Release Notes

We are pleased to announce the PMN12 release. In this release we introduce 54 new species-specific metabolic pathway databases, which brings the total number of species-specific databases to 76.  The 76 species cover the green plant lineage widely, including green algae, a moss, a club moss, a basal flowering plant, and higher plants of monocots and eudicots. They include major crops from grains to vegetables and fruits. Several medicinal plants are also added to this release, such as Madagascar periwinkle (Catharanthus roseus), red sage (Salvia miltiorrhiza) and flax (Linum usitatissimum). The new release also expands the number of species in three plant families: 17 species in Poaceae, 13 in Brassicaceae and 6 in Fabaceae.

Examples of new species-specific metabolic pathway databases:

Bread wheat

Carrot

Spinach

Sweet orange

Sugar beet

Madagascar periwinkle

Please find complete list of databases here.

An important note about downloading complete PMN databases:

The following five databases were constructed from genome releases which are under prepublication data usage restrictions and thus can only be accessed by online searching and browsing at the PMN web site: AhalleriCyc (version 1.0) (Arabidopsis halleri), LperrieriCyc (1.0) (Leersia perrieri), ObrachyanthaCyc (1.0) (Oryza brachyantha), OpunctataCyc (1.0) (Oryza punctate), OrufipogonCyc (1.0) (Oryza rufipogon). Please see detailed data policy at the corresponding species page from Phytozome (https://phytozome.jgi.doe.gov/pz/portal.html) or EnsemblPlants (http://plants.ensembl.org/index.html).

CornCyc (version 8.0) was constructed from the maize B73 RefGen_V4 genome release, which is also under prepublication data usage restrictions. We communicated with the genome release provider and was allowed to provide the PMN users full access to the CornCyc database, online browsing and complete download. However we ask that you respect the data usage restrictions posted on http://plants.ensembl.org/Zea_mays/Info/Index. The preprint of the maize B73 RefGen_V4 genome paper can be found at http://biorxiv.org/content/early/2016/12/19/079004.