Preparation:
| Sampleprep ID: | SP003907 |
| Sampleprep Summary: | 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. |
Combined analysis:
| Analysis ID | AN006185 | AN006186 |
|---|---|---|
| Analysis type | MS | MS |
| Chromatography type | HILIC | HILIC |
| Chromatography system | LC20 Ultra High Performance Liquid Chromatograph (Shimadzu) | LC20 Ultra High Performance Liquid Chromatograph (Shimadzu) |
| Column | Waters ACQUITY UPLC HSS T3 (100 x 2.1mm,1.8um) | Waters ACQUITY UPLC HSS T3 (100 x 2.1mm,1.8um) |
| 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 | ug/g | μg/g |
Chromatography:
| Chromatography ID: | CH004695 |
| Instrument Name: | LC20 Ultra High Performance Liquid Chromatograph (Shimadzu) |
| Column Name: | Waters ACQUITY UPLC HSS T3 (100 x 2.1mm,1.8um) |
| Column Temperature: | 40℃ |
| Flow Gradient: | At the beginning of the analysis (0 minutes), the analysis was performed at A flow rate of 0.4 mL/min with a ratio of 95% solvent A and 5% solvent B. Over the next 11 minutes, the proportion of solvent A gradually decreases to 10%, while the proportion of solvent B correspondingly increases to 90% and maintains this proportion until 12 minutes. At 12.1 minutes, the solvent ratio is quickly adjusted back to the initial condition, i.e. 95% for solvent A and 5% for solvent B, and maintained until 14 minutes in preparation for the next analysis run. |
| 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: | MS005889 |
| Analysis ID: | AN006185 |
| Instrument Name: | ABI Sciex 6600 TripleTOF |
| Instrument Type: | Triple TOF |
| MS Type: | ESI |
| MS Comments: | In the positive and negative ion mode of mass spectrometry analysis, the mass spectrum conditions are fine-tuned to ensure accuracy. Specifically, the ionization voltage is set to 5500 volts in ESI+ mode and -4500 volts in ESI-mode. The atomizer gas pressure is uniformly adjusted to 50psi to achieve a stable ionization process. The cluster voltage is 60 volts in ESI+ mode and -60 volts in ESI-mode to optimize ion transport and detection. The curtain gas pressure is set to 35psi to effectively control the ion path into the mass spectrometer. The system temperature is maintained at 550 degrees Celsius, providing a suitable thermal environment for mass spectrometry analysis. The auxiliary heating gas pressure is set to 60 psi to further ensure ionization efficiency. Finally, the impact energy of ESI+ mode is set to 30 volts, and the impact energy of ESI- mode is set to -30 volts to meet the requirements of ion fragmentation under different mass spectrum conditions. These carefully designed parameters together ensure the high sensitivity and resolution of mass spectrometry analysis. |
| Ion Mode: | POSITIVE |
| MS ID: | MS005890 |
| Analysis ID: | AN006186 |
| Instrument Name: | ABI Sciex 6600 TripleTOF |
| Instrument Type: | Triple TOF |
| MS Type: | ESI |
| MS Comments: | In the positive and negative ion mode of mass spectrometry analysis, the mass spectrum conditions are fine-tuned to ensure accuracy. Specifically, the ionization voltage is set to 5500 volts in ESI+ mode and -4500 volts in ESI-mode. The atomizer gas pressure is uniformly adjusted to 50psi to achieve a stable ionization process. The cluster voltage is 60 volts in ESI+ mode and -60 volts in ESI-mode to optimize ion transport and detection. The curtain gas pressure is set to 35psi to effectively control the ion path into the mass spectrometer. The system temperature is maintained at 550 degrees Celsius, providing a suitable thermal environment for mass spectrometry analysis. The auxiliary heating gas pressure is set to 60 psi to further ensure ionization efficiency. Finally, the impact energy of ESI+ mode is set to 30 volts, and the impact energy of ESI- mode is set to -30 volts to meet the requirements of ion fragmentation under different mass spectrum conditions. These carefully designed parameters together ensure the high sensitivity and resolution of mass spectrometry analysis. |
| Ion Mode: | NEGATIVE |
