#METABOLOMICS WORKBENCH liuhaijiao_0611_20210125_044243 DATATRACK_ID:2418 STUDY_ID:ST001713 ANALYSIS_ID:AN002788 PROJECT_ID:PR001097 VERSION 1 CREATED_ON February 23, 2021, 1:17 am #PROJECT PR:PROJECT_TITLE Study on metabolites of Panax notoginseng under different densities PR:PROJECT_TYPE Ms qualitative research PR:PROJECT_SUMMARY At the moderate planting density, the primary metabolism (starch and sucrose PR:PROJECT_SUMMARY metabolism) of the plants were significantly enhanced. However, the strong PR:PROJECT_SUMMARY intraspecific competition at the higher planting densities resulted in stress as PR:PROJECT_SUMMARY well as the accumulation of antioxidants (gentiobiose, oxalic acid, PR:PROJECT_SUMMARY dehydroascorbic acid) and other stress resistance-related metabolites. PR:PROJECT_SUMMARY Interestingly, the planting at low densities with low intraspecific competition PR:PROJECT_SUMMARY disturbed normal carbohydrate metabolism by upregulating galactose metabolism. PR:INSTITUTE Yunnan Agricultural University PR:DEPARTMENT Crop Protection Institute PR:LABORATORY Key Laboratory for Agro-biodiversity and Pest Control of Ministry of Education PR:LAST_NAME Liu PR:FIRST_NAME haijiao PR:ADDRESS 452 Fengyuan road, kunming, Yunnan, 650051, China PR:EMAIL 15832256149@163.com PR:PHONE +8615288149641 PR:FUNDING_SOURCE This work was supported by the National Key Research and Development Program of PR:FUNDING_SOURCE China (2017YFC1702502; 2018YFD0201100), Yunnan provincial key programs of Yunnan PR:FUNDING_SOURCE Eco-friendly Food International Cooperation Research Center project under grant PR:FUNDING_SOURCE (2019ZG00901), the Yunnan Academician Workstation of Chinese Academy of PR:FUNDING_SOURCE Engineering (2018IC063), the Young and Middle-aged Academic and Technical PR:FUNDING_SOURCE Leaders Reserve Programme in Yunnan Province (2017HB024), the Yunnan Ten PR:FUNDING_SOURCE Thousand Talents Plan Young & Elite Talents Project and Program for Innovative PR:FUNDING_SOURCE Research Team in Science and Technology in University of Yunnan Province (to PR:FUNDING_SOURCE Shusheng Zhu) #STUDY ST:STUDY_TITLE Effects of different planting densities on the metabolism of Panax notoginseng ST:STUDY_TYPE Planting density experiment ST:STUDY_SUMMARY At the moderate planting density, the primary metabolism (starch and sucrose ST:STUDY_SUMMARY metabolism) of the plants were significantly enhanced. However, the strong ST:STUDY_SUMMARY intraspecific competition at the higher planting densities resulted in stress as ST:STUDY_SUMMARY well as the accumulation of antioxidants (gentiobiose, oxalic acid, ST:STUDY_SUMMARY dehydroascorbic acid) and other stress resistance-related metabolites. ST:STUDY_SUMMARY Interestingly, the planting at low densities with low intraspecific competition ST:STUDY_SUMMARY disturbed normal carbohydrate metabolism by upregulating galactose metabolism. ST:INSTITUTE Yunnan Agricultural University ST:DEPARTMENT College of Plant Protection ST:LABORATORY Key Laboratory for Agro-biodiversity and Pest Control of