@article{rahman_standish_d'arcangelo_quesada-ocampo_2021, title={Clade-Specific Biosurveillance of Pseudoperonospora cubensis Using Spore Traps for Precision Disease Management of Cucurbit Downy Mildew}, volume={111}, ISSN={["1943-7684"]}, url={https://doi.org/10.1094/PHYTO-06-20-0231-R}, DOI={10.1094/PHYTO-06-20-0231-R}, abstractNote={ Pseudoperonospora cubensis is an obligate oomycete and cause of cucurbit downy mildew (CDM), the most destructive foliar disease affecting cucurbit hosts. Annual epidemics develop throughout the United States as windborne sporangia travel great distances and survive prolonged exposure to solar radiation. Recent genomic evidence suggests that P. cubensis isolates display host adaptation based on their respective clade. Early detection is key for fungicide application timing, and identification of the host-adapted clade provides information on the risk of infection for specific cucurbit crops. In this study, a multiplex quantitative PCR assay was developed based on species- and clade-specific nuclear genomic markers. The assay detected as few as 10 sporangia or DNA at 100 fg/ml for both clades and was validated in the field by deploying rotorod spore samplers in cucurbit sentinel plots located at two research stations in North Carolina. Using this assay, sporangia DNA was detected in spore trap sampling rods before signs of P. cubensis or CDM symptoms were observed in the sentinel plots. Both clade 1 and clade 2 DNA were detected in late-season cucumber and watermelon plots but only clade 2 DNA was detected in the early-season cucumber plots. These results will significantly improve disease management of CDM by monitoring inoculum levels to determine the cucurbit crops at risk of infection throughout each growing season. }, number={2}, journal={PHYTOPATHOLOGY}, publisher={Scientific Societies}, author={Rahman, A. and Standish, J. R. and D'Arcangelo, K. N. and Quesada-Ocampo, L. M.}, year={2021}, month={Feb}, pages={312–320} }
 @article{rahman_gongora-castillo_bowman_childs_gent_martin_quesada-ocampo_2019, title={Genome Sequencing and Transcriptome Analysis of the Hop Downy Mildew Pathogen Pseudoperonospora humuli Reveal Species-Specific Genes for Molecular Detection}, volume={109}, ISSN={["1943-7684"]}, url={https://doi.org/10.1094/PHYTO-11-18-0431-R}, DOI={10.1094/PHYTO-11-18-0431-R}, abstractNote={Pseudoperonospora humuli is an obligate oomycete pathogen of hop (Humulus lupulus) that causes downy mildew, an important disease in most production regions in the Northern Hemisphere. The pathogen can cause a systemic infection in hop, overwinter in the root system, and infect propagation material. Substantial yield loss may occur owing to P. humuli infection of strobiles (seed cones), shoots, and cone-bearing branches. Fungicide application and cultural practices are the primary methods to manage hop downy mildew. However, effective, sustainable, and cost-effective management of downy mildew can be improved by developing early detection systems to inform on disease risk and timely fungicide application. However, no species-specific diagnostic assays or genomic resources are available for P. humuli. The genome of the P. humuli OR502AA isolate was partially sequenced using Illumina technology and assembled with ABySS. The assembly had a minimum scaffold length of 500 bp and an N50 (median scaffold length of the assembled genome) of 19.2 kbp. A total number of 18,656 genes were identified using MAKER standard gene predictions. Additionally, transcriptome assemblies were generated using RNA-seq and Trinity for seven additional P. humuli isolates. Bioinformatics analyses of next generation sequencing reads of P. humuli and P. cubensis (a closely related sister species) identified 242 candidate species-specific P. humuli genes that could be used as diagnostic molecular markers. These candidate genes were validated using polymerase chain reaction against a diverse collection of isolates from P. humuli, P. cubensis, and other oomycetes. Overall, four diagnostic markers were found to be uniquely present in P. humuli. These candidate markers identified through comparative genomics can be used for pathogen diagnostics in propagation material, such as rhizomes and vegetative cuttings, or adapted for biosurveillance of airborne sporangia, an important source of inoculum in hop downy mildew epidemics.}, number={8}, journal={PHYTOPATHOLOGY}, publisher={Scientific Societies}, author={Rahman, A. and Gongora-Castillo, E. and Bowman, M. J. and Childs, K. L. and Gent, D. H. and Martin, F. N. and Quesada-Ocampo, L. M.}, year={2019}, month={Aug}, pages={1354–1366} }
