#METABOLOMICS WORKBENCH jrenaud86_20191216_121902 DATATRACK_ID:1870 STUDY_ID:ST001293 ANALYSIS_ID:AN002154 PROJECT_ID:PR000875 VERSION 1 CREATED_ON December 22, 2019, 4:06 pm #PROJECT PR:PROJECT_TITLE Metabolomic profiling of fungal pathogens responsible for root rot in American PR:PROJECT_TITLE ginseng PR:PROJECT_SUMMARY Ginseng root is an economically valuable crop in Canada at high risk of yield PR:PROJECT_SUMMARY loss caused by the pathogenic fungus Ilyonectria mors-panacis, formerly known as PR:PROJECT_SUMMARY Cylindrocarpon destructans. While this pathogen has been well-characterized from PR:PROJECT_SUMMARY morphological and genetic perspectives, little is known the secondary PR:PROJECT_SUMMARY metabolites it produces and their role in pathogenicity. We used an untargeted PR:PROJECT_SUMMARY LC-MS/MS-based approach paired with global natural products social molecular PR:PROJECT_SUMMARY networking (GNPS) to compare the metabolite profiles of virulent and avirulent PR:PROJECT_SUMMARY Ilyonectria strains. The ethyl acetate liquid culture extracts of 22 I. PR:PROJECT_SUMMARY mors-panacis strains and closely related species were analyzed by LC-MS/MS. PR:PROJECT_SUMMARY Principal component analysis of LC-MS features resulted in two distinct groups, PR:PROJECT_SUMMARY which corresponded to virulent and avirulent Ilyonectria strains. Virulent PR:PROJECT_SUMMARY strains produced more types of compounds than the avirulent strains. The PR:PROJECT_SUMMARY previously reported I. mors-panacis antifungal compound radicicol was present. PR:PROJECT_SUMMARY Additionally, a number of related resorcyclic acid lactones (RALs) were PR:PROJECT_SUMMARY putatively identified, namely pochonins and several additional derivatives of PR:PROJECT_SUMMARY radicicol. Pochonins have not been previously reported in Ilyonectria spp. and PR:PROJECT_SUMMARY have documented antimicrobial activity. This research contributes to our PR:PROJECT_SUMMARY understanding of I. mors-panacis natural products and its pathogenic PR:PROJECT_SUMMARY relationship with ginseng. PR:INSTITUTE Agriculture and Agri-Food Canada PR:LAST_NAME Renaud PR:FIRST_NAME Justin PR:ADDRESS 1391 Sandford Street, London, Ontario, LN5V 4T3, Canada PR:EMAIL justin.renaud@agr.gc.ca PR:PHONE 519-953-6698 #STUDY ST:STUDY_TITLE Determining secondary metabolite profile of Ilyonectria spp. pathogenic to ST:STUDY_TITLE ginseng root ST:STUDY_SUMMARY This experiment aims to ascertain a profile of secondary metabolites produced by ST:STUDY_SUMMARY Ilyonectria species capable of causing disappearing root rot in ginseng. ST:STUDY_SUMMARY Ilyonectria isolates were grown on potato dextrose agar for 20 days, then plugs ST:STUDY_SUMMARY were taken from the cultures and extracted with ethyl acetate. Extracts were ST:STUDY_SUMMARY analyzed by LC-HRMS and tandem HRMS. Data were analyzed by Principal component ST:STUDY_SUMMARY analysis and molecular networking with GNPS. ST:INSTITUTE Agriculture and Agri-Food Canada ST:LAST_NAME Renaud ST:FIRST_NAME Justin ST:ADDRESS 1391 Sandford Street, London, Ontario, LN5V 4T3, Canada ST:EMAIL justin.renaud@agr.gc.ca ST:PHONE 519-953-6698 ST:TOTAL_SUBJECTS 22 #SUBJECT SU:SUBJECT_TYPE Fungi SU:SUBJECT_SPECIES Ilyonectria mors-panacis;Ilyonectria rufa;Ilyonectria robusta;Ilyonectria torresensis;Ilyonectria estremocensis;Neonectria obtusispora SU:SUBJECT_SPECIES Ilyonectria mors-panacis;Ilyonectria rufa;Ilyonectria robusta;Ilyonectria torresensis;Ilyonectria estremocensis;Neonectria obtusispora #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 - 139398_Ilyonectria_robusta-140KfullMSneg Virulence:Virulent RAW_FILE_NAME=139398_Ilyonectria_robusta-140KfullMSneg.raw SUBJECT_SAMPLE_FACTORS - 139398_Ilyonectria_robusta-140KfullMSpos Virulence:Virulent