Ministry of Education ST:LAST_NAME Haijiao ST:FIRST_NAME Liu ST:ADDRESS 452 Fengyuan road, Kunming, Yunnan, China ST:EMAIL 15832256149@163.com ST:PHONE +8615288149641 #SUBJECT SU:SUBJECT_TYPE Plant SU:SUBJECT_SPECIES Panax notoginseng SU:TAXONOMY_ID 44586 SU:GENDER Not applicable #SUBJECT_SAMPLE_FACTORS: SUBJECT(optional)[tab]SAMPLE[tab]FACTORS(NAME:VALUE pairs separated by |)[tab]Raw file names and additional sample data SUBJECT_SAMPLE_FACTORS Panax notoginseng 8cm_1 Treatment:8cm RAW_FILE_NAME=8cm_1.raw SUBJECT_SAMPLE_FACTORS Panax notoginseng 8cm_2 Treatment:8cm RAW_FILE_NAME=8cm_2.raw SUBJECT_SAMPLE_FACTORS Panax notoginseng 8cm_3 Treatment:8cm RAW_FILE_NAME=8cm_3.raw SUBJECT_SAMPLE_FACTORS Panax notoginseng 8cm_4 Treatment:8cm RAW_FILE_NAME=8cm_4.raw SUBJECT_SAMPLE_FACTORS Panax notoginseng 10cm_1 Treatment:10cm RAW_FILE_NAME=10cm_1.raw SUBJECT_SAMPLE_FACTORS Panax notoginseng 10cm_2 Treatment:10cm RAW_FILE_NAME=10cm_2.raw SUBJECT_SAMPLE_FACTORS Panax notoginseng 10cm_3 Treatment:10cm RAW_FILE_NAME=10cm_3.raw SUBJECT_SAMPLE_FACTORS Panax notoginseng 10cm_4 Treatment:10cm RAW_FILE_NAME=10cm_4.raw SUBJECT_SAMPLE_FACTORS Panax notoginseng 15cm_1 Treatment:15cm RAW_FILE_NAME=15cm_1.raw SUBJECT_SAMPLE_FACTORS Panax notoginseng 15cm_2 Treatment:15cm RAW_FILE_NAME=15cm_2.raw SUBJECT_SAMPLE_FACTORS Panax notoginseng 15cm_3 Treatment:15cm RAW_FILE_NAME=15cm_3.raw SUBJECT_SAMPLE_FACTORS Panax notoginseng 15cm_4 Treatment:15cm RAW_FILE_NAME=15cm_4.raw SUBJECT_SAMPLE_FACTORS Panax notoginseng 20cm_1 Treatment:20cm RAW_FILE_NAME=20cm_1.raw SUBJECT_SAMPLE_FACTORS Panax notoginseng 20cm_2 Treatment:20cm RAW_FILE_NAME=20cm_2.raw SUBJECT_SAMPLE_FACTORS Panax notoginseng 20cm_3 Treatment:20cm RAW_FILE_NAME=20cm_3.raw SUBJECT_SAMPLE_FACTORS Panax notoginseng 20cm_4 Treatment:20cm RAW_FILE_NAME=20cm_4.raw SUBJECT_SAMPLE_FACTORS Panax notoginseng 30cm_1 Treatment:30cm RAW_FILE_NAME=30cm_1.raw SUBJECT_SAMPLE_FACTORS Panax notoginseng 30cm_2 Treatment:30cm RAW_FILE_NAME=30cm_2.raw SUBJECT_SAMPLE_FACTORS Panax notoginseng 30cm_3 Treatment:30cm RAW_FILE_NAME=30cm_3.raw SUBJECT_SAMPLE_FACTORS Panax notoginseng 30cm_4 Treatment:30cm RAW_FILE_NAME=30cm_4.raw #COLLECTION CO:COLLECTION_SUMMARY Fresh fibrous root of Panax notoginseng were washed with sterile water and then CO:COLLECTION_SUMMARY flash-frozen in liquid N2 CO:SAMPLE_TYPE Fibrous root #TREATMENT TR:TREATMENT_SUMMARY The experimental design for P. notoginseng cultivation is as follows: Each TR:TREATMENT_SUMMARY plastic basin (65×40×18 cm) contains about 40 kg natural soil, which was TR:TREATMENT_SUMMARY collected from a pine forest in Xundian Country, Yunnan, China (103.29°E, TR:TREATMENT_SUMMARY 25.51°N; altitude of 1960 m), then sieved to remove the residue of plant. The TR:TREATMENT_SUMMARY soil had the following characteristics: pH 5.17, electrical conductivity 458 μS TR:TREATMENT_SUMMARY cm-1, available potassium (K) 6.90 mg kg-1, available phosphate (P) 5.18 mg TR:TREATMENT_SUMMARY kg-1, alkali-hydrolyzable nitrogen (N) 172.38 mg kg-1 and organic matter 47830 TR:TREATMENT_SUMMARY mg kg-1. 