@article{guo_betzen_salcedo_he_bowden_fellers_jordan_akhunova_rouse_szabo_et al._2022, title={Population genomics of Puccinia graminis f.sp. tritici highlights the role of admixture in the origin of virulent wheat rust races}, volume={13}, ISSN={["2041-1723"]}, DOI={10.1038/s41467-022-34050-w}, abstractNote={Abstract Puccinia graminis f.sp. tritici (Pgt) causes stem rust disease in wheat that can result in severe yield losses. The factors driving the evolution of its virulence and adaptation remain poorly characterized. We utilize long-read sequencing to develop a haplotype-resolved genome assembly of a U.S. isolate of Pgt. Using Pgt haplotypes as a reference, we characterize the structural variants (SVs) and single nucleotide polymorphisms in a diverse panel of isolates. SVs impact the repertoire of predicted effectors, secreted proteins involved in host-pathogen interaction, and show evidence of purifying selection. By analyzing global and local genomic ancestry we demonstrate that the origin of 8 out of 12 Pgt clades is linked with either somatic hybridization or sexual recombination between the diverged donor populations. Our study shows that SVs and admixture events appear to play an important role in broadening Pgt virulence and the origin of highly virulent races, creating a resource for studying the evolution of Pgt virulence and preventing future epidemic outbreaks.}, number={1}, journal={NATURE COMMUNICATIONS}, author={Guo, Yuanwen and Betzen, Bliss and Salcedo, Andres and He, Fei and Bowden, Robert L. and Fellers, John P. and Jordan, Katherine W. and Akhunova, Alina and Rouse, Mathew N. and Szabo, Les J. and et al.}, year={2022}, month={Oct} }
 @misc{salcedo_purayannur_standish_miles_thiessen_quesada-ocampo_2021, title={Fantastic Downy Mildew Pathogens and How to Find Them: Advances in Detection and Diagnostics}, volume={10}, ISSN={["2223-7747"]}, url={https://doi.org/10.3390/plants10030435}, DOI={10.3390/plants10030435}, abstractNote={Downy mildews affect important crops and cause severe losses in production worldwide. Accurate identification and monitoring of these plant pathogens, especially at early stages of the disease, is fundamental in achieving effective disease control. The rapid development of molecular methods for diagnosis has provided more specific, fast, reliable, sensitive, and portable alternatives for plant pathogen detection and quantification than traditional approaches. In this review, we provide information on the use of molecular markers, serological techniques, and nucleic acid amplification technologies for downy mildew diagnosis, highlighting the benefits and disadvantages of the technologies and target selection. We emphasize the importance of incorporating information on pathogen variability in virulence and fungicide resistance for disease management and how the development and application of diagnostic assays based on standard and promising technologies, including high-throughput sequencing and genomics, are revolutionizing the development of species-specific assays suitable for in-field diagnosis. Our review provides an overview of molecular detection technologies and a practical guide for selecting the best approaches for diagnosis.}, number={3}, journal={PLANTS-BASEL}, publisher={MDPI AG}, author={Salcedo, Andres F. and Purayannur, Savithri and Standish, Jeffrey R. and Miles, Timothy and Thiessen, Lindsey and Quesada-Ocampo, Lina M.}, year={2021}, month={Mar} }