Tracking 19th Century Late Blight from Archival Documents using Text Analytics and Geoparsing

In 1845, Ireland\u27s potato crop was struck by a devastating potato disease that killed Ireland’s crop caused devastation for seven years and led to mass starvation and emigration from the country. The cause of the potato destruction was a fungus-like plant pathogen. There are several theories about the origin of the disease and the source of the 19th century outbreaks. We use historical documents contemporary to that time to investigate spatial information that might inform these mysteries. We present methodologies for automatically extracting information from these voluminous data sources. We identify and map geographic locations that are proximate in the text to key terms related to potato blight. Data sources include agricultural documents with extensive discussions of crop yields and failures, seed export and import, and weather conditions, along with location names. We apply natural language processing tools and geoparsing to automate text mining of the data within narrative passages. We couple these to mine the relationships between locations and reports of potato disease. Results are displayed in an interactive Web mapping tool for users to spatially explore the pertinent data for trends in the emergence of 19th century late blight

Genomic characterization of a South American <i>Phytophthora </i>hybrid mandates reassessment of the geographic origins of <i>Phytophthora infestans</i>

As the oomycete pathogen causing potato late blight disease, Phytophthora infestans triggered the famous 19th-century Irish potato famine and remains the leading cause of global commercial potato crop destruction. But the geographic origin of the genotype that caused this devastating initial outbreak remains disputed, as does the New World center of origin of the species itself. Both Mexico and South America have been proposed, generating considerable controversy. Here, we readdress the pathogen’s origins using a genomic data set encompassing 71 globally sourced modern and historical samples of P. infestans and the hybrid species P. andina, a close relative known only from the Andean highlands. Previous studies have suggested that the nuclear DNA lineage behind the initial outbreaks in Europe in 1845 is now extinct. Analysis of P. andina’s phased haplotypes recovered eight haploid genome sequences, four of which represent a previously unknown basal lineage of P. infestans closely related to the famine-era lineage. Our analyses further reveal that clonal lineages of both P. andina and historical P. infestans diverged earlier than modern Mexican lineages, casting doubt on recent claims of a Mexican center of origin. Finally, we use haplotype phasing to demonstrate that basal branches of the clade comprising Mexican samples are occupied by clonal isolates collected from wild Solanum hosts, suggesting that modern Mexican P. infestans diversified on Solanum tuberosum after a host jump from a wild species and that the origins of P. infestans are more complex than was previously thought

Fungicide Sensitivity of US Genotypes of Phytophthora infestans to Six Oomycete-Targeted Compounds

Phytophthora infestans causes potato late blight, an important and costly disease of potato and tomato crops. Seven clonal lineages of P. infestans identified recently in the United States were tested for baseline sensitivity to six oomycete-targeted fungicides. A subset of the dominant lineages (n = 45) collected between 2004 and 2012 was tested in vitro on media amended with a range of concentrations of either azoxystrobin, cyazofamid, cymoxanil, fluopicolide, mandipropamid, or mefenoxam. Dose-response curves and values for the effective concentration at which 50% of growth was suppressed were calculated for each isolate. The US-8 and US-11 clonal lineages were insensitive to mefenoxam while the US-20, US-21, US-22, US-23, and US-24 clonal lineages were sensitive to mefenoxam. Insensitivity to azoxystrobin, cyazofamid, cymoxanil, fluopicolide, or mandipropamid was not detected within any lineage. Thus, current U.S. populations of P. infestans remained sensitive to mefenoxam during the displacement of the US-22 lineage by US-23 over the past 5 years

DNA barcoding of oomycetes with cytochrome c oxidase subunit I and internal transcribed spacer

Oomycete species occupy many different environments and many ecological niches. The genera Phytophthora and Pythium for example, contain many plant pathogens which cause enormous damage to a wide range of plant species. Proper identification to the species level is a critical first step in any investigation of oomycetes, whether it is research driven or compelled by the need for rapid and accurate diagnostics during a pathogen outbreak. The use of DNA for oomycete species identification is well established, but DNA barcoding with cytochrome c oxidase subunit I (COI) is a relatively new approach that has yet to be assessed over a significant sample of oomycete genera. In this study we have sequenced COI, from 1205 isolates representing 23 genera. A comparison to internal transcribed spacer (ITS) sequences from the same isolates showed that COI identification is a practical option; complementary because it uses the mitochondrial genome instead of nuclear DNA. In some cases COI was more discriminative than ITS at the species level. This is in contrast to the large ribosomal subunit, which showed poor species resolution when sequenced from a subset of the isolates used in this study. The results described in this paper indicate that COI sequencing and the dataset generated are a valuable addition to the currently available oomycete taxonomy resources, and that both COI, the default DNA barcode supported by GenBank, and ITS, the de facto barcode accepted by the oomycete and mycology community, are acceptable and complementary DNA barcodes to be used for identification of oomycetes

Reconstructing genome evolution in historic samples of the Irish potato famine pathogen

