We have released the genome of Catharanthus roseus variety Sunstorm Apricot as described in Kellner et al. 2015. See the genome browser, BLAST search site, and Dryad download page for access to the data.
Methods for transcriptome assembly as performed in the MPGR project are described in Gongora-Castillo et al. 2012. Analysis of the Camptotheca acuminata, Catharanthus roseus, and Rauvolfia serpentina transcriptomes are described in PLoS ONE and analysis of the Valeriana officinalius transcriptome assembly is described in Yeo et al. 2013. For more information about the release of the Final Version of the transcriptome data, please see the press release.
Expression data released for 14 medicinal plants.Expression levels for the representative transcript (the longest transcript isoform) are provided from an array of tissues that were sequenced using RNA-seq for expression abundances. Expression levels are provided in FPKM values (Fragments per kilobase per transcript per million mapped reads). The information can be downloaded from the MPC Download site.
The Medicinal Plant Metabolomics Resource website, the metabolomics partner of the Medicinal Plant Genomics Resource, is available with metabolomics data from Atropa belladonna and Digitalis purpurea. Metabolite data from the remaining 12 medicinal plant species covered by this project will be made available soon. A press release is available with complete information about this metabolite resource.
We have released a set of functional annotation search tools for the assembled transcriptomes for each of the 14 medicinal plant species using keywords, Pfam domains, and sequence identifiers. The transcript and predicted protein sequences for the transcript assemblies are provided. Note that the assembly process using Velvet and Oases generates isoforms and each isoform has been annotated. Functional annotation includes alignments to UniRef, identification of InterPro domains, alignments to Arabidopsis thaliana genes, and alignment to ESTs and peptides from existing public sequences for these 14 medicinal plants. Expression levels for the representative transcript (the longest transcript isoform) are provided from an array of tissues that were sequenced using RNA-seq for expression abundances. Expression levels are provided in the form of FPKM values (Fragments per kilobase per transcript per million mapped reads). Note alternative isoforms generated from Oases are not annotated for expression abundances
The final transcriptome assemblies for 14 medicinal plants have been completed and these datasets are now available for searching via an anonymous search window, or the information can be downloaded directly from an MPC Download site or via the NCBI SRA site
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We are providing our first assemblies of the transcriptomes of 11 medicinal plant species: Atropa belladonna, Catharanthus roseus, Digitalis purpurea, Dioscorea villosa, Echinacea purpurea, Hoodia gordonii, Hypericum perforatum, Panax quinquefolius, Rauvolfia serpentina, Rosmarinus officinalis, Valeriana officials.
Assemblies can be searched through our BLAST search page (See "Search Tools", select "BLAST Search"). Individual contigs can be retrieved using the Contig Search Tool (See Search Tools", select "Contig Search").
New Website released for Medicinal Plant Genomics Resource. Species Overview pages that contain information about drug uses, clinical trials and metabolites have been added for all species within MPGR.