Development of a genomics-based LAMP (Loop-Mediated Isothermal Amplification) assay for detection of Pseudomonas fuscovaginae from rice
The vast amount of data available through next-generation sequencing technology is facilitating the design of diagnostic marker systems. This study reports the use of draft genome sequences from the bacterial plant pathogen Pseudomonas fuscovaginae, the cause of sheath brown rot of rice, to describe...
| Main Authors: | , , , , , , , |
|---|---|
| Format: | Journal Article |
| Language: | Inglés |
| Published: |
Scientific Societies
2014
|
| Online Access: | https://hdl.handle.net/10568/165509 |
| _version_ | 1855538071571791872 |
|---|---|
| author | Ash, Gavin J. Lang, Jillian M. Triplett, Lindsay R. Stodart, Benjamin J. Verdier, Valérie Vera Cruz, Casiana Rott, Philippe Leach, Jan E. |
| author_browse | Ash, Gavin J. Lang, Jillian M. Leach, Jan E. Rott, Philippe Stodart, Benjamin J. Triplett, Lindsay R. Vera Cruz, Casiana Verdier, Valérie |
| author_facet | Ash, Gavin J. Lang, Jillian M. Triplett, Lindsay R. Stodart, Benjamin J. Verdier, Valérie Vera Cruz, Casiana Rott, Philippe Leach, Jan E. |
| author_sort | Ash, Gavin J. |
| collection | Repository of Agricultural Research Outputs (CGSpace) |
| description | The vast amount of data available through next-generation sequencing technology is facilitating the design of diagnostic marker systems. This study reports the use of draft genome sequences from the bacterial plant pathogen Pseudomonas fuscovaginae, the cause of sheath brown rot of rice, to describe the genetic diversity within a worldwide collection of strains representing the species. Based on a comparative analysis with the draft sequences, primers for a loop-mediated isothermal amplification (LAMP) assay were developed to identify P. fuscovaginae. The assay reported here reliably differentiated strains of P. fuscovaginae isolated from rice from a range of other bacteria that are commonly isolated from rice and other plants using a primer combination designated Pf8. The LAMP assay identified P. fuscovaginae purified DNA, live or heat-killed cells from pure cultures, and detected the bacterium in extracts or exudates from infected host plant material. The P. fuscovaginae LAMP assay is a suitable diagnostic tool for the glasshouse and laboratory and could be further developed for in-field surveys. |
| format | Journal Article |
| id | CGSpace165509 |
| institution | CGIAR Consortium |
| language | Inglés |
| publishDate | 2014 |
| publishDateRange | 2014 |
| publishDateSort | 2014 |
| publisher | Scientific Societies |
| publisherStr | Scientific Societies |
| record_format | dspace |
| spelling | CGSpace1655092025-12-08T09:54:28Z Development of a genomics-based LAMP (Loop-Mediated Isothermal Amplification) assay for detection of Pseudomonas fuscovaginae from rice Ash, Gavin J. Lang, Jillian M. Triplett, Lindsay R. Stodart, Benjamin J. Verdier, Valérie Vera Cruz, Casiana Rott, Philippe Leach, Jan E. The vast amount of data available through next-generation sequencing technology is facilitating the design of diagnostic marker systems. This study reports the use of draft genome sequences from the bacterial plant pathogen Pseudomonas fuscovaginae, the cause of sheath brown rot of rice, to describe the genetic diversity within a worldwide collection of strains representing the species. Based on a comparative analysis with the draft sequences, primers for a loop-mediated isothermal amplification (LAMP) assay were developed to identify P. fuscovaginae. The assay reported here reliably differentiated strains of P. fuscovaginae isolated from rice from a range of other bacteria that are commonly isolated from rice and other plants using a primer combination designated Pf8. The LAMP assay identified P. fuscovaginae purified DNA, live or heat-killed cells from pure cultures, and detected the bacterium in extracts or exudates from infected host plant material. The P. fuscovaginae LAMP assay is a suitable diagnostic tool for the glasshouse and laboratory and could be further developed for in-field surveys. 2014-07 2024-12-19T12:55:09Z 2024-12-19T12:55:09Z Journal Article https://hdl.handle.net/10568/165509 en Scientific Societies Ash, Gavin J.; Lang, Jillian M.; Triplett, Lindsay R.; Stodart, Benjamin J.; Verdier, Valérie; Cruz, Casiana Vera; Rott, Philippe and Leach, Jan E. 2014. Development of a genomics-based LAMP (Loop-Mediated Isothermal Amplification) assay for detection of Pseudomonas fuscovaginae from rice. Plant Disease, Volume 98 no. 7 p. 909-915 |
| spellingShingle | Ash, Gavin J. Lang, Jillian M. Triplett, Lindsay R. Stodart, Benjamin J. Verdier, Valérie Vera Cruz, Casiana Rott, Philippe Leach, Jan E. Development of a genomics-based LAMP (Loop-Mediated Isothermal Amplification) assay for detection of Pseudomonas fuscovaginae from rice |
| title | Development of a genomics-based LAMP (Loop-Mediated Isothermal Amplification) assay for detection of Pseudomonas fuscovaginae from rice |
| title_full | Development of a genomics-based LAMP (Loop-Mediated Isothermal Amplification) assay for detection of Pseudomonas fuscovaginae from rice |
| title_fullStr | Development of a genomics-based LAMP (Loop-Mediated Isothermal Amplification) assay for detection of Pseudomonas fuscovaginae from rice |
| title_full_unstemmed | Development of a genomics-based LAMP (Loop-Mediated Isothermal Amplification) assay for detection of Pseudomonas fuscovaginae from rice |
| title_short | Development of a genomics-based LAMP (Loop-Mediated Isothermal Amplification) assay for detection of Pseudomonas fuscovaginae from rice |
| title_sort | development of a genomics based lamp loop mediated isothermal amplification assay for detection of pseudomonas fuscovaginae from rice |
| url | https://hdl.handle.net/10568/165509 |
| work_keys_str_mv | AT ashgavinj developmentofagenomicsbasedlamploopmediatedisothermalamplificationassayfordetectionofpseudomonasfuscovaginaefromrice AT langjillianm developmentofagenomicsbasedlamploopmediatedisothermalamplificationassayfordetectionofpseudomonasfuscovaginaefromrice AT triplettlindsayr developmentofagenomicsbasedlamploopmediatedisothermalamplificationassayfordetectionofpseudomonasfuscovaginaefromrice AT stodartbenjaminj developmentofagenomicsbasedlamploopmediatedisothermalamplificationassayfordetectionofpseudomonasfuscovaginaefromrice AT verdiervalerie developmentofagenomicsbasedlamploopmediatedisothermalamplificationassayfordetectionofpseudomonasfuscovaginaefromrice AT veracruzcasiana developmentofagenomicsbasedlamploopmediatedisothermalamplificationassayfordetectionofpseudomonasfuscovaginaefromrice AT rottphilippe developmentofagenomicsbasedlamploopmediatedisothermalamplificationassayfordetectionofpseudomonasfuscovaginaefromrice AT leachjane developmentofagenomicsbasedlamploopmediatedisothermalamplificationassayfordetectionofpseudomonasfuscovaginaefromrice |