LAMP detection assays for boxwood blight pathogens: A comparative genomics approach

Malapi-Wight, Martha; Demers, Jill E.; Veltri, Daniel; Marra, Robert E.; Crouch, Jo Anne

doi:10.1038/srep26140

Title: LAMP detection assays for boxwood blight pathogens: A comparative genomics approach

Journal Article · Fri May 20 00:00:00 EDT 2016 · Scientific Reports

DOI:https://doi.org/10.1038/srep26140· OSTI ID:1282973

Malapi-Wight, Martha ^[1]; Demers, Jill E. ^[2]; Veltri, Daniel ^[3]; Marra, Robert E. ^[4]; Crouch, Jo Anne ^[2]

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

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.

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Research Organization:: United States Dept. of Agriculture, Agricultural Research Service (ARS), Beltsville, MD (United States)

Sponsoring Organization:: USDOE

Grant/Contract Number:: AC05-06OR23100

OSTI ID:: 1282973

Journal Information:: Scientific Reports, Vol. 6; ISSN 2045-2322

Publisher:: Nature Publishing GroupCopyright Statement

Country of Publication:: United States

Language:: English

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Cited by: 22 works

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Related Subjects

59 BASIC BIOLOGICAL SCIENCES
mediated isothermal amplification
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cylindrocladium-buxicola
virus diagnostics
visual detection
plant-pathogens
stem blight
box blight
1st report
dna

Title: LAMP detection assays for boxwood blight pathogens: A comparative genomics approach

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