COST Webpage of the Action:

Very useful organizations, projects, and resource pages

Medicinal Plant Genomics Resource - http://medicinalplantgenomics.msu.edu/

Transcriptome assemblies for 14 medicinal plants, together with expression data and functional annotation, plus metabolomics data for some of the species.

Atropa belladonna, Camptotheca acuminate, Cannabis sativa, Catharanthus roseus, Digitalis purpurea, Dioscorea villosa, Echinacea purpurea, Ginkgo biloba, Hoodia gordonii, Hypericum perforatum, Panax quinquefolius, Rauvolfia serpentina, Rosmarinus officinalis, Valeriana officinalis


PhytoMetaSyn - http://www.phytometasyn.ca/

Synthetic Biosystems for the Production of High Value Plant Metabolites

The objective of the  PhytoMetaSyn Project is to determine the metabolic pathways of selected plants by which the plants produce high value added metabolites and reproduce these pathways in the common yeast cell.

The key deliverables of this project are: (1) A public resource of genomic and metabolomic information for 75 plants producing bioactive natural products; (2) engineered yeast strains that produce high-value plant natural products; (3) the extensive cataloguing of new enzymes for use as biocatalysts in plug-and-play synthetic biology applications; (4) the invention of efficient functional genomics approaches for elucidating novel metabolic pathways and identifying unknown biosynthetic genes from non-model plants; and (5) a thorough analysis of related regulatory, ethical, and economic issues, including consultations with the public, which will help to ensure that technology development is not just scientifically sound, but is also socially robust.


The 1KP Project -  http://www.onekp.com/

The 1000 plants (oneKP or 1KP) initiative is a public-private partnership generating large scale gene sequence information for 1000 different species of plants. Major supporters include Alberta's Department of Advanced Education and Technology (AET), Silicon Valley based Musea Ventures, Beijing Genomics Institute in Shenzhen, University of Alberta, and Alberta's Informatics Circle of Research Excellence (iCORE).


Transcriptome Project - http://www.uic.edu/pharmacy/MedPlTranscriptome/index.html

Transcriptome characterization, sequencing, and assembly of medicinal plants relevant to human health



Tools for PNP research
suggested by participants of the WG3 meeting in Warsaw, Sep. 2014

Cytoscape -  a tool for network visualization with great systems biology applications.

As can be found in the tutorial: (1) It is very easy to create plots for papers; (2) It can import biological data directly - so there is no need for searching the internet and parsing files; (3) Useful systems-related apps (for example) are GeneMania, BINGO that are good for gene function prediction.


UCSC genome browser  - the most widely used genome browser (some say it is much better than NCBI and EMBL). The browser allows analyzing specific positions in the studied genome. You can show in one window almost any available information for the studied locus - e.g., genes, gene annotations, known SNPs, alternative splicing variants and many more. You can also easily upload sequencing results and compare your own experiment to what is currently known.

Tutorials for the first two tools, please see here


EXPANDER -analysis of gene expression and NGS data. It seamlessly integrates in one package all analysis steps, including: (1) Data preprocessing and normalization, (2) Identification of differential genes (including methods suitable for NGS data analysis); (3) Clustering and biclustering;

It also supports down-stream enrichment analyses of:

  - GO functional categories

  - TF binding sites in promoter regions

  - MicroRNA sites in 3'-UTRs and

  - Biological pathways and

  - Chromosomal locations

To learn more about this tool see this Nature protocol 


Learned Societies of interest

Phytochemical Society of Europe (PSE)

Society for Medicinal Plant and Natural Product Research (GA)




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