We are pleased to announce the PMN13 release. In this release we introduce 24 new organism-specific metabolic pathway databases, which brings the total number of organism pathway databases to 100! New species include nine crops, two medicinal plants, four ornamental plants, two wild relatives of domesticated crops, two grasses, a succulent, a basal eudicot, two lower plants and a green alga:
Anacardium occidentale (cashew); Asparagus officinalis (asparagus); Capsicum annuum (pepper); Chenopodium quinoa (quinoa); Corchorus capsularis (white jute); Dioscorea rotundata (white yam); Helianthus annuus (sun flower); Humulus lupulus (hop); Solanum melongena (eggplant); Calotropis gigantea (a medicinal plant); Camptotheca acuminata (a medicinal plant); Dianthus caryophyllus (carnation); Petunia axillaris (white petunia); Rosa chinensis (rose); Rosa multiflora (rose); Olea europaea (a wild olive); Solanum pennellii (a wild tomato); Miscanthus sinensis (Chinese silver grass); Panicum hallii (Hall's panicgrass); Kalanchoe fedtschenkoi (a succulent); Aquilegia coerulea (a basal eudicot); Sphagnum fallax (a moss); Marchantia polymorpha (a liverwort) and Chromochloris zofingiensis (a unicellular green alga).
The full list of 100 species and details of the database constructions can be found here.
We also updated the pan-plant pathway database PlantCyc (version 13.0). PlantCyc database now includes only literature-curated enzymes and pathways. Using the new virtual data integration feature (provided by Pathway Tools software version 21.5 and up), users can select up to 10 organism pathway databases from which their predicted enzymes will be displayed onto PlantCyc pathway diagrams.
Please note that the following 11 databases were constructed or updated from genome releases which are under prepublication data usage restrictions:
AcoeruleaCyc (Aquilegia coerulea), AhalleriCyc (Arabidopsis halleri), AhypochondriacusCyc (Amaranthus hypochondriacus), CashewCyc (Anacardium occidentale), CommonbeanCyc (Phaseolus vulgaris), MsinensisCyc (Miscanthus sinensis), PhalliiCyc (Panicum hallii), SfallaxCyc (Sphagnum fallax), SorghumbicolorCyc (Sorghum bicolor), SviridisCyc (Setaria viridis), SwitchgrassCyc (Panicum virgatum). Please see detailed data policy at the corresponding species pages from Phytozome (v12).
