Summary of Study ST001293

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 PR000875. The data can be accessed directly via it's Project DOI: 10.21228/M8KM4W 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.

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Study IDST001293
Study TitleDetermining secondary metabolite profile of Ilyonectria spp. pathogenic to ginseng root
Study SummaryThis experiment aims to ascertain a profile of secondary metabolites produced by Ilyonectria species capable of causing disappearing root rot in ginseng. Ilyonectria isolates were grown on potato dextrose agar for 20 days, then plugs were taken from the cultures and extracted with ethyl acetate. Extracts were analyzed by LC-HRMS and tandem HRMS. Data were analyzed by Principal component analysis and molecular networking with GNPS.
Institute
Agriculture and Agri-Food Canada
Last NameRenaud
First NameJustin
Address1391 Sandford Street, London, Ontario, LN5V 4T3, Canada
Emailjustin.renaud@agr.gc.ca
Phone519-953-6698
Submit Date2019-12-16
Total Subjects22
Raw Data AvailableYes
Raw Data File Type(s)raw(Thermo)
Analysis Type DetailLC-MS
Release Date2020-04-15
Release Version1
Justin Renaud Justin Renaud
https://dx.doi.org/10.21228/M8KM4W
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

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Project:

Project ID:PR000875
Project DOI:doi: 10.21228/M8KM4W
Project Title:Metabolomic profiling of fungal pathogens responsible for root rot in American ginseng
Project Summary:Ginseng root is an economically valuable crop in Canada at high risk of yield loss caused by the pathogenic fungus Ilyonectria mors-panacis, formerly known as Cylindrocarpon destructans. While this pathogen has been well-characterized from morphological and genetic perspectives, little is known the secondary metabolites it produces and their role in pathogenicity. We used an untargeted LC-MS/MS-based approach paired with global natural products social molecular networking (GNPS) to compare the metabolite profiles of virulent and avirulent Ilyonectria strains. The ethyl acetate liquid culture extracts of 22 I. mors-panacis strains and closely related species were analyzed by LC-MS/MS. Principal component analysis of LC-MS features resulted in two distinct groups, which corresponded to virulent and avirulent Ilyonectria strains. Virulent strains produced more types of compounds than the avirulent strains. The previously reported I. mors-panacis antifungal compound radicicol was present. Additionally, a number of related resorcyclic acid lactones (RALs) were putatively identified, namely pochonins and several additional derivatives of radicicol. Pochonins have not been previously reported in Ilyonectria spp. and have documented antimicrobial activity. This research contributes to our understanding of I. mors-panacis natural products and its pathogenic relationship with ginseng.
Institute:Agriculture and Agri-Food Canada
Last Name:Renaud
First Name:Justin
Address:1391 Sandford Street, London, Ontario, LN5V 4T3, Canada
Email:justin.renaud@agr.gc.ca
Phone:519-953-6698

Subject:

Subject ID:SU001367
Subject Type:Fungi
Subject Species:Ilyonectria mors-panacis;Ilyonectria rufa;Ilyonectria robusta;Ilyonectria torresensis;Ilyonectria estremocensis;Neonectria obtusispora
Species Group:Fungi

Factors:

Subject type: Fungi; Subject species: Ilyonectria mors-panacis;Ilyonectria rufa;Ilyonectria robusta;Ilyonectria torresensis;Ilyonectria estremocensis;Neonectria obtusispora (Factor headings shown in green)

