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We examined the evolutionary history ofPhytophthora infestansand its close relatives in the 1c clade. We used whole genome sequence data from 69 isolates ofPhytophthoraspecies in the 1c clade and conducted a range of genomic analyses including nucleotide diversity evaluation, maximum likelihood trees, network assessment, time to most recent common ancestor and migration analysis. We consistently identified distinct and later divergence of the two MexicanPhytophthoraspecies,P.mirabilisandP.ipomoeae, fromP.infestansand other 1c clade species.Phytophthora infestansexhibited more recent divergence from other 1c clade species ofPhytophthorafrom South America,P.andinaandP.betacei. Speciation in the 1c clade and evolution ofP.infestansoccurred in the Andes.P.andina–P.betacei–P.infestansformed a species complex with indistinct species boundaries, hybridizations between the species, and short times to common ancestry. Furthermore, the distinction between modern Mexican and South AmericanP.infestansproved less discrete, suggesting gene flow between populations over time. Admixture analysis indicated a complex relationship among these populations, hinting at potential gene flow across these regions. HistoricP.infestans, collected from 1845–1889, were the first to diverge from all otherP.infestanspopulations. Modern South American populations diverged next followed by Mexican populations which showed later ancestry. Both populations were derived from historicP.infestans. Based on the time of divergence ofP.infestansfrom its closest relatives,P.andinaandP.betaceiin the Andean region, we consider the Andes to be the center of origin ofP.infestans, with modern globalization contributing to admixture betweenP.infestanspopulations today from Mexico, the Andes and Europe. 

Abstract In 1843, a hitherto unknown plant pathogen entered the US and spread to potato fields in the northeast. By 1845, the pathogen had reached Ireland leading to devastating famine. Questions arose immediately about the source of the outbreaks and how the disease should be managed. The pathogen, now known asPhytophthora infestans, still continues to threaten food security globally. A wealth of untapped knowledge exists in both archival and modern documents, but is not readily available because the details are hidden in descriptive text. In this work, we (1) used text analytics of unstructured historical reports (1843–1845) to map US late blight outbreaks; (2) characterized theories on the source of the pathogen and remedies for control; and (3) created modern late blight intensity maps using Twitter feeds. The disease spread from 5 to 17 states and provinces in the US and Canada between 1843 and 1845. Crop losses, Andean sources of the pathogen, possible causes and potential treatments were discussed. Modern disease discussion on Twitter included near-global coverage and local disease observations. Topic modeling revealed general disease information, published research, and outbreak locations. The tools described will help researchers explore and map unstructured text to track and visualize pandemics. 

Rapid detection of plant diseases before they escalate can improve disease control. Our team has developed rapid nucleic acid extraction methods with microneedles (MN) and combined these with LAMP assays for pathogen detection in the field. In this work, we developed LAMP assays for early blight (Alternaria linariae, A. alternata, and A. solani) and bacterial spot of tomato (Xanthomonas perforans) and validated these LAMP assays and two previously developed LAMP assays for tomato spotted wilt virus and late blight. Tomato plants were inoculated and disease severity was measured. Extractions were performed using MN and LAMP assays were run in tubes (with hydroxynaphthol blue) on a heat block or on a newly designed microfluidic slide chip on a heat block or a slide heater. Fluorescence on the microfluidic chip slides was visualized using EvaGreen and photographed on a smartphone. Plants inoculated with X. perforans or tomato spotted wilt virus tested positive prior to visible disease symptoms, while P. infestans and A. linariae were detected at the time of visual disease symptoms. LAMP assays were more sensitive than PCR and the limit of detection was 1 pg of DNA for both A. linariae and X. perforans. The LAMP assay designed for early blight detected all three species of Alternaria that infect tomato and is thus an Alternaria spp. assay. This study demonstrates the utility of rapid MN extraction followed by LAMP on a microfluidic chip for rapid diagnosis of four important tomato pathogens. 

A leaf-attachable multimodal plant wearable sensor was developed for monitoring biotic and abiotic stresses in real time.