Recent News

Big news! PMN has just received a new grant from the National Science Foundation's Plant Genome Research Program (PGRP). Worth $3 million over four years, this grant will allow us to significantly expand PMN in size, scope, and usefulness. In addition to our PI, Dr. Sue Rhee here at Michigan State University, whose lab created PMN and has operated and maintained it for more than 15 years, we have now also brought on collaborators Dr. Hiroshi Maeda at the University of Wisconsin-Madison, and Dr. Phillipp Zerbe from the University of California, Davis. Both these labs have tremendous expertise in the functional characterization of enzymes, and they have signed on to work with us to discover new enzymes as well as new functions for previously-known enzymes in a multitude of plant species. Newly-characterized enzymes will be represented in PMN directly in the appropriate species database, but will also be included in the dataset we use to make computational predictions of enzymes in all PMN species, so the impact of these new data will reach beyond their species of origin. These labs will form the core of an Enzyme Consortium, a collaboration of computational and experimental groups focused on identifying and filling gaps in our understanding of plant enzymes and metabolism.

As another major objective, we plan to massively increase the number of plant and green alge species databases in PMN, from the current total of 127 to more than 1000 by the end of the grant period. To achieve this increase, we will be overhauling the computational pipeline we use to create and update the PMN databases, making it faster, easier, more reproducible, and more scalable. Even better, we will be releasing the upgraded pipeline publicly as a Singularity container, so interested users can reproduce our results and generate their own plant databases comparable to the ones in PMN. Our next release, PMN 16, is due out in mid-2024 and will be the first to be built using the new pipeline.

We will also be releasing a new version of our Ensemble Enzyme Prediction Pipeline (E2P2) software [insert link to github], a core piece of the pipeline that predicts enzyme function from amino acid sequences. E2P2 is an ensemble classifier, meaning it combines the predictions of different classifier software to produce a final set of predictions, and the new E2P2 version 5 will be modularized so that users can easily add and swap out classifiers using a standardized interface. The default classifiers will be blastp [link to ncbi blast+] and DeepEC [link to paper], the latter replacing PRIAM which is no longer maintained, but users will be able to easily add more if desired.

Finally, we will be developing educational resources and materials to help K-12 teachers engage students from diverse backgrounds with plant science, helping to fostering the next generation of leaders in the field.

We're super excited to take PMN to the next level, and we can't wait to get started!

Update 2: The PMN databases are now back up. We thank you for your patience during the move.

Update: Due to unexpected difficulties with the server move, PMN downtime has been extended into March 16th. We expect to have PMN back up later today. We again apologize for the inconvenience.

Original Post: Due to a server move, pmn.plantcyc.org (the part of the site that contains the databases), will be down for part or all of March 15th. We apologize for the inconvenience.

PMN Databases will be offline on July 8th due to datacenter maintenance

We are pleased to announce the PMN14 release. In this release we introduce 25 new organism-specific metabolic pathway databases, which brings the total number of organism pathway databases to 125!  New species include ten crops, six wild crop-relatives, three ornamentals, two oak trees, a model plant, our first gymnosperm, our first parasitic plant, and a green alga.

Arabidopsis thaliana Landsberg, Cajanus cajan (pigeon pea),  Camellia sinensis (tea), Chlorella variabilis (a green alga), Citrullus lanatus (watermelon), Cucumis melo (Cantaloupe, Honeydew, and related melons),  Cuscuta campestris (a parasitic plant), Elaeis guineensis (African oil palm), Ginkgo biloba, Hevea brasiliensis (rubber tree), Lactuca sativa (lettuce), Musa balbisiana (a wild banana), Nelumbo nuficera (sacred lotus), Oryza barthii (African wild rice), Oryza longistaminanta (another wild rice), Oryza meridionalis (Australian wild rice), Oryza nivara (still another wild rice), Phoenix dactylifera (date palm), Phyllostachys edulis (Moso bamboo), Prunis avium (cherry), Pyrus communis (European pear), Quercus lobata (valley oak), Quercus suber (cork oak), Saccharum spontanaeum (wild sugar cane), and Tarenaya hassleriana (Spider flower).

The full list of 125 species and details of the database constructions can be found here.

We have also updated the pan-plant pathway database PlantCyc (version 14.0). The PlantCyc database includes only literature-curated enzymes and pathways, including from species that do not have a full genome database in PMN.  

Please note that the following 8 databases were constructed or updated from genome releases which are under prepublication data usage restrictions:

AhalleriCyc (Arabidopsis halleri), CashewCyc (Anacardium occidentale), CommonbeanCyc (Phaseolus vulgaris), MsinensisCyc (Miscanthus sinensis), PhalliiCyc (Panicum hallii), SfallaxCyc (Sphagnum fallax), SviridisCyc (Setaria viridis), SwitchgrassCyc (Panicum virgatum). Please see detailed data policy at the corresponding species pages from Phytozome (v12.1).