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| − | == SJAPGEM description ==
| + | {{#ask: [[Category:reaction]] [[reconstruction category::annotation]] |
| − | | + | | ?common-name |
| − | ''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 ([http://www.fao.org/fishery/culturedspecies/Laminaria_japonica/en#tcNA008C Chen J., FAO website, accessed on january 10th, 2019]).
| + | | ?ec-number |
| − | Its draft genome sequence was published in 2015 ([http://doi.org/10.1038/ncomms7986 Ye et al., Nature Communications]). The genome version used here underwent an additional round of cleaning for bacterial contaminants using Taxoblast ([https://doi.org/10.7717/peerj.4073 Dittami and Corre, 2017]). The paper describing this GEM reconstruction in more detail was published in 2019 ([https://doi.org/10.3390/antiox8110564 Nègre et al., Antioxidants]). In this study, extensive manual curation was performed on the carotenoid biosynthesis pathway (CAROTENOID-PWY) and on the first cycle of xanthophylls (PWY-5945). In a follow-up study (Girard et al., in preparation) we are now curating the sterol biosynthesis pathways (PWY-8191, PWY-8238).
| + | | ?reconstruction tool |
| − | | + | | ?reconstruction source |
| − | == Automatic reconstruction with [http://aureme.genouest.org AuReMe] ==
| + | | ?reconstruction comment |
| − | Model summary: [[MEDIA:summary.txt|summary]]
| + | | ?nb gene associated |
| − | | + | | ?nb pathway associated |
| − | Download '''AuReMe''' Input/Output [LINK OR MEDIA data]
| + | }} |
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| − | The automatic reconstruction of ''Saccharina japonica'' results to a Genome scale [[MEDIA:S.japonica carotenoid curated.sbml|Model]] containing 3345 reactions, 2211 metabolites, 5021 genes and 1389 pathways. This GeM was obtained based on the following sources:
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| − | * Based on annotation data:
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| − | ** Tool: [http://bioinformatics.ai.sri.com/ptools/ Pathway tools]
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| − | *** Creation of a metabolic network containing 2552 reactions
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| − | * Based on orthology data:
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| − | ** Tool: [http://pathtastic.gforge.inria.fr Pantograph]
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| − | *** From template ''NANNOCHLOROPSIS_SALINA'' ([https://doi.org/10.1186/s12918-017-0441-1 Loira et al., 2017]) creation of a metabolic network containing: 589 reactions
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| − | *** From template ''ARABIDOPSIS_THALIANA'' ([https://doi.org/10.1104/pp.109.148817 De Oliveira dal'Molin et al., 2010]) creation of a metabolic network containing: 419 reactions
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| − | *** From template ''[http://gem-aureme.irisa.fr/ectogem/ ECTOCARPUS_SILICULOSUS]'' creation of a metabolic network containing: 1492 reactions
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| − | * Based on expertise:
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| − | ** 64 reaction(s) added
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| − | * Based on gap-filling:
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| − | ** Tool: [https://pypi.python.org/pypi/meneco meneco]
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| − | *** 106 reaction(s) added
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| − | == Collaborative curation ==
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| − | * Suggest reactions to add or remove:
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| − | ** Download this [[MEDIA:Add_delete_reaction.csv|form]]
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| − | * Suggest new reactions to create and add:
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| − | ** Download this [[MEDIA:Reaction_creator.csv|form]]
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| − | * '''Follow the examples given in the form(s) to correctly share your suggestions'''
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| − | * Send the filled form(s) to: gabriel.markov@sb-roscoff.fr
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