PWY-5885

SJAPGEM description

Saccharina japonica is the most cultivated alga worldwide, with nearly 8 millions tons of dry weight harvested in 2014, representing more than US $1.3 billion value (Chen J., FAO website, accessed on january 10th, 2019). Its draft genome sequence was published in 2015 (Ye et al., Nature Communications). The genome version used here underwent an additional round of cleaning for bacterial contaminants using Taxoblast (Dittami and Corre, 2017). The paper describing this GEM reconstruction in more detail is in preparation. Manual curation is ongoing on carotenoid biosynthesis pathway (CAROTENOID-PWY) and on the first cycle of xanthophylls (PWY-5945).

Automatic reconstruction with AuReMe

Model summary: summary

Download AuReMe Input/Output [LINK OR MEDIA data]

The automatic reconstruction of Saccharina japonica results to a Genome scale Model containing 3345 reactions, 2211 metabolites, 5021 genes and 1389 pathways. This GeM was obtained based on the following sources:

• Based on annotation data:
  • Tool: Pathway tools
    • Creation of a metabolic network containing 2552 reactions
• Based on orthology data:
  • Tool: Pantograph
    • From template NANNOCHLOROPSIS_SALINA (Loira et al., 2017) creation of a metabolic network containing: 589 reactions
    • From template ARABIDOPSIS_THALIANA (De Oliveira dal'Molin et al., 2010) creation of a metabolic network containing: 419 reactions
    • From template ECTOCARPUS_SILICULOSUS creation of a metabolic network containing: 1492 reactions
• Based on expertise:
  • 64 reaction(s) added
• Based on gap-filling:
  • Tool: meneco
    • 106 reaction(s) added

Collaborative curation

• Suggest reactions to add or remove:
  • Download this form
• Suggest new reactions to create and add:
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• Follow the examples given in the form(s) to correctly share your suggestions
• Send the filled form(s) to: gabriel.markov@sb-roscoff.fr