RAW_FILE_NAME=139398_Ilyonectria_robusta-140KfullMSpos.raw SUBJECT_SAMPLE_FACTORS - 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PotatoDextroseAgar_blankmedia-MS2pos Virulence:Blank RAW_FILE_NAME=PotatoDextroseAgar_blankmedia-MS2pos.raw SUBJECT_SAMPLE_FACTORS - QC1-140KfullMSneg Virulence:Quality Control RAW_FILE_NAME=QC1-140KfullMSneg.raw SUBJECT_SAMPLE_FACTORS - QC1-140KfullMSpos Virulence:Quality Control RAW_FILE_NAME=QC1-140KfullMSpos.raw SUBJECT_SAMPLE_FACTORS - QC2-140KfullMSneg Virulence:Quality Control RAW_FILE_NAME=QC2-140KfullMSneg.raw SUBJECT_SAMPLE_FACTORS - QC2-140KfullMSpos Virulence:Quality Control RAW_FILE_NAME=QC2-140KfullMSpos.raw SUBJECT_SAMPLE_FACTORS - QC3-140KfullMSneg Virulence:Quality Control RAW_FILE_NAME=QC3-140KfullMSneg.raw SUBJECT_SAMPLE_FACTORS - QC3-140KfullMSpos Virulence:Quality Control RAW_FILE_NAME=QC3-140KfullMSpos.raw SUBJECT_SAMPLE_FACTORS - QC4-140KfullMSneg Virulence:Quality Control RAW_FILE_NAME=QC4-140KfullMSneg.raw SUBJECT_SAMPLE_FACTORS - QC4-140KfullMSpos Virulence:Quality Control RAW_FILE_NAME=QC4-140KfullMSpos.raw SUBJECT_SAMPLE_FACTORS - QC5-140KfullMSneg Virulence:Quality Control RAW_FILE_NAME=QC5-140KfullMSneg.raw SUBJECT_SAMPLE_FACTORS - QC5-140KfullMSpos Virulence:Quality Control RAW_FILE_NAME=QC5-140KfullMSpos.raw SUBJECT_SAMPLE_FACTORS - Radicicol_seedspectra_MS2pos Virulence:GNPS Seed spectra RAW_FILE_NAME=Radicicol_seedspectra_MS2pos.raw SUBJECT_SAMPLE_FACTORS - unknown_compound1_seedspectra_MS2pos Virulence:GNPS Seed spectra RAW_FILE_NAME=unknown_compound1_seedspectra_MS2pos.raw SUBJECT_SAMPLE_FACTORS - unknown_compound2_seedspectra_MS2pos Virulence:GNPS Seed spectra RAW_FILE_NAME=unknown_compound2_seedspectra_MS2pos.raw #COLLECTION CO:COLLECTION_SUMMARY Fungal isolates obtained from the Canadian Fungal Culture Collection (CFCC) at CO:COLLECTION_SUMMARY Agriculture and Agri-Food Canada were grown on potato dextrose agar for 20 days CO:COLLECTION_SUMMARY at 21 C. CO:SAMPLE_TYPE Fungal cells #TREATMENT TR:TREATMENT_SUMMARY All fungal isolates were grown on potato dextrose agar (2.4%, w/v) with 3.47E-5 TR:TREATMENT_SUMMARY zinc sulfate heptahydrate and 3.13E-5 copper sulfate. Plates were grown for 20 TR:TREATMENT_SUMMARY days at 21 C in the dark. #SAMPLEPREP SP:SAMPLEPREP_SUMMARY Cultures were sampled by taking six 0.5-cm plugs from each plate. Plugs were SP:SAMPLEPREP_SUMMARY extracted with 4 mL of ethyl acetate, then dried by centrifugal vacuum SP:SAMPLEPREP_SUMMARY evaporation. Dried extracts were reconstituted in 1 mL of 3:1 methanol:water and SP:SAMPLEPREP_SUMMARY were filtered through 0.45 um PTFE filters (Chromatographic Specialties, Inc.). SP:SAMPLEPREP_SUMMARY Composite quality control samples were made by combining 50 uL from each SP:SAMPLEPREP_SUMMARY completed extract. #CHROMATOGRAPHY CH:CHROMATOGRAPHY_SUMMARY Samples were resolved with a reversed-phase column (C-18) CH:CHROMATOGRAPHY_TYPE Reversed phase CH:INSTRUMENT_NAME Agilent 1290 Infinity CH:COLUMN_NAME Agilent Zorbax EclipsePlus C-18 (50 x 2.1 mm, 1.8 um) CH:FLOW_GRADIENT 0% B for 0.5 minutes, increased to 100% B over 3 minutes, held at 100% B for 2.5 CH:FLOW_GRADIENT minutes, decreased to 0% B over 0.5 minutes, then held at 0% B for 1 minute CH:FLOW_RATE 0.3 mL/min CH:COLUMN_TEMPERATURE 35 CH:SOLVENT_A 0.1% (v/v) formic acid in water CH:SOLVENT_B 0.1% (v/v) formic acid in acetonitrile CH:SAMPLE_INJECTION 5 uL CH:CAPILLARY_VOLTAGE 3900 V #ANALYSIS AN:ANALYSIS_TYPE MS #MS MS:INSTRUMENT_NAME Thermo Q Exactive Orbitrap MS:INSTRUMENT_TYPE Orbitrap MS:MS_TYPE ESI MS:ION_MODE NEGATIVE MS:MS_COMMENTS Data were acquired by untargeted LC-DDA MS:MS_RESULTS_FILE ST001293_AN002154_Results.txt UNITS:Integrated peak area Has m/z:Yes Has RT:Yes RT units:Minutes #END