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Terzyme: a tool for identification and analysis of the plant terpenome
BACKGROUND: Terpenoid hydrocarbons represent the largest and most ancient group of phytochemicals, such that the entire chemical library of a plant is often referred to as its ‘terpenome’. Besides having numerous pharmacological properties, terpenes contribute to the scent of the rose, the flavors o...
Autores principales: | , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
BioMed Central
2018
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5761147/ https://www.ncbi.nlm.nih.gov/pubmed/29339971 http://dx.doi.org/10.1186/s13007-017-0269-0 |
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author | Priya, Piyush Yadav, Archana Chand, Jyoti Yadav, Gitanjali |
author_facet | Priya, Piyush Yadav, Archana Chand, Jyoti Yadav, Gitanjali |
author_sort | Priya, Piyush |
collection | PubMed |
description | BACKGROUND: Terpenoid hydrocarbons represent the largest and most ancient group of phytochemicals, such that the entire chemical library of a plant is often referred to as its ‘terpenome’. Besides having numerous pharmacological properties, terpenes contribute to the scent of the rose, the flavors of cinnamon and the yellow of sunflowers. Rapidly increasing -omics datasets provide an unprecedented opportunity for terpenome detection, paving the way for automated web resources dedicated to phytochemical predictions in genomic data. RESULTS: We have developed Terzyme, a predictive algorithm for identification, classification and assignment of broad substrate unit to terpene synthase (TPS) and prenyl transferase (PT) enzymes, known to generate the enormous structural and functional diversity of terpenoid compounds across the plant kingdom. Terzyme uses sequence information, plant taxonomy and machine learning methods for predicting TPSs and PTs in genome and proteome datasets. We demonstrate a significant enrichment of the currently identified terpenome by running Terzyme on more than 40 plants. CONCLUSIONS: Terzyme is the result of a rigorous analysis of evolutionary relationships between hundreds of characterized sequences of TPSs and PTs with known specificities, followed by analysis of genome-wide gene distribution patterns, ontology based clustering and optimization of various parameters for building accurate profile Hidden Markov Models. The predictive webserver and database is freely available at http://nipgr.res.in/terzyme.html and would serve as a useful tool for deciphering the species-specific phytochemical potential of plant genomes. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s13007-017-0269-0) contains supplementary material, which is available to authorized users. |
format | Online Article Text |
id | pubmed-5761147 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2018 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-57611472018-01-16 Terzyme: a tool for identification and analysis of the plant terpenome Priya, Piyush Yadav, Archana Chand, Jyoti Yadav, Gitanjali Plant Methods Research BACKGROUND: Terpenoid hydrocarbons represent the largest and most ancient group of phytochemicals, such that the entire chemical library of a plant is often referred to as its ‘terpenome’. Besides having numerous pharmacological properties, terpenes contribute to the scent of the rose, the flavors of cinnamon and the yellow of sunflowers. Rapidly increasing -omics datasets provide an unprecedented opportunity for terpenome detection, paving the way for automated web resources dedicated to phytochemical predictions in genomic data. RESULTS: We have developed Terzyme, a predictive algorithm for identification, classification and assignment of broad substrate unit to terpene synthase (TPS) and prenyl transferase (PT) enzymes, known to generate the enormous structural and functional diversity of terpenoid compounds across the plant kingdom. Terzyme uses sequence information, plant taxonomy and machine learning methods for predicting TPSs and PTs in genome and proteome datasets. We demonstrate a significant enrichment of the currently identified terpenome by running Terzyme on more than 40 plants. CONCLUSIONS: Terzyme is the result of a rigorous analysis of evolutionary relationships between hundreds of characterized sequences of TPSs and PTs with known specificities, followed by analysis of genome-wide gene distribution patterns, ontology based clustering and optimization of various parameters for building accurate profile Hidden Markov Models. The predictive webserver and database is freely available at http://nipgr.res.in/terzyme.html and would serve as a useful tool for deciphering the species-specific phytochemical potential of plant genomes. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s13007-017-0269-0) contains supplementary material, which is available to authorized users. BioMed Central 2018-01-10 /pmc/articles/PMC5761147/ /pubmed/29339971 http://dx.doi.org/10.1186/s13007-017-0269-0 Text en © The Author(s) 2018 Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated. |
spellingShingle | Research Priya, Piyush Yadav, Archana Chand, Jyoti Yadav, Gitanjali Terzyme: a tool for identification and analysis of the plant terpenome |
title | Terzyme: a tool for identification and analysis of the plant terpenome |
title_full | Terzyme: a tool for identification and analysis of the plant terpenome |
title_fullStr | Terzyme: a tool for identification and analysis of the plant terpenome |
title_full_unstemmed | Terzyme: a tool for identification and analysis of the plant terpenome |
title_short | Terzyme: a tool for identification and analysis of the plant terpenome |
title_sort | terzyme: a tool for identification and analysis of the plant terpenome |
topic | Research |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5761147/ https://www.ncbi.nlm.nih.gov/pubmed/29339971 http://dx.doi.org/10.1186/s13007-017-0269-0 |
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