mb_sample_id local_sample_id Virulence
SA093977251609_Ilyonectria_rufa-MS2posAvirulent
SA093978Neonectria_obtusisporum-140KfullMSnegAvirulent
SA093979251609_Ilyonectria_rufa-MS2negAvirulent
SA093980226721_Ilyonectria_rufa-MS2posAvirulent
SA093981226721_Ilyonectria_rufa-MS2negAvirulent
SA093982Neonectria_obtusisporum-140KfullMSposAvirulent
SA093983Neonectria_obtusisporum-MS2negAvirulent
SA093984226730_Ilyonectria_estremocensis-MS2negAvirulent
SA093985226730_Ilyonectria_estremocensis-140KfullMSposAvirulent
SA093986226730_Ilyonectria_estremocensis-140KfullMSnegAvirulent
SA093987Neonectria_obtusisporum-MS2posAvirulent
SA093988226730_Ilyonectria_estremocensis-MS2posAvirulent
SA093989226721_Ilyonectria_rufa-140KfullMSposAvirulent
SA093990144524_Ilyonectria_torresensis-140KfullMSposAvirulent
SA093991144524_Ilyonectria_torresensis-140KfullMSnegAvirulent
SA093992251608_Ilyonectria_rufa-140KfullMSposAvirulent
SA093993251608_Ilyonectria_rufa-140KfullMSnegAvirulent
SA093994226721_Ilyonectria_rufa-140KfullMSnegAvirulent
SA093995144524_Ilyonectria_torresensis-MS2negAvirulent
SA093996251608_Ilyonectria_rufa-MS2posAvirulent
SA093997144524_Ilyonectria_torresensis-MS2posAvirulent
SA093998251609_Ilyonectria_rufa-140KfullMSposAvirulent
SA093999251608_Ilyonectria_rufa-MS2negAvirulent
SA094000251609_Ilyonectria_rufa-140KfullMSnegAvirulent
SA094001PotatoDextroseAgar_blankmedia-MS2negBlank
SA094002PotatoDextroseAgar_blankmedia-140KfullMSnegBlank
SA094003PotatoDextroseAgar_blankmedia-140KfullMSposBlank
SA094004PotatoDextroseAgar_blankmedia-MS2posBlank
SA094005unknown_compound1_seedspectra_MS2posGNPS Seed spectra
SA094006Radicicol_seedspectra_MS2posGNPS Seed spectra
SA094007unknown_compound2_seedspectra_MS2posGNPS Seed spectra
SA094008QC4-140KfullMSnegQuality Control
SA094009QC4-140KfullMSposQuality Control
SA094010QC5-140KfullMSnegQuality Control
SA094011QC5-140KfullMSposQuality Control
SA094012QC3-140KfullMSposQuality Control
SA094013QC2-140KfullMSposQuality Control
SA094014QC1-140KfullMSposQuality Control
SA094015QC1-140KfullMSnegQuality Control
SA094016QC3-140KfullMSnegQuality Control
SA094017QC2-140KfullMSnegQuality Control
SA094018251607_Ilyonectria_mors-panacis-140KfullMSnegVirulent
SA094019251607_Ilyonectria_mors-panacis-140KfullMSposVirulent
SA094020251607_Ilyonectria_mors-panacis-MS2negVirulent
SA094021251606_Ilyonectria_mors-panacis-MS2posVirulent
SA094022251606_Ilyonectria_mors-panacis-MS2negVirulent
SA094023251606_Ilyonectria_mors-panacis-140KfullMSnegVirulent
SA094024251606_Ilyonectria_mors-panacis-140KfullMSposVirulent
SA094025251607_Ilyonectria_mors-panacis-MS2posVirulent
SA094026251605_Ilyonectria_mors-panacis-MS2posVirulent
SA094027251610_Ilyonectria_mors-panacis-140KfullMSposVirulent
SA094028251611_Ilyonectria_mors-panacis-MS2posVirulent
SA094029251611_Ilyonectria_mors-panacis-MS2negVirulent
SA094030251610_Ilyonectria_mors-panacis-MS2negVirulent
SA094031251611_Ilyonectria_mors-panacis-140KfullMSposVirulent
SA094032251611_Ilyonectria_mors-panacis-140KfullMSnegVirulent
SA094033251610_Ilyonectria_mors-panacis-MS2posVirulent
SA094034251610_Ilyonectria_mors-panacis-140KfullMSnegVirulent
SA094035251604_Ilyonectria_mors-panacis-140KfullMSnegVirulent
SA094036230337_Ilyonectria_mors-panacis-140KfullMSnegVirulent
SA094037226729_Ilyonectria_robusta-MS2posVirulent
SA094038226729_Ilyonectria_robusta-MS2negVirulent
SA094039226729_Ilyonectria_robusta-140KfullMSposVirulent
SA094040230337_Ilyonectria_mors-panacis-140KfullMSposVirulent
SA094041230337_Ilyonectria_mors-panacis-MS2negVirulent
SA094042230338_Ilyonectria_mors-panacis-MS2negVirulent
SA094043230338_Ilyonectria_mors-panacis-140KfullMSposVirulent
SA094044230338_Ilyonectria_mors-panacis-140KfullMSnegVirulent
SA094045230337_Ilyonectria_mors-panacis-MS2posVirulent
SA094046226729_Ilyonectria_robusta-140KfullMSnegVirulent
SA094047226727_Ilyonectria_mors-panacis-MS2posVirulent
SA094048220159_Ilyonectria_mors-panacis-140KfullMSnegVirulent
SA094049139398_Ilyonectria_robusta-MS2posVirulent
SA094050139398_Ilyonectria_robusta-MS2negVirulent
SA094051139398_Ilyonectria_robusta-140KfullMSposVirulent
SA094052220159_Ilyonectria_mors-panacis-140KfullMSposVirulent
SA094053220159_Ilyonectria_mors-panacis-MS2negVirulent
SA094054226727_Ilyonectria_mors-panacis-MS2negVirulent
SA094055226727_Ilyonectria_mors-panacis-140KfullMSposVirulent
SA094056226727_Ilyonectria_mors-panacis-140KfullMSnegVirulent
SA094057220159_Ilyonectria_mors-panacis-MS2posVirulent
SA094058230338_Ilyonectria_mors-panacis-MS2posVirulent
SA094059234582_Ilyonectria_mors-panacis-140KfullMSnegVirulent
SA094060251603_Ilyonectria_mors-panacis-MS2posVirulent
SA094061251603_Ilyonectria_mors-panacis-MS2negVirulent
SA094062251603_Ilyonectria_mors-panacis-140KfullMSposVirulent
SA094063251603_Ilyonectria_mors-panacis-140KfullMSnegVirulent
SA094064139398_Ilyonectria_robusta-140KfullMSnegVirulent
SA094065251604_Ilyonectria_mors-panacis-140KfullMSposVirulent
SA094066251605_Ilyonectria_mors-panacis-140KfullMSposVirulent
SA094067251605_Ilyonectria_mors-panacis-140KfullMSnegVirulent
SA094068251604_Ilyonectria_mors-panacis-MS2posVirulent
SA094069251604_Ilyonectria_mors-panacis-MS2negVirulent
SA094070251602_Ilyonectria_mors-panacis-MS2posVirulent
SA094071251602_Ilyonectria_mors-panacis-MS2negVirulent
SA094072251601_Ilyonectria_mors-panacis-140KfullMSnegVirulent
SA094073234582_Ilyonectria_mors-panacis-MS2posVirulent
SA094074234582_Ilyonectria_mors-panacis-MS2negVirulent
SA094075234582_Ilyonectria_mors-panacis-140KfullMSposVirulent
SA094076251601_Ilyonectria_mors-panacis-140KfullMSposVirulent
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Collection:

