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16bestgem description

This page presents a multispecies comparison of metabolism across brown algae, using a subset of data from the Phaeoexplorer project. The selected species are a compromise between assembly quality and phylogenetic coverage. This version contains 13 algae and 3 outgroup species for which genomes were sequenced with long reads and 14 public genomes.

Automatic reconstruction with AuCoMe

Genome-scale metabolic networks for the algae were inferred using the AuCoMe program, as described in Belcour et al., 2023. The following table gives direct access to the individual summary table below for numbers of genes and reactions. You can also browse the wiki using the Metacyc IDs of individual enzymes, metabolites or reactions, and you will see in which cases gene-protein-reaction association were found across all species.

Description of the 30 species

• 17 species are Phaeophyceae:

Organism	Reactions	Metabolites	Genes	Pathways	Sequencing with	Models
Ascophyllum nodosum	2773	3232	4989	1395	Nanopore & completed with Illumina	sbml
Chordaria linearis	2783	3240	3986	1387	Nanopore & completed with Illumina	sbml
Desmarestia herbacea	2764	3190	4089	1387	Nanopore & completed with Illumina	sbml
Dictyota dichotoma	2726	3193	4142	1385	Nanopore & completed with Illumina	sbml
Ectocarpus crouaniorum	2800	3267	4049	1400	Nanopore & completed with Illumina	sbml
Ectocarpus fasciculatus	2776	3230	4355	1390	Nanopore & completed with Illumina	sbml
Ectocarpus siliculosus	2826	3277	4106	1396	Nanopore & completed with Illumina	sbml
Ectocarpus species6	2790	3242	4460	1400	Nanopore & completed with Illumina	sbml
Ectocarpus species7	2777	3228	5148	1390	Public genome	sbml
Fucus serratus	2772	3227	5126	1380	Nanopore & completed with Illumina	sbml
Pleurocladia lacustris	2738	3197	3890	1387	Nanopore & completed with Illumina	sbml
Porterinema fluviatile	2762	3219	3861	1381	Nanopore & completed with Illumina	sbml
Pylaiella littoralis	2805	3273	4071	1394	Nanopore & completed with Illumina	sbml
Saccharina japonica	3012	3490	5534	1451	Public genome	sbml
Saccharina latissima	2745	3225	4235	1400	Nanopore & completed with Illumina	sbml
Scytosiphon promiscuus	2788	3242	4117	1396	Nanopore & completed with Illumina	sbml
Undaria pinnatifida	2789	3251	5000	1394	Public genome	sbml

• 13 species are outgroups:

Organism	Phylogeny	Reactions	Metabolites	Genes	Pathways	Sequencing with	Models
Aphanomyces euteiches	Saprolegniaceae	2778	3213	5207	1362	Public genome	sbml
Aureococcus anophagefferens	Pelagophyceae	2800	3223	3994	1422	Public genome	sbml
Fistulifera solaris	Diatoms	2789	3224	5517	1384	Public genome	sbml
Fragilariopsis cylindrus	Diatoms	2865	3354	3578	1443	Public genome	sbml
Heterosigma akashiwo	Chattonellaceae	2561	3035	3827	1346	Nanopore & completed with Illumina	sbml
Nannochloropsis gaditana	Eustigmatophyceae	2887	3328	3300	1433	Public genome	sbml
Nannochloropsis oceanica	Eustigmatophyceae	2887	3323	3363	1444	Public genome	sbml
Phaeodactylum tricornutum	Diatoms	2694	3142	2952	1392	Public genome	sbml
Phytophthora infestans	Peronosporaceae	2653	3054	4598	1336	Public genome	sbml
Pythium ultimum	Pythiaceae	2615	3018	4269	1328	Public genome	sbml
Saprolegnia parasitica	Saprolegniaceae	2723	3149	5156	1351	Public genome	sbml
Schizocladia ischiensis	Schizocladia	2891	3366	4617	1446	Nanopore & completed with Illumina	sbml
Thalassiosira pseudonana	Diatoms	2712	3123	3135	1396	Public genome	sbml

Collaborative curation

Curation based on expert analysis of some gene families is always very welcome, using the procedure described below.

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