4, 12, 15, 28, 45 healthy one-year old seedlings were planted in TR:TREATMENT_SUMMARY January 3, 2016 at a plant spacing of 30 cm, 20 cm, 15 cm, 10 cm and 8 cm, TR:TREATMENT_SUMMARY respectively. There were four repeats for each treatment, and a total of 20 TR:TREATMENT_SUMMARY plastic basins were placed in a completely randomized block design in TR:TREATMENT_SUMMARY greenhouse. The fresh fibrous root of P. notoginseng was collected in November TR:TREATMENT_SUMMARY 30, 2016. #SAMPLEPREP SP:SAMPLEPREP_SUMMARY Approximately 60 mg of frozen powder fibrous roots and 1 mL of methanol (CH3OH) SP:SAMPLEPREP_SUMMARY containing 0.5 mg of ribitol were added into a prechilled 2 mL lock-cap SP:SAMPLEPREP_SUMMARY centrifuge tube, then vortexed for 10 s. A 300 μL extraction aliquot SP:SAMPLEPREP_SUMMARY (H2O:methanol:chloroform=1:2.5:1, v:v:v) was added and ultrasonically extracted SP:SAMPLEPREP_SUMMARY for 30 min at 37°C. Then, the sample was centrifuged (1600 g, 3 min) to SP:SAMPLEPREP_SUMMARY separate the polar and nonpolar phases. Then the upper polar phase was SP:SAMPLEPREP_SUMMARY transferred to a fresh centrifuge tube and added 200 μL sterile water, and then SP:SAMPLEPREP_SUMMARY vortexed and centrifuged (1600 g, 4°C for 3 min). A 250 μL aliquot of the SP:SAMPLEPREP_SUMMARY upper phase was transferred to a fresh centrifuge tube, dried for 3-4 h at room SP:SAMPLEPREP_SUMMARY temperature using a SpeedVac (Christ, Germany). Adding 80 μL of methoxyamine SP:SAMPLEPREP_SUMMARY hydrochloride solution (20 mg mL-1 dissolved in pyridine) to each sample and SP:SAMPLEPREP_SUMMARY incubating for 90 min at 30°C to protect carbonyl moieties. And then, 40 μL SP:SAMPLEPREP_SUMMARY N-methyl-N-(trimethylsilyl)-trifluoroacetamide (MSTFA) was added and incubating SP:SAMPLEPREP_SUMMARY at 37°C for 30 min to trimethylsilylate the acidic protons. After this step, SP:SAMPLEPREP_SUMMARY the sample was centrifuged (1600 g, 4°C for 3 min), then the supernatant was SP:SAMPLEPREP_SUMMARY stored at 4°C for further analysis. #CHROMATOGRAPHY CH:CHROMATOGRAPHY_TYPE GC CH:INSTRUMENT_NAME Shimadzu GCMS-QP2010 ultra CH:COLUMN_NAME Agilent HP5-MS (30m x 0.25mm, 0.25 um) #ANALYSIS AN:ANALYSIS_TYPE MS #MS MS:INSTRUMENT_NAME Shimadzu QP2010 Ultra MS:INSTRUMENT_TYPE GC-TOF MS:MS_TYPE EI MS:ION_MODE UNSPECIFIED MS:MS_COMMENTS Mass spectra were obtained in electron impact (EI) ionization mode at 70 eV by MS:MS_COMMENTS monitoring the full-scan range (m/z 45-600);the raw peak obtained by data MS:MS_COMMENTS baseline filtering and calibration, peak alignment, deconvolution analysis and MS:MS_COMMENTS peak identification using MS-DIAL with the Fiehn library. The peak areas of MS:MS_COMMENTS metabolites in raw MS-Dial output (Supplementary Table S2) were normalization by MS:MS_COMMENTS sum, transformation by log and scaling by Pareto method on Metaboanalyst 4.0 MS:MS_COMMENTS (http://www.metaboanalyst.ca/MetaboAnalyst/) MS:MS_RESULTS_FILE ST001713_AN002788_Results.txt UNITS:Peak area Has m/z:Yes Has RT:Yes RT units:Minutes #END