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
Email	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

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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.

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.