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Virus‐induced gene silencing database for phenomics and functional genomics in Nicotiana benthamiana
Virus‐induced gene silencing (VIGS) is an important forward and reverse genetics method for the study of gene function in many plant species, especially Nicotiana benthamiana. However, despite the widespread use of VIGS, a searchable database compiling the phenotypes observed with this method is lac...
Autores principales: | , , , , , , , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
John Wiley and Sons Inc.
2018
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6508541/ https://www.ncbi.nlm.nih.gov/pubmed/31245720 http://dx.doi.org/10.1002/pld3.55 |
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author | Senthil‐Kumar, Muthappa Wang, Mingyi Chang, Junil Ramegowda, Venkategowda del Pozo, Olga Liu, Yule Doraiswamy, Vanthana Lee, Hee‐Kyung Ryu, Choong‐Min Wang, Keri Xu, Ping Van Eck, Joyce Chakravarthy, Suma Dinesh‐Kumar, Savithramma P. Martin, Gregory B. Mysore, Kirankumar S. |
author_facet | Senthil‐Kumar, Muthappa Wang, Mingyi Chang, Junil Ramegowda, Venkategowda del Pozo, Olga Liu, Yule Doraiswamy, Vanthana Lee, Hee‐Kyung Ryu, Choong‐Min Wang, Keri Xu, Ping Van Eck, Joyce Chakravarthy, Suma Dinesh‐Kumar, Savithramma P. Martin, Gregory B. Mysore, Kirankumar S. |
author_sort | Senthil‐Kumar, Muthappa |
collection | PubMed |
description | Virus‐induced gene silencing (VIGS) is an important forward and reverse genetics method for the study of gene function in many plant species, especially Nicotiana benthamiana. However, despite the widespread use of VIGS, a searchable database compiling the phenotypes observed with this method is lacking. Such a database would allow researchers to know the phenotype associated with the silencing of a large number of individual genes without experimentation. We have developed a VIGS phenomics and functional genomics database (VPGD) that has DNA sequence information derived from over 4,000 N. benthamiana VIGS clones along with the associated silencing phenotype for approximately 1,300 genes. The VPGD has a built‐in BLAST search feature that provides silencing phenotype information of specific genes. In addition, a keyword‐based search function could be used to find a specific phenotype of interest with the corresponding gene, including its Gene Ontology descriptions. Query gene sequences from other plant species that have not been used for VIGS can also be searched for their homologs and silencing phenotype in N. benthamiana. VPGD is useful for identifying gene function not only in N. benthamiana but also in related Solanaceae plants such as tomato and potato. The database is accessible at http://vigs.noble.org. |
format | Online Article Text |
id | pubmed-6508541 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2018 |
publisher | John Wiley and Sons Inc. |
record_format | MEDLINE/PubMed |
spelling | pubmed-65085412019-06-26 Virus‐induced gene silencing database for phenomics and functional genomics in Nicotiana benthamiana Senthil‐Kumar, Muthappa Wang, Mingyi Chang, Junil Ramegowda, Venkategowda del Pozo, Olga Liu, Yule Doraiswamy, Vanthana Lee, Hee‐Kyung Ryu, Choong‐Min Wang, Keri Xu, Ping Van Eck, Joyce Chakravarthy, Suma Dinesh‐Kumar, Savithramma P. Martin, Gregory B. Mysore, Kirankumar S. Plant Direct Original Research Virus‐induced gene silencing (VIGS) is an important forward and reverse genetics method for the study of gene function in many plant species, especially Nicotiana benthamiana. However, despite the widespread use of VIGS, a searchable database compiling the phenotypes observed with this method is lacking. Such a database would allow researchers to know the phenotype associated with the silencing of a large number of individual genes without experimentation. We have developed a VIGS phenomics and functional genomics database (VPGD) that has DNA sequence information derived from over 4,000 N. benthamiana VIGS clones along with the associated silencing phenotype for approximately 1,300 genes. The VPGD has a built‐in BLAST search feature that provides silencing phenotype information of specific genes. In addition, a keyword‐based search function could be used to find a specific phenotype of interest with the corresponding gene, including its Gene Ontology descriptions. Query gene sequences from other plant species that have not been used for VIGS can also be searched for their homologs and silencing phenotype in N. benthamiana. VPGD is useful for identifying gene function not only in N. benthamiana but also in related Solanaceae plants such as tomato and potato. The database is accessible at http://vigs.noble.org. John Wiley and Sons Inc. 2018-04-23 /pmc/articles/PMC6508541/ /pubmed/31245720 http://dx.doi.org/10.1002/pld3.55 Text en © 2018 The Authors. Plant Direct published by American Society of Plant Biologists, Society for Experimental Biology and John Wiley & Sons Ltd. This is an open access article under the terms of the http://creativecommons.org/licenses/by/4.0/ License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Original Research Senthil‐Kumar, Muthappa Wang, Mingyi Chang, Junil Ramegowda, Venkategowda del Pozo, Olga Liu, Yule Doraiswamy, Vanthana Lee, Hee‐Kyung Ryu, Choong‐Min Wang, Keri Xu, Ping Van Eck, Joyce Chakravarthy, Suma Dinesh‐Kumar, Savithramma P. Martin, Gregory B. Mysore, Kirankumar S. Virus‐induced gene silencing database for phenomics and functional genomics in Nicotiana benthamiana |
title | Virus‐induced gene silencing database for phenomics and functional genomics in Nicotiana benthamiana
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title_full | Virus‐induced gene silencing database for phenomics and functional genomics in Nicotiana benthamiana
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title_fullStr | Virus‐induced gene silencing database for phenomics and functional genomics in Nicotiana benthamiana
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title_full_unstemmed | Virus‐induced gene silencing database for phenomics and functional genomics in Nicotiana benthamiana
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title_short | Virus‐induced gene silencing database for phenomics and functional genomics in Nicotiana benthamiana
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title_sort | virus‐induced gene silencing database for phenomics and functional genomics in nicotiana benthamiana |
topic | Original Research |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6508541/ https://www.ncbi.nlm.nih.gov/pubmed/31245720 http://dx.doi.org/10.1002/pld3.55 |
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