Recent News

We are pleased to announce the launch of a new website feature, the Metabolic Cluster Viewer. We have run our PlantClusterFinder software on nine of the PMN species' genomes, and the Cluster Viewer allows you to search and view the results without having to download and run the cluster finder yourself. The species currently available are Arabidopsis thaliana, Glycine max (soybean), Medicago truncatula (wild relative of alfalfa), Oryza sativa (rice), Populus trichocarpa (poplar), Senna tora (a wild legume), Solanum lycopersicum (tomato), Vitis vinifera (grape), and Zea mays (maize).

The tool will show a gene diagram of the cluster and a list of genes, with EC numbers and Metacyc IDs of catalyzed reactions and GO terms for each gene. It will also show co-expression data of the genes from the ATTED-II database if available.

The Cluster Viewer can be accessed from the PMN Data menu under PMN Tools, where BLAST has also been moved.

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).

We are pleased to announce the PMN10 release. In this release, we introduce 5 new metabolic pathway databases for species including tomato, potato, two diploid progenitors of the bread wheat, Aegilops tauschii  (D-genome) and Triticum Urartu (A-genome), and the great duckweed (Spirodela polyrhiza). We substantially updated the 17 existing species-specific databases and the multi-species database PlantCyc. PMN now hosts 23 databases in total.

The computational predictions of enzyme functions in PMN 10 are based on an enhanced Ensemble Enzyme Prediction Pipeline (E2P2 v3.0), with increased precision and a 62% increase of enzyme function space. We also made the following major changes to the scope and rules used in PMNs databases:

1. To reinforce the PMNs focus on small molecule metabolism, enzymes that metabolize macromolecules such as serine protein kinase are excluded from the pathway databases.
2. In our enzyme to reaction association, EC number-based enzyme predictions are transferred to distinct MetaCyc reaction IDs. To reduce false-positive associations, when multiple MetaCyc reactions exist for the same EC number, only the MetaCyc reaction corresponding to the official EC reaction is used for annotation.
3. When multiple splice variants of a gene locus exist in a genome, only the protein sequence that represents the longest coding sequence is included in the pathway database.