Population Structure of Peronospora effusa in the Southwestern United States

Peronospora effusa is an obligate pathogen that causes downy mildew on spinach and is considered the most economically important disease of spinach. The objective of the current research was to assess genetic diversity of known historical races and isolates collected in 2014 from production fields in Yuma, Arizona and Salinas Valley, California. Candidate neutral single nucleotide polymorphisms (SNPs) were identified by comparing sequence data from reference isolates of known races of the pathogen collected in 2009 and 2010. Genotypes were assessed using targeted sequencing on genomic DNA extracted directly from infected plant tissue. Genotyping 26 historical and 167 contemporary samples at 46 SNP loci revealed 82 unique multi-locus genotypes. The unique genotypes clustered into five groups and the majority of isolates collected in 2014 were genetically closely related, regardless of source location. The historical samples, representing several races, showed greater genetic differentiation. Overall, the SNP data indicate much of the genotypic variation found within fields was produced during asexual development, whereas overall genetic diversity may be influenced by sexual recombination on broader geographical and temporal scales

Phytophthora foliorum sp. nov., a new species causing leaf blight of azalea

a b s t r a c t A previously unknown Phytophthora was recovered more than 60 times from evergreen hybrid azalea leaves collected during surveys for the sudden oak death pathogen Phytophthora ramorum in California and Tennessee. The novel Phytophthora was discovered when genomic DNA from this species cross-reacted with the ITS-based diagnostic PCR primers used to screen plants for the presence of P. ramorum. This species had caducous, semi-papillate sporangia, was homothallic with both paragynous and amphigynous antheridia, and was pathogenic on both wounded and intact azalea leaves. Nuclear and mitochondrial sequence data indicate that this species is related to, but distinct from, P. ramorum. AFLP analysis indicates that the isolates of this species have limited genotypic diversity and share no markers with P. ramorum. This paper presents the formal description of P. foliorum as a new species and underscores the need for caution when relying solely on DNA-based diagnostic tools

Whole genome comparisons reveal panmixia among fall armyworm (Spodoptera frugiperda) from diverse locations

Background: The fall armyworm (Spodoptera frugiperda (J.E. Smith)) is a highly polyphagous agricultural pest with long-distance migratory behavior threatening food security worldwide. This pest has a host range of > 80 plant species, but two host strains are recognized based on their association with corn (C-strain) or rice and smaller grasses (R-strain). The population genomics of the United States (USA) fall armyworm remains poorly characterized to date despite its agricultural threat. Results: In this study, the population structure and genetic diversity in 55 S. frugiperda samples from Argentina, Brazil, Kenya, Puerto Rico and USA were surveyed to further our understanding of whole genome nuclear diversity. Comparisons at the genomic level suggest a panmictic S. frugiperda population, with only a minor reduction in gene flow between the two overwintering populations in the continental USA, also corresponding to distinct host strains at the mitochondrial level. Two maternal lines were detected from analysis of mitochondrial genomes. We found members from the Eastern Hemisphere interspersed within both continental USA overwintering subpopulations, suggesting multiple individuals were likely introduced to Africa. Conclusions: Our research is the largest diverse collection of United States S. frugiperda whole genome sequences characterized to date, covering eight continental states and a USA territory (Puerto Rico). The genomic resources presented provide foundational information to understand gene flow at the whole genome level among S. frugiperda populations. Based on the genomic similarities found between host strains and laboratory vs. field samples, our findings validate the experimental use of laboratory strains and the host strain differentiation based on mitochondria and sex-linked genetic markers extends to minor genome wide differences with some exceptions showing mixture between host strains is likely occurring in field populations.Fil: Schlum, Katrina A.. University of Tennessee; Estados UnidosFil: Lamour, Kurt. University of Tennessee; Estados UnidosFil: Placidi de Bortoli, Caroline. University of Tennessee; Estados UnidosFil: Banerjee, Rahul. University of Tennessee; Estados UnidosFil: Meagher, Robert. United States Department Of Agriculture. Center For Medical Agric And Vet Entomology; Estados UnidosFil: Pereira, Eliseu. Universidade Federal de Viçosa; BrasilFil: Murúa, María Gabriela. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Tucumán. Instituto de Tecnología Agroindustrial del Noroeste Argentino. Provincia de Tucumán. Ministerio de Desarrollo Productivo. Estación Experimental Agroindustrial "Obispo Colombres" (p). Instituto de Tecnología Agroindustrial del Noroeste Argentino; ArgentinaFil: Sword, Gregory A.. Texas A&M University; Estados UnidosFil: Tessnow, Ashley E.. Texas A&M University; Estados UnidosFil: Viteri Dillon, Diego. Universidad de Puerto Rico; Puerto RicoFil: Linares Ramirez, Angela M.. Universidad de Puerto Rico; Puerto RicoFil: Akutse, Komivi S.. International Centre Of Insect Physiology And Ecology; KeniaFil: Schmidt Jeffris, Rebecca. United States Department Of Agriculture. Center For Medical Agric And Vet Entomology; Estados UnidosFil: Huang, Fangneng. State University of Louisiana; Estados UnidosFil: Reisig, Dominic. North Carolina State University; Estados UnidosFil: Emrich, Scott J.. University of Tennessee; Estados UnidosFil: Jurat Fuentes, Juan Luis. University of Tennessee; Estados Unido

Genomic surveillance uncovers a pandemic clonal lineage of the wheat blast fungus

Wheat, one of the most important food crops, is threatened by a blast disease pandemic. Here, we show that a clonal lineage of the wheat blast fungus recently spread to Asia and Africa following two independent introductions from South America. Through a combination of genome analyses and laboratory experiments, we show that the decade-old blast pandemic lineage can be controlled by the Rmg8 disease resistance gene and is sensitive to strobilurin fungicides. However, we also highlight the potential of the pandemic clone to evolve fungicide-insensitive variants and sexually recombine with African lineages. This underscores the urgent need for genomic surveillance to track and mitigate the spread of wheat blast outside of South America and to guide preemptive wheat breeding for blast resistance

Genome sequences of two Phytophthora species responsible for Sudden Oak Death and Soybean Root Rot provide novel insights into their evolutionary origins and mechanisms of pathogenesis

The approximately 60 species of Phytophthora are all destructive pathogens, causing rots of roots, stems, leaves and fruits of a wide range of agriculturally and ornamentally important plants (1). Some species, such as P. cinnamomi, P. parasitica and P. cactorum, each attack hundreds of different plant host species, whereas others are more restricted. Some of the crops where Phytophthora infections cause the greatest financial losses include potato, soybean, tomato, alfalfa, tobacco, peppers, cucurbits, pineapple, strawberry, raspberry and a wide range of perennial tree crops, especially citrus, avocado, almonds, walnuts, apples and cocoa, and they also heavily affect the ornamental, nursery and forestry industries. The economic damage overall to crops in the United States by Phytophthora species is estimated in the tens of billions of dollars, including the costs of control measures, and worldwide it is many times this amount (1). In the northern midwest of the U.S., P. sojae causes $200 million in annual losses to soybean alone, and worldwide causes around$1-2 billion in losses per year. P. infestans infections resulted in the Irish potato famine last century and continues to be a difficult and worsening problem for potato and tomato growers worldwide, with worldwide costs estimated at $5 billion per year

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

Lizard in Vietnam

For some reason I really like this lizard that was looking at me while I collected diseased plants in Vietnam. Zoom in on him – he’s cool.https://trace.tennessee.edu/utiaphoto_2013/1069/thumbnail.jp

Oomycete genetics and genomics : diversity, interactions, and research tools /

Includes bibliographical references and index