 @article{crandall_rahman_quesada-ocampo_martin_bilodeau_miles_2018, title={Advances in Diagnostics of Downy Mildews: Lessons Learned from Other Oomycetes and Future Challenges}, volume={102}, ISSN={["1943-7692"]}, url={https://doi.org/10.1094/PDIS-09-17-1455-FE}, DOI={10.1094/pdis-09-17-1455-fe}, abstractNote={ Downy mildews are plant pathogens that damage crop quality and yield worldwide. Among the most severe and notorious crop epidemics of downy mildew occurred on grapes in the mid-1880s, which almost destroyed the wine industry in France. Since then, there have been multiple outbreaks on sorghum and millet in Africa, tobacco in Europe, and recent widespread epidemics on lettuce, basil, cucurbits, and spinach throughout North America. In the mid-1970s, loss of corn to downy mildew in the Philippines was estimated at US$23 million. Today, crops that are susceptible to downy mildews are worth at least $7.5 billion of the United States’ economy. Although downy mildews cause devastating economic losses in the United States and globally, this pathogen group remains understudied because they are difficult to culture and accurately identify. Early detection of downy mildews in the environment is critical to establish pathogen presence and identity, determine fungicide resistance, and understand how pathogen populations disperse. Knowing when and where pathogens emerge is also important for identifying critical control points to restrict movement and to contain populations. Reducing the spread of pathogens also decreases the likelihood of sexual recombination events and discourages the emergence of novel virulent strains. A major challenge in detecting downy mildews is that they are obligate pathogens and thus cannot be cultured in artificial media to identify and maintain specimens. However, advances in molecular detection techniques hold promise for rapid and in some cases, relatively inexpensive diagnosis. In this article, we discuss recent advances in diagnostic tools that can be used to detect downy mildews. First, we briefly describe downy mildew taxonomy and genetic loci used for detection. Next, we review issues encountered when identifying loci and compare various traditional and novel platforms for diagnostics. We discuss diagnosis of downy mildew traits and issues to consider when detecting this group of organisms in different environments. We conclude with challenges and future directions for successful downy mildew detection. }, number={2}, journal={PLANT DISEASE}, publisher={Scientific Societies}, author={Crandall, Sharifa G. and Rahman, Alamgir and Quesada-Ocampo, Lina M. and Martin, Frank N. and Bilodeau, Guillaume J. and Miles, Timothy D.}, year={2018}, month={Feb}, pages={265–275} }
 @article{rahman_miles_martin_quesada-ocampo_2017, title={Molecular approaches for biosurveillance of the cucurbit downy mildew pathogen, Pseudoperonospora cubensis}, volume={39}, ISSN={["1715-2992"]}, url={https://doi.org/10.1080/07060661.2017.1357661}, DOI={10.1080/07060661.2017.1357661}, abstractNote={Abstract Globalization has allowed for rapid movement of plant pathogens that threaten food security. Successful disease management largely depends on timely and accurate detection of plant pathogens causing epidemics. Thus, biosurveillance of epidemic plant pathogens such as Pseudoperonospora cubensis, the causal agent of cucurbit downy mildew, is becoming a priority to prevent disease outbreaks and deploy successful control efforts. Next Generation Sequencing (NGS) facilitates rapid development of genomics resources needed to generate molecular diagnostics assays for P. cubensis. Having information regarding the presence or absence of the pathogen, amount of inoculum, crop risk, time to initiate fungicide applications, and effective fungicides to apply would significantly contribute to reducing losses to cucurbit downy mildew. In this article, we discuss approaches to identify unique loci for rapid molecular diagnostics using genomic data, to develop molecular diagnostic tools that discriminate economically important pathogen alleles (i.e. mating type and fungicide resistance), and how to use molecular diagnostics with current and future spore trap strategies for biosurveillance purposes of important downy mildew pathogens. The combined use of these technologies within the already existent disease management framework has the potential to improve disease control.}, number={3}, journal={CANADIAN JOURNAL OF PLANT PATHOLOGY}, publisher={Informa UK Limited}, author={Rahman, Alamgir and Miles, Timothy D. and Martin, Frank N. and Quesada-Ocampo, Lina M.}, year={2017}, pages={282–296} }