MAGE-TAB Version 1.1 Comment[MetaboBank accession] MTBKS24 Study Title Transcriptomic and Metabolomic Reprogramming from Roots to Haustoria in the Parasitic Plant, Thesium chinense Study Description Most plants show remarkable developmental plasticity in the generation of diverse types of new organs upon external stimuli, allowing them to adapt to their environment. Haustorial formation in parasitic plants is an example of such developmental reprogramming, but its molecular mechanism is largely unknown. In this study, we performed field-omics using transcriptomics and metabolomics to profile the molecular switch occurring in haustorial formation of the root parasitic plant, Thesium chinense, collected from its natural habitat. RNA-sequencing with de novo assembly revealed that the transcripts of very long chain fatty acid (VLCFA) biosynthesis genes, auxin biosynthesis/signaling-related genes and lateral root developmental genes are highly abundant in the haustoria. Gene co-expression network analysis identified a network module linking VLCFAs and the auxin-responsive lateral root development pathway. GC-TOF-MS analysis consistently revealed a unique metabolome profile with many types of fatty acids in the T. chinense root system, including the accumulation of a 25-carbon long chain saturated fatty acid in the haustoria. Our field-omics data provide evidence supporting the hypothesis that the molecular developmental machinery used for lateral root formation in non-parasitic plants has been co-opted into the developmental reprogramming of haustorial formation in the linage of parasitic plants. Experimental Design organism part comparison design Experimental Factor Name tissue Extraction phase Experimental Factor Type tissue Extraction phase Person Last Name Takahashi Fukushima Ichihashi Shirasu Person First Name Mikiko Atsushi Yasunori Ken Person Mid Initials Person Affiliation RIKEN Center for Sustainable Resource Science RIKEN Center for Sustainable Resource Science; Department of Agricultural and Life Science, Kyoto Prefectural University RIKEN Center for Sustainable Resource Science RIKEN Center for Sustainable Resource Science Person Roles submitter submitter submitter submitter PubMed ID 29281058 Publication DOI Protocol Name Sample collection Extraction Chromatography Mass spectrometry Data processing Metabolite identification Protocol Type Sample collection Extraction Chromatography Mass spectrometry Data processing Metabolite identification Protocol Description Thesium chinense is a perennial herb that has branched stems up to 60 cm in length. Thesium chinense can parasitize a diverse range of species from many plant families, and disturbs grasslands and riversides. It develops narrow linear leaves and has greenish-white, cylindrical flowers that are approximately 2 mm long. Samples were collected near the Kizu River, Kyoto Prefecture, Japan on February 3, 2015 and September 16, 2016. Eight sections of 30-30-20 (depth) cm3 turf, containing at least two T. chinense plants and their hosts, such as A. capillaris, E. curvula and L. juncea, were randomly collected and then seven and four biological replicates made from pooled tissues of all plants were prepared for transcriptome and metabolome analyses, respectively. In order to minimize any surface tissue contamination, tissue samples were carefully collected using hand sectioning with a razor blade and rinsed using 70% ethanol or tap water for transcriptome and metabolome analyses, respectively, immediately frozen in liquid nitrogen and stored at -80 degree C until sample preparation. Extraction mixture comprised of chloroform : methanol : milliQ water (1 : 3 : 1 by vol.), following the addition of milliQ water to fractionate the lipophilic and polar phases. Lipophilic fraction was subjected to GC-MS analysis. Column name: 30 m long, 0.25 mm internal diameter fused-silica capillary column with a chemically bound 0.25micro liter film Rtx-5 Sil MS staionary phase (RESTEK, Bellefonte, USA); Column type: low polarity; Flow gas: Helium; Flow rate: 1.0 ml/min; Instrument: Agilent 6890N Gas Chromatograph (Agilent Technologies, Wilmingston, USA); Temperature gradient: The temperture program started with a 2-min isothermal step at 80 degrees C and this was followed by temperature ramping at 30 degrees C to a final temperature of 320 degrees C. Acquisition rate: 30 spectra/s; Capilary temperature: 300.0 degree C; Fragmentation method: EI; Instrument: Pegasus III TOF mass spectrometer (LECO, St. Joseph, MI, USA); Ion isolation: EI; Ion isolation energy: 70.0 eV; Ion mode: Positive; Ion source: GC; Ion source temperature: 230.0 degree C; Mass analyser: TOF; Retenition index method: Alkane standard mixtures (C8-C20 and C21-C40) ; Scan MZ range: m/z 60-800. the raw data of detected metabolites were transferred from the ChromaTOF software in the NetCDF format to the MATLAB software, version 2011b (MathWorks) The resolved MS spectra were matched against reference mass spectra using the NIST mass spectral search program for the NIST/EPA/NIH mass spectral library (version 2.0) and our custom software for peak annotation written in JAVA. The metabolites were identified by comparison with RIs from the library databases (GMD and our own library) and with those of authentic standards, and the metabolites were defined as annotated metabolites on comparison with mass spectra and RIs from these two libraries. Protocol Parameters Post extraction;Derivatization;Extraction phase Chromatography instrument;Autosampler model;Column model;Column type;Guard column Scan polarity;Scan m/z range;Instrument;Ion source;Mass analyzer Protocol Hardware Protocol Software Public Release Date 2020-10-05 Term Source Name RIKEN Plant Metabolome MetaDatabase (RPMM) Term Source File http://metabobank.riken.jp/pmm/db/plantMetabolomics Term Source Version SDRF File MTBKS24.sdrf.txt Comment[Study type] untargeted metabolite profiling Comment[Experiment type] gas chromatography-mass spectrometry Comment[Submission type] GC-MS Comment[BioProject] PRJDB15525 Comment[Related study] RPMM:RPMM0026 Comment[Contributor] Comment[Submission Date] 2019-10-05 Comment[Last Update Date] 2025-01-24