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phaeogem description

This page presents a multispecies comparison of metabolism across brown algae, using mainly data from the Phaeoexplorer project. This version contains 21 species sequenced with long reads and 23 species sequences with short reads, as well as 18 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 where found across all species.

Description of the 62 species

• 46 species are Phaeophyceae:

Organism	Reactions	Metabolites	Genes	Pathways	Sequencing with	Models
Ascophyllum nodosum	2902	3373	5566	1427	Nanopore & completed with Illumina	sbml
Chordaria linearis	2933	3384	4306	1430	Nanopore & completed with Illumina	sbml
Choristocarpus tenellus	2705	3178	4163	1358	Nanopore & completed with Illumina	sbml
Cladosiphon okamuranus	3018	3532	5217	1458	Public genome	sbml
Desmarestia dudresnayi	3161	3627	8012	1497	Illumina	sbml
Desmarestia herbacea	2920	3361	4344	1433	Nanopore & completed with Illumina	sbml
Dictyota dichotoma	2859	3311	4558	1422	Nanopore & completed with Illumina	sbml
Discosporangium mesarthrocarpum	3525	4011	8630	1678	Nanopore & completed with Illumina	sbml
Ectocarpus crouaniorum	2923	3387	4384	1432	Nanopore & completed with Illumina	sbml
Ectocarpus fasciculatus	2900	3354	4769	1419	Nanopore & completed with Illumina	sbml
Ectocarpus siliculosus	2933	3390	4397	1430	Nanopore & completed with Illumina	sbml
Ectocarpus species1	2937	3403	4729	1447	Illumina	sbml
Ectocarpus species2	2811	3279	4761	1399	Illumina	sbml
Ectocarpus species3	2833	3291	4721	1401	Illumina	sbml
Ectocarpus species5	2902	3353	5051	1468	Illumina	sbml
Ectocarpus species6	2930	3395	4746	1434	Nanopore & completed with Illumina	sbml
Ectocarpus species7	2900	3368	5510	1422	Public genome	sbml
Ectocarpus species8	2958	3474	8341	1455	Illumina	sbml
Ectocarpus species9	2867	3333	4863	1418	Illumina	sbml
Ectocarpus species12	4137	4503	12990	1808	Illumina	sbml
Ectocarpus species13	2822	3257	5725	1398	Illumina	sbml
Ectocarpus subulatus	2997	3467	8381	1441	Public genome	sbml
Feldmannia mitchelliae	2885	3336	4478	1421	Illumina	sbml
Fucus distichus	2873	3379	5555	1430	Illumina	sbml
Fucus serratus	2893	3352	5539	1406	Nanopore & completed with Illumina	sbml
Halopteris paniculata	2777	3232	4928	1405	Illumina	sbml
Hapterophycus canaliculatus	3097	3564	9329	1490	Illumina	sbml
Heribaudiella fluviatilis	3631	4077	10416	1627	Illumina	sbml
Himanthalia elongata	2691	3151	5233	1387	Illumina	sbml
Laminaria digitata	3970	4386	12651	1782	Nanopore & completed with Illumina	sbml
Laminarionema elsbetiae	2865	3305	4638	1409	Illumina	sbml
Macrocystis pyrifera	3650	4106	7257	1657	Illumina	sbml
Myriotrichia clavaeformis	2922	3391	4884	1431	Illumina	sbml
Pelvetia canaliculata	3371	3807	5933	1600	Illumina	sbml
Pleurocladia lacustris	2866	3340	4235	1414	Nanopore & completed with Illumina	sbml
Porterinema fluviatile	2887	3341	4201	1418	Nanopore & completed with Illumina	sbml
Pylaiella littoralis	2924	3375	4533	1423	Nanopore & completed with Illumina	sbml
Saccharina japonica	3011	3495	5538	1453	Public genome	sbml
Saccharina latissima	2848	3317	4494	1418	Nanopore & completed with Illumina	sbml
Saccorhiza dermatodea	2736	3207	4912	1364	Illumina	sbml
Saccorhiza polyschides	2876	3407	4934	1439	Illumina	sbml
Sargassum fusiforme	3020	3471	5620	1439	Public genome	sbml
Scytosiphon promiscuus	2906	3358	4463	1426	Nanopore & completed with Illumina	sbml
Sphacelaria rigidula	2266	2744	3694	1281	Nanopore & completed with Illumina	sbml
Sphaerotrichia firma	2878	3341	5154	1427	Illumina	sbml
Undaria pinnatifida	2884	3325	5706	1413	Public genome	sbml

• 16 species are composing the outgroup

Organism	Phylogeny	Reactions	Metabolites	Genes	Pathways	Sequencing with	Models
Aphanomyces euteiches	Saprolegniaceae	2796	3234	5193	1388	Public genome	sbml
Aureococcus anophagefferens	Pelagophyceae	2895	3336	4131	1455	Public genome	sbml
Chrysoparadoxa australica	Chrysoparadoxa	3777	4182	5896	1746	Illumina	sbml
Fistulifera solaris	Diatoms	2893	3317	5768	1428	Public genome	sbml
Fragilariopsis cylindrus	Diatoms	2972	3406	3613	1459	Public genome	sbml
Heterosigma akashiwo	Chattonellaceae	2597	3053	3835	1348	Nanopore & completed with Illumina	sbml
Nannochloropsis gaditana	Eustigmatophyceae	3012	3461	3420	1480	Public genome	sbml
Nannochloropsis oceanica	Eustigmatophyceae	3015	3475	3466	1481	Public genome	sbml
Phaeodactylum tricornutum	Diatoms	2799	3224	2994	1422	Public genome	sbml
Phaeothamnion wetherbeei	Phaeothamniophyceae	3980	4408	7863	1805	Nanopore & completed with Illumina	sbml
Phytophthora infestans	Peronosporaceae	2685	3068	4636	1357	Public genome	sbml
Pythium ultimum	Pythiaceae	2676	3069	4267	1351	Public genome	sbml
Saprolegnia parasitica	Saprolegniaceae	2781	3188	5156	1382	Public genome	sbml
Schizocladia ischiensis	Schizocladia	2989	3420	4888	1470	Nanopore & completed with Illumina	sbml
Thalassiosira pseudonana	Diatoms	2752	3152	3200	1422	Public genome	sbml
Tribonema minus	Xanthophyceae	2908	3364	4565	1421	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