ResearchPad - downy-mildew https://www.researchpad.co Default RSS Feed en-us © 2020 Newgen KnowledgeWorks <![CDATA[Genome reconstruction of the non-culturable spinach downy mildew <i>Peronospora effusa</i> by metagenome filtering]]> https://www.researchpad.co/article/elastic_article_13800 Peronospora effusa (previously known as P. farinosa f. sp. spinaciae, and here referred to as Pfs) is an obligate biotrophic oomycete that causes downy mildew on spinach (Spinacia oleracea). To combat this destructive many disease resistant cultivars have been bred and used. However, new Pfs races rapidly break the employed resistance genes. To get insight into the gene repertoire of Pfs and identify infection-related genes, the genome of the first reference race, Pfs1, was sequenced, assembled, and annotated. Due to the obligate biotrophic nature of this pathogen, material for DNA isolation can only be collected from infected spinach leaves that, however, also contain many other microorganisms. The obtained sequences can, therefore, be considered a metagenome. To filter and obtain Pfs sequences we utilized the CAT tool to taxonomically annotate ORFs residing on long sequences of a genome pre-assembly. This study is the first to show that CAT filtering performs well on eukaryotic contigs. Based on the taxonomy, determined on multiple ORFs, contaminating long sequences and corresponding reads were removed from the metagenome. Filtered reads were re-assembled to provide a clean and improved Pfs genome sequence of 32.4 Mbp consisting of 8,635 scaffolds. Transcript sequencing of a range of infection time points aided the prediction of a total of 13,277 gene models, including 99 RxLR(-like) effector, and 14 putative Crinkler genes. Comparative analysis identified common features in the predicted secretomes of different obligate biotrophic oomycetes, regardless of their phylogenetic distance. Their secretomes are generally smaller, compared to hemi-biotrophic and necrotrophic oomycete species. We observe a reduction in proteins involved in cell wall degradation, in Nep1-like proteins (NLPs), proteins with PAN/apple domains, and host translocated effectors. The genome of Pfs1 will be instrumental in studying downy mildew virulence and for understanding the molecular adaptations by which new isolates break spinach resistance.

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<![CDATA[A Quantitative Dynamic Simulation of Bremia lactucae Airborne Conidia Concentration above a Lettuce Canopy]]> https://www.researchpad.co/article/5989daafab0ee8fa60baa9fa

Lettuce downy mildew, caused by the oomycete Bremia lactucae Regel, is a major threat to lettuce production worldwide. Lettuce downy mildew is a polycyclic disease driven by airborne spores. A weather-based dynamic simulation model for B. lactucae airborne spores was developed to simulate the aerobiological characteristics of the pathogen. The model was built using the STELLA platform by following the system dynamics methodology. The model was developed using published equations describing disease subprocesses (e.g., sporulation) and assembled knowledge of the interactions among pathogen, host, and weather. The model was evaluated with four years of independent data by comparing model simulations with observations of hourly and daily airborne spore concentrations. The results show an accurate simulation of the trend and shape of B. lactucae temporal dynamics of airborne spore concentration. The model simulated hourly and daily peaks in airborne spore concentrations. More than 95% of the simulation runs, the daily-simulated airborne conidia concentration was 0 when airborne conidia were not observed. Also, the relationship between the simulated and the observed airborne spores was linear. In more than 94% of the simulation runs, the proportion of the linear variation in the hourly-observed values explained by the variation in the hourly-simulated values was greater than 0.7 in all years except one. Most of the errors came from the deviation from the 1:1 line, and the proportion of errors due to the model bias was low. This model is the only dynamic model developed to mimic the dynamics of airborne inoculum and represents an initial step towards improved lettuce downy mildew understanding, forecasting and management.