Responsible for the Irish potato famine of 1845–49, the oomycete pathogen Phytophthora infestans caused persistent, devastating outbreaks of potato late blight across Europe in the 19th century. Despite continued interest in the history and spread of the pathogen, the genome of the famine-era strain remains entirely unknown. Here we characterize temporal genomic changes in introduced P. infestans. We shotgun sequence five 19th-century European strains from archival herbarium samples—including the oldest known European specimen, collected in 1845 from the first reported source of introduction. We then compare their genomes to those of extant isolates. We report multiple distinct genotypes in historical Europe and a suite of infection-related genes different from modern strains. At virulence-related loci, several now-ubiquitous genotypes were absent from the historical gene pool. At least one of these genotypes encodes a virulent phenotype in modern strains, which helps explain the 20th century’s episodic replacements of European P. infestans lineages

Genetic modification for disease resistance: a position paper

This Position Paper was prepared by members of the Task Force on Global Food Security of the International Society for Plant Pathology. An objective approach is proposed to the assessment of the potential of genetic modification (GM) to reduce the impact of crop diseases. The addition of GM to the plant breeder’s conventional toolbox facilitates gene-by-gene introduction into breeding programmes of well defined characters, while also allowing access to genes from a greatly extended range of organisms. The current status of GM crops is outlined. GM could make an additional contribution to food security but its potential has been controversial, sometimes because of fixed views that GM is unnatural and risky. These have no factual basis: GM technology, where adopted, is widely regulated and no evidence has been reported of adverse consequences for human health. The potential benefits of GM could be particularly valuable for the developing world but there are numerous constraints. These include cost, inadequate seed supply systems, reluctance to adopt unfamiliar technology, concern about markets, inadequacy of local regulatory systems, mismatch between research and growers’ needs, and limited technical resources. The lower cost of new gene-editing methods should open the practice of GM beyond multinational corporations. As yet there are few examples of utilization of GM-based resistance to plant diseases. Two cases, papaya ringspot virus and banana xanthomonas wilt, are outlined. In the developing world there are many more potential cases whose progress is prevented by the absence of adequate biosafety regulation. It is concluded that there is untapped potential for using GM to introduce disease resistance. An objective approach to mobilizing this potential is recommended, to address the severe impact of plant disease on food security

An Ephemeral Sexual Population of Phytophthora infestans in the Northeastern United States and Canada

Phytophthora infestans, the causal agent of late blight disease, has been reported in North America since the mid-nineteenth century. In the United States the lack of or very limited sexual reproduction has resulted in largely clonal populations of P. infestans. In 2010 and 2011, but not in 2012 or 2013, 20 rare and diverse genotypes of P. infestans were detected in a region that centered around central New York State. The ratio of A1 to A2 mating types among these genotypes was close to the 50:50 ratio expected for sexual recombination. These genotypes were diverse at the glucose-6-phosphate isomerase locus, differed in their microsatellite profiles, showed different banding patterns in a restriction fragment length polymorphism assay using a moderately repetitive and highly polymorphic probe (RG57), were polymorphic for four different nuclear genes and differed in their sensitivity to the systemic fungicide mefenoxam. The null hypothesis of linkage equilibrium was not rejected, which suggests the population could be sexual. These new genotypes were monomorphic in their mitochondrial haplotype that was the same as US-22. Through parentage exclusion testing using microsatellite data and sequences of four nuclear genes, recent dominant lineages US-8, US-11, US-23, and US-24 were excluded as possible parents for these genotypes. Further analyses indicated that US-22 could not be eliminated as a possible parent for 14 of the 20 genotypes. We conclude that US-22 could be a parent of some, but not all, of the new genotypes found in 2010 and 2011. There were at least two other parents for this population and the genotypic characteristics of the other parents were identified

The Top 10 oomycete pathogens in molecular plant pathology

Oomycetes form a deep lineage of eukaryotic organisms that includes a large number of plant pathogens which threaten natural and managed ecosystems. We undertook a survey to query the community for their ranking of plant-pathogenic oomycete species based on scientific and economic importance. In total, we received 263 votes from 62 scientists in 15 countries for a total of 33 species. The Top 10 species and their ranking are: (1) Phytophthora infestans; (2, tied) Hyaloperonospora arabidopsidis; (2, tied) Phytophthora ramorum; (4) Phytophthora sojae; (5) Phytophthora capsici; (6) Plasmopara viticola; (7) Phytophthora cinnamomi; (8, tied) Phytophthora parasitica; (8, tied) Pythium ultimum; and (10) Albugo candida. This article provides an introduction to these 10 taxa and a snapshot of current research. We hope that the list will serve as a benchmark for future trends in oomycete research.Keywords: microbiology, diversity, genomics, oomycetes plant patholog

Global historic pandemics caused by the FAM-1 genotype of Phytophthora infestans on six continents

Abstract The FAM-1 genotype of Phytophthora infestans caused late blight in the 1840s in the US and Europe and was responsible for the Irish famine. We sampled 140 herbarium specimens collected between 1845 and 1991 from six continents and used 12-plex microsatellite genotyping (SSR) to identify FAM-1 and the mtDNA lineage (Herb-1/Ia) present in historic samples. FAM-1 was detected in approximately 73% of the historic specimens and was found on six continents. The US-1 genotype was found later than FAM-1 on all continents except Australia/Oceania and in only 27% of the samples. FAM-1 was the first genotype detected in almost all the former British colonies from which samples were available. The data from historic outbreak samples suggest the FAM-1 genotype was widespread, diverse, and spread to Asia and Africa from European sources. The famine lineage spread to six continents over 144 years, remained widespread and likely spread during global colonization from Europe. In contrast, modern lineages of P. infestans are rapidly displaced and sexual recombination occurs in some regions