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Home - Citation

If you find any of the data made accessible here useful and use them in your own work, please cite the following two publications in your papers:

Facchini P.J., Bohlmann J., Covello P.S., De Luca V., Mahadevan R., Page J.E., Ro D.K., Sensen C.W., Storms R., Martin V.J. (2012) Synthetic biosystems for the production of high-value plant metabolites. Trends Biotechnol. 30:127-131  http://dx.doi.org/10.1016/j.tibtech.2011.10.001

Xiao M., Zhang Y., Chen X., Lee E.J., Barber C., Chakrabarty R., Desgagné-Penix I., Haslam T., Kim Y.-B., Liu E., MacNervin G., Masada-Atsumi S., Reed D., Stout J., Zerbe P., Zhang Y., Bohlmann J., Covello P., De Luca V., Page J., Ro D.-K., Martin V., Facchini P., Sensen C.W. (2013) Tanscriptome analysis based on next-generation sequencing of non-model plants producing specialized metabolites of biotechnological interest. J. Biotechnol. 166:122-134   http://dx.doi.org/10.1016/j.jbiotec.2013.04.004

- The Phytometasyn team



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 such that the yeast cells produce the same compounds.


It has been said that plants are the world's best chemists.  Through biosynthetic pathways incorporating genes and enzymes, they can synthesize a immense diversity of molecules.  These molecules are referred to as metabolites, as they are a result of the metabolic processes of the plants.   These metabolites have been used as traditional medicines and  the commercial potential of these metabolites has recently been recognized.  Commercial applications of the metabolites include pharmaceuticals (analgesics, cough suppressants anticancer drugs), flavouring agents, insecticides, fragrances and industrial applications such as resins. The production of these metabolites by plants however, has limited opportunities for commercialization given the quantities of metabolites produced by the plants,  challenges in harvesting the plants and extracting the desired metabolite and the time required for plant growth. If however, the pathways resulting in the production of these metabolites in plants could be transferred to other organisms,  the potential for the commercialization of these high value metabolites may be possible.


Read more: Synthetic Biosystems for the Production of High Value Plant Metabolites

Project Overview Diagram



Publications of the Principal Investigators for the PhytoMetaSyn Project can be viewed on the websites as listed for each Investigator in the section titled Our People. Publications arising directly out of the research activities of the PhytoMetaSyn project include the following:


Read more: Publications

Data Access and Release Policy

Data will be released to public databases in accordance with Genome Canada's policy on Data Release and Resource Sharing.  Various methods will be used to share the data generated on this project including:


Read more: Data Access

Plant Assembly Download

The project is releasing all transcriptome assemblies we have generated from both 454 and Illumina sequencing data. Currently 167 assemblies sets for 74 plant species are complete and available for download.


Read more: plantDownload

briaskThumb_citrus_maxima0.jpgBLAST Portal for Project Transcriptomes

 We have made our first assembled transcriptome based on 454 sequencing available for BLAST analysis. The remaining 33 assembled transcriptomes will be added shortly, with databases for all 75 plant species available by February 2012. Future updates will also include assemblies based on Illumina sequencing for each species.

To the Blast Search >>


Read more: BLAST Project Transcriptomes

Plants Next Generation Sequence Data on Short Read Archive (SRA)

Plants RNA has been sequenced using both 454 and Illumina (GA and HiSeq) technologies. Raw reads are submitted to SRA database. You can go to  SRA web site to search for the data using the accession number in the following table.


Read more: Plant_SRA_Data

Plants of Interest

Approximately seventy-five plant species are being studied in the project. The plant species were selected on the basis of the following criteria:(1) the natural product composition of the species; (2) the commercial importance of the plant and/or the natural products; and (3) the availability of sufficient tissue for RNA and metabolite isolation.


Read more: Plants

Project Organization and Management 

The project has in place a management structure which facilitates decision - making and control, freeing the researchers up to undertake the research activities of the project.


Read more: Organization


 The total project budget is $13,602,100 over 4 years of which Genome Canada contributed $6,443,100.  Other project funders include Genome British Columbia, Genome Alberta, Genome Prairie, Genome Quebec, the National Research Council, Ontario Ministry of Innovation and Research, Agriculture and Agri-Food Canada, Canada Foundation for Innovation (CFI),  Brock University and industry.


Read more: Funding


 GE3LS stands for genomics and its related ethical, economic, environmental, legal and social aspects. GE3LS research complement the role of natural scientists by bringing to the table a fuller diversity of perspectives in helping to shape and address critical questions at the interface of science and society. GE3LS research is carried out by academic researchers from an ever-expanding range of perspectives and disciplinary backgrounds including, but not limited to: social science, law, commerce, communications and journalism studies, bioethics, political science and public policy


Read more: GE3LS

briaskThumb_citrus_maxima0.jpgThe Science Advisory Board

 The reseach team receives advice and guidance from an external group of experts in the related research disciplines. The members of the Scientific Advisory Board work with the project researchers to maximize the successful outcome of the project.


Read more: SAB