LAMP detection assays for boxwood blight pathogens: A comparative genomics approach
Abstract
Rapid and accurate molecular diagnostic tools are critical to efforts to minimize the impact and spread of emergent pathogens. The identification of diagnostic markers for novel pathogens presents several challenges, especially in the absence of information about population diversity and where genetic resources are limited. The objective of this study was to use comparative genomics datasets to find unique target regions suitable for the diagnosis of two fungal species causing a newly emergent blight disease of boxwood. Candidate marker regions for loop-mediated isothermal amplification (LAMP) assays were identified from draft genomes of Calonectria henricotiae and C. pseudonaviculata, as well as three related species not associated with this disease. To increase the probability of identifying unique targets, we used three approaches to mine genome datasets, based on (i) unique regions, (ii) polymorphisms, and (iii) presence/absence of regions across datasets. From a pool of candidate markers, we demonstrate LAMP assay specificity by testing related fungal species, common boxwood pathogens, and environmental samples containing 445 diverse fungal taxa. In conclusion, this comparative-genomics-based approach to the development of LAMP diagnostic assays is the first of its kind for fungi and could be easily applied to diagnostic marker development for other newly emergent plant pathogens.
- Authors:
-
- United States Dept. of Agriculture, Agricultural Research Service (ARS), Systematic Mycology and Microbiology Laboratory, Beltsville, MD (United States); United States Dept. of Agriculture, Animal and Plant Health Inspection Service (APHIS), Plant Germplasm Quarantine Program, Beltsville, MD (United States)
- United States Dept. of Agriculture, Agricultural Research Service (ARS), Systematic Mycology and Microbiology Laboratory, Beltsville, MD (United States)
- Oak Ridge Inst. for Science and Education, ARS Research Participation Program, Oak Ridge, TN (United States); United States Dept. of Agriculture, Agricultural Research Service (ARS), Systematic Mycology and Microbiology Laboratory, Beltsville, MD (United States)
- Connecticut Agricultural Experiment Station, New Haven, CT (United States). Dept. of Plant Pathology and Ecology
- Publication Date:
- Research Org.:
- United States Dept. of Agriculture, Agricultural Research Service (ARS), Beltsville, MD (United States)
- Sponsoring Org.:
- USDOE
- OSTI Identifier:
- 1282973
- Grant/Contract Number:
- AC05-06OR23100
- Resource Type:
- Accepted Manuscript
- Journal Name:
- Scientific Reports
- Additional Journal Information:
- Journal Volume: 6; Journal ID: ISSN 2045-2322
- Publisher:
- Nature Publishing Group
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 59 BASIC BIOLOGICAL SCIENCES; mediated isothermal amplification; calonectria-pseudonaviculata; cylindrocladium-buxicola; virus diagnostics; visual detection; plant-pathogens; stem blight; box blight; 1st report; dna
Citation Formats
Malapi-Wight, Martha, Demers, Jill E., Veltri, Daniel, Marra, Robert E., and Crouch, Jo Anne. LAMP detection assays for boxwood blight pathogens: A comparative genomics approach. United States: N. p., 2016.
Web. doi:10.1038/srep26140.
Malapi-Wight, Martha, Demers, Jill E., Veltri, Daniel, Marra, Robert E., & Crouch, Jo Anne. LAMP detection assays for boxwood blight pathogens: A comparative genomics approach. United States. https://doi.org/10.1038/srep26140
Malapi-Wight, Martha, Demers, Jill E., Veltri, Daniel, Marra, Robert E., and Crouch, Jo Anne. Fri .
"LAMP detection assays for boxwood blight pathogens: A comparative genomics approach". United States. https://doi.org/10.1038/srep26140. https://www.osti.gov/servlets/purl/1282973.
@article{osti_1282973,
title = {LAMP detection assays for boxwood blight pathogens: A comparative genomics approach},
author = {Malapi-Wight, Martha and Demers, Jill E. and Veltri, Daniel and Marra, Robert E. and Crouch, Jo Anne},
abstractNote = {Rapid and accurate molecular diagnostic tools are critical to efforts to minimize the impact and spread of emergent pathogens. The identification of diagnostic markers for novel pathogens presents several challenges, especially in the absence of information about population diversity and where genetic resources are limited. The objective of this study was to use comparative genomics datasets to find unique target regions suitable for the diagnosis of two fungal species causing a newly emergent blight disease of boxwood. Candidate marker regions for loop-mediated isothermal amplification (LAMP) assays were identified from draft genomes of Calonectria henricotiae and C. pseudonaviculata, as well as three related species not associated with this disease. To increase the probability of identifying unique targets, we used three approaches to mine genome datasets, based on (i) unique regions, (ii) polymorphisms, and (iii) presence/absence of regions across datasets. From a pool of candidate markers, we demonstrate LAMP assay specificity by testing related fungal species, common boxwood pathogens, and environmental samples containing 445 diverse fungal taxa. In conclusion, this comparative-genomics-based approach to the development of LAMP diagnostic assays is the first of its kind for fungi and could be easily applied to diagnostic marker development for other newly emergent plant pathogens.},
doi = {10.1038/srep26140},
journal = {Scientific Reports},
number = ,
volume = 6,
place = {United States},
year = {Fri May 20 00:00:00 EDT 2016},
month = {Fri May 20 00:00:00 EDT 2016}
}
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