Cunha2022 - Inner Bark Model for Quercus suber

  public model
Model Identifier
MODEL2205040002
Short description
Inner Bark GSM Model for Quercus suber
Format
SBML (L3V1)
Related Publication
  • The first multi-tissue diel genome-scale metabolic model of a woody plant highlights suberin biosynthesis pathways in Quercus suber
  • Emanuel Cunha, Miguel Silva, Ines Chaves, Huseyin Demirci, Davide Rafael Lagoa, Diogo Lima, Miguel Rocha, Isabel Rocha, Oscar Dias
  • BioRxiv, pre-print , 3/ 2021 , DOI: 10.1101/2021.03.09.434537
  • 1 Centre of Biological Engineering, Universidade do Minho, 4710-057 Braga, Portugal 2 LABBELS – Associate Laboratory, Braga, Guimarães, Portugal 3 Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Avenida da República, 7 Quinta do Marquês, 2780-157 Oeiras, Portugal 4 iBET, Instituto de Biologia Experimental e Tecnológica, Apartado 12, 2781-901 Oeiras, Portugal 5 SnT/University of Luxembourg, Luxembourg
  • In the last decade, genome-scale metabolic models have been increasingly used to study plant metabolic behavior at the tissue and multi-tissue level under different environmental conditions. Quercus suber, also known as the cork oak tree, is one of the most important forest communities of the Mediterranean/Iberian region. In this work, we present the genome-scale metabolic model of the Q. suber (iEC7871), the first of a woody plant. The metabolic model comprises 7871 genes, 6231 reactions, and 6481 metabolites across eight compartments. Transcriptomics data was integrated into the model to obtain tissue-specific models for the leaf, inner bark, and phellogen, with specific biomass compositions. The tissue-specific models were merged into a diel multi-tissue metabolic model to predict interactions among the three tissues at the light and dark phases. The metabolic models were also used to analyze the pathways associated with the synthesis of suberin monomers. Nevertheless, the models developed in this work can provide insights into other aspects of the metabolism of Q. suber, such as its secondary metabolism and cork formation.
Contributors
Submitter of the first revision: Emanuel Cunha
Submitter of this revision: Emanuel Cunha

Metadata information

hasProperty
Mathematical Modelling Ontology Constraint-based model

Curation status
Non-curated

Modelling approach(es)


Connected external resources

SBGN view in Newt Editor

Name Description Size Actions

Model files

QuercusSuberInnerBark.xml SBML L3V1 Inner Bark GSM model for Quercus suber 23.22 MB Preview | Download

Additional files

FROG_report_InnerBark.zip FROG report for Inner Bark 135.42 KB Preview | Download
Qsuber_ibark.html Memote report 6.50 MB Preview | Download
miniFROG Report_Cunha2022_inner_bark.xlsx miniFROG report 55.32 KB Preview | Download

  • Model originally submitted by : Emanuel Cunha
  • Submitted: May 4, 2022 3:44:01 PM
  • Last Modified: May 4, 2022 3:44:01 PM
Revisions
  • Version: 2 public model Download this version
    • Submitted on: May 4, 2022 3:44:01 PM
    • Submitted by: Emanuel Cunha
    • With comment: Model revised without commit message