Collection ID:CO001362
Collection Summary:Fungal isolates obtained from the Canadian Fungal Culture Collection (CFCC) at Agriculture and Agri-Food Canada were grown on potato dextrose agar for 20 days at 21 C.
Sample Type:Fungal cells

Treatment:

Treatment ID:TR001382
Treatment Summary:All fungal isolates were grown on potato dextrose agar (2.4%, w/v) with 3.47E-5 zinc sulfate heptahydrate and 3.13E-5 copper sulfate. Plates were grown for 20 days at 21 C in the dark.

Sample Preparation:

Sampleprep ID:SP001375
Sampleprep Summary:Cultures were sampled by taking six 0.5-cm plugs from each plate. Plugs were extracted with 4 mL of ethyl acetate, then dried by centrifugal vacuum evaporation. Dried extracts were reconstituted in 1 mL of 3:1 methanol:water and were filtered through 0.45 um PTFE filters (Chromatographic Specialties, Inc.). Composite quality control samples were made by combining 50 uL from each completed extract.

Combined analysis:

Analysis ID AN002151 AN002152 AN002153 AN002154
Analysis type MS MS MS MS
Chromatography type Reversed phase Reversed phase Reversed phase Reversed phase
Chromatography system Agilent 1290 Infinity Agilent 1290 Infinity Agilent 1290 Infinity Agilent 1290 Infinity
Column Agilent Zorbax Eclipse Plus C18 (50 x 2.1mm,1.8um) Agilent Zorbax Eclipse Plus C18 (50 x 2.1mm,1.8um) Agilent Zorbax Eclipse Plus C18 (50 x 2.1mm,1.8um) Agilent Zorbax Eclipse Plus C18 (50 x 2.1mm,1.8um)
MS Type ESI ESI ESI ESI
MS instrument type Orbitrap Orbitrap Orbitrap Orbitrap
MS instrument name Thermo Q Exactive Orbitrap Thermo Q Exactive Orbitrap Thermo Q Exactive Orbitrap Thermo Q Exactive Orbitrap
Ion Mode POSITIVE POSITIVE NEGATIVE NEGATIVE
Units Integrated peak area Integrated peak area Integrated peak area Integrated peak area

Chromatography:

Chromatography ID:CH001574
Chromatography Summary:Samples were resolved with a reversed-phase column (C-18)
Instrument Name:Agilent 1290 Infinity
Column Name:Agilent Zorbax Eclipse Plus C18 (50 x 2.1mm,1.8um)
Column Temperature:35
Flow Gradient:0% B for 0.5 minutes, increased to 100% B over 3 minutes, held at 100% B for 2.5 minutes, decreased to 0% B over 0.5 minutes, then held at 0% B for 1 minute
Flow Rate:0.3 mL/min
Sample Injection:5 uL
Solvent A:100% water; 0.1% formic acid
Solvent B:100% acetonitrile; 0.1% formic acid
Capillary Voltage:3900 V
Chromatography Type:Reversed phase

MS:

MS ID:MS002002
Analysis ID:AN002151
Instrument Name:Thermo Q Exactive Orbitrap
Instrument Type:Orbitrap
MS Type:ESI
MS Comments:Data were acquired by single-stage LC-HRMS (140,000 resolution)
Ion Mode:POSITIVE
  
MS ID:MS002003
Analysis ID:AN002152
Instrument Name:Thermo Q Exactive Orbitrap
Instrument Type:Orbitrap
MS Type:ESI
MS Comments:Data were acquired by untargeted LC-DDA
Ion Mode:POSITIVE
  
MS ID:MS002004
Analysis ID:AN002153
Instrument Name:Thermo Q Exactive Orbitrap
Instrument Type:Orbitrap
MS Type:ESI
MS Comments:Data were acquired by single-stage LC-HRMS (140,000 resolution)
Ion Mode:NEGATIVE
  
MS ID:MS002005
Analysis ID:AN002154
Instrument Name:Thermo Q Exactive Orbitrap
Instrument Type:Orbitrap
MS Type:ESI
MS Comments:Data were acquired by untargeted LC-DDA
Ion Mode:NEGATIVE
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