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CathaCyc, a metabolic pathway database built from Catharanthus roseus RNA-Seq data

(2013) PLANT AND CELL PHYSIOLOGY. 54(5). p.673-685
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Abstract
drugs vinblastine and vincristine. The TIA pathway operates in a complex metabolic network that steers plant growth and survival. Pathway databases and metabolic networks reconstructed from 'omics' sequence data can help to discover missing enzymes, study metabolic pathway evolution and, ultimately, engineer metabolic pathways. To date, such databases have mainly been built for model plant species with sequenced genomes. Although genome sequence data are not available for most medicinal plant species, next-generation sequencing is now extensively employed to create comprehensive medicinal plant transcriptome sequence resources. Here we report on the construction of CathaCyc, a detailed metabolic pathway database, from C. roseus RNA-Seq data sets. CathaCyc (version 1.0) contains 390 pathways with 1,347 assigned enzymes and spans primary and secondary metabolism. Curation of the pathways linked with the synthesis of TIAs and triterpenoids, their primary metabolic precursors, and their elicitors, the jasmonate hormones, demonstrated that RNA-Seq resources are suitable for the construction of pathway databases. CathaCyc is accessible online ( ext-link-type="uri" xlink:href="http://www.cathacyc.org" xmlns:xlink="http://www.w3.org/1999/xlink">http://www.cathacyc.org) and offers a range of tools for the visualization and analysis of metabolic networks and 'omics' data. Overlay with expression data from publicly available RNA-Seq resources demonstrated that two well-characterized C. roseus terpenoid pathways, those of TIAs and triterpenoids, are subject to distinct regulation by both developmental and environmental cues. We anticipate that databases such as CathaCyc will become key to the study and exploitation of the metabolism of medicinal plants.
Keywords
BIOCYC COLLECTION, PHENOLIC-COMPOUNDS, MOLECULAR-CLONING, METACYC DATABASE, SYSTEMS BIOLOGY, HAIRY ROOTS, ENZYMES, Transcriptome, INDOLE ALKALOID BIOSYNTHESIS, MADAGASCAR PERIWINKLE, CLASS-III PEROXIDASE, Metabolism, Madagascar periwinkle, Deep sequencing, Catharanthus roseus, BioCyc

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Chicago
Van Moerkercke, Alex, Michele Fabris, Jacob Pollier, Gino Baart, Stephane Rombauts, Ghulam Hasnain, Heiko Rischer, Johan Memelink, Kirsi-Marja Oksman-Caldentey, and Alain Goossens. 2013. “CathaCyc, a Metabolic Pathway Database Built from Catharanthus Roseus RNA-Seq Data.” Plant and Cell Physiology 54 (5): 673–685.
APA
Van Moerkercke, A., Fabris, M., Pollier, J., Baart, G., Rombauts, S., Hasnain, G., Rischer, H., et al. (2013). CathaCyc, a metabolic pathway database built from Catharanthus roseus RNA-Seq data. PLANT AND CELL PHYSIOLOGY, 54(5), 673–685.
Vancouver
1.
Van Moerkercke A, Fabris M, Pollier J, Baart G, Rombauts S, Hasnain G, et al. CathaCyc, a metabolic pathway database built from Catharanthus roseus RNA-Seq data. PLANT AND CELL PHYSIOLOGY. 2013;54(5):673–85.
MLA
Van Moerkercke, Alex, Michele Fabris, Jacob Pollier, et al. “CathaCyc, a Metabolic Pathway Database Built from Catharanthus Roseus RNA-Seq Data.” PLANT AND CELL PHYSIOLOGY 54.5 (2013): 673–685. Print.
@article{4098862,
  abstract     = {drugs vinblastine and vincristine. The TIA pathway operates in a complex metabolic network that steers plant growth and survival. Pathway databases and metabolic networks reconstructed from 'omics' sequence data can help to discover missing enzymes, study metabolic pathway evolution and, ultimately, engineer metabolic pathways. To date, such databases have mainly been built for model plant species with sequenced genomes. Although genome sequence data are not available for most medicinal plant species, next-generation sequencing is now extensively employed to create comprehensive medicinal plant transcriptome sequence resources. Here we report on the construction of CathaCyc, a detailed metabolic pathway database, from C. roseus RNA-Seq data sets. CathaCyc (version 1.0) contains 390 pathways with 1,347 assigned enzymes and spans primary and secondary metabolism. Curation of the pathways linked with the synthesis of TIAs and triterpenoids, their primary metabolic precursors, and their elicitors, the jasmonate hormones, demonstrated that RNA-Seq resources are suitable for the construction of pathway databases. CathaCyc is accessible online ( ext-link-type="uri" xlink:href="http://www.cathacyc.org" xmlns:xlink="http://www.w3.org/1999/xlink">http://www.cathacyc.org) and offers a range of tools for the visualization and analysis of metabolic networks and 'omics' data. Overlay with expression data from publicly available RNA-Seq resources demonstrated that two well-characterized C. roseus terpenoid pathways, those of TIAs and triterpenoids, are subject to distinct regulation by both developmental and environmental cues. We anticipate that databases such as CathaCyc will become key to the study and exploitation of the metabolism of medicinal plants.},
  author       = {Van Moerkercke, Alex and Fabris, Michele and Pollier, Jacob and Baart, Gino and Rombauts, Stephane and Hasnain, Ghulam and Rischer, Heiko and Memelink, Johan and Oksman-Caldentey, Kirsi-Marja and Goossens, Alain},
  issn         = {0032-0781},
  journal      = {PLANT AND CELL PHYSIOLOGY},
  keywords     = {BIOCYC COLLECTION,PHENOLIC-COMPOUNDS,MOLECULAR-CLONING,METACYC DATABASE,SYSTEMS BIOLOGY,HAIRY ROOTS,ENZYMES,Transcriptome,INDOLE ALKALOID BIOSYNTHESIS,MADAGASCAR PERIWINKLE,CLASS-III PEROXIDASE,Metabolism,Madagascar periwinkle,Deep sequencing,Catharanthus roseus,BioCyc},
  language     = {eng},
  number       = {5},
  pages        = {673--685},
  title        = {CathaCyc, a metabolic pathway database built from Catharanthus roseus RNA-Seq data},
  url          = {http://dx.doi.org/10.1093/pcp/pct039},
  volume       = {54},
  year         = {2013},
}

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