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<![CDATA[Nocturnal Fanning Suppresses Downy Mildew Epidemics in Sweet Basil]]> https://www.researchpad.co/article/5989da80ab0ee8fa60b9a3b5

Downy mildew is currently the most serious disease of sweet basil around the world. The oomycete causal agent Peronospora belbahrii requires ≥ 4h free leaf moisture for infection and ≥7.5h of water-saturated atmosphere (relative humidity RH≥95%) at night for sporulation. We show here that continued nocturnal fanning (wind speed of 0.4–1.5 m/s) from 8pm to 8am dramatically suppressed downy mildew development. In three experiments conducted during 2015, percent infected leaves in regular (non-fanned) net-houses reached a mean of 89.9, 94.3 and 96.0% compared to1.2, 1.7 and 0.5% in adjacent fanned net-houses, respectively. Nocturnal fanning reduced the number of hours per night with RH≥95% thus shortened the dew periods below the threshold required for infection or sporulation. In experiments A, B and C, the number of nights with ≥4h of RH≥95% was 28, 10 and 17 in the non-fanned net-houses compared to 5, 0 and 5 in the fanned net-houses, respectively. In the third experiment leaf wetness sensors were installed. Dew formation was strongly suppressed in the fanned net-house as compared to the non-fanned net-house. Healthy potted plants became infected and sporulated a week later if placed one night in the non-fanned house whereas healthy plants placed during that night in the fanned house remained healthy. Infected potted basil plants sporulated heavily after one night of incubation in the non-fanned house whereas almost no sporulation occurred in similar plants incubated that night in the fanned house. The data suggest that nocturnal fanning is highly effective in suppressing downy mildew epidemics in sweet basil. Fanning prevented the within-canopy RH from reaching saturation, reduced dew deposition on the leaves, and hence prevented both infection and sporulation of P. belbahrii.

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<![CDATA[Transcriptome analysis of Phytophthora litchii reveals pathogenicity arsenals and confirms taxonomic status]]> https://www.researchpad.co/article/5989db5cab0ee8fa60be0205

Litchi downy blight, caused by Peronophythora litchii, is one of the major diseases of litchi and has caused severe economic losses. P. litchii has the unique ability to produce downy mildew like sporangiophores under artificial culture. The pathogen had been placed in a new family Peronophytophthoraceae by some authors. In this study, the whole transcriptome of P. litchii from mycelia, sporangia, and zoospores was sequenced for the first time. A set of 23637 transcripts with an average length of 1284 bp was assembled. Using six open reading frame (ORF) predictors, 19267 representative ORFs were identified and were annotated by searching against several public databases. There were 4666 conserved gene families and various sets of lineage-specific genes among P. litchii and other four closely related oomycetes. In silico analyses revealed 490 pathogen-related proteins including 128 RXLR and 22 CRN effector candidates. Based on the phylogenetic analysis of 164 single copy orthologs from 22 species, it is validated that P. litchii is in the genus Phytophthora. Our work provides valuable data to elucidate the pathogenicity basis and ascertain the taxonomic status of P. litchii.

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<![CDATA[Population Structure of Peronospora effusa in the Southwestern United States]]> https://www.researchpad.co/article/5989da48ab0ee8fa60b8c500

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.

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<![CDATA[Effects of Heat Shock on Photosynthetic Properties, Antioxidant Enzyme Activity, and Downy Mildew of Cucumber (Cucumis sativus L.)]]> https://www.researchpad.co/article/5989db09ab0ee8fa60bc989f

Heat shock is considered an abiotic stress for plant growth, but the effects of heat shock on physiological responses of cucumber plant leaves with and without downy mildew disease are still not clear. In this study, cucumber seedlings were exposed to heat shock in greenhouses, and the responses of photosynthetic properties, carbohydrate metabolism, antioxidant enzyme activity, osmolytes, and disease severity index of leaves with or without the downy mildew disease were measured. Results showed that heat shock significantly decreased the net photosynthetic rate, actual photochemical efficiency, photochemical quenching coefficient, and starch content. Heat shock caused an increase in the stomatal conductance, transpiration rate, antioxidant enzyme activities, total soluble sugar content, sucrose content, soluble protein content and proline content for both healthy leaves and downy mildew infected leaves. These results demonstrate that heat shock activated the transpiration pathway to protect the photosystem from damage due to excess energy in cucumber leaves. Potential resistance mechanisms of plants exposed to heat stress may involve higher osmotic regulation capacity related to an increase of total accumulations of soluble sugar, proline and soluble protein, as well as higher antioxidant enzymes activity in stressed leaves. Heat shock reduced downy mildew disease severity index by more than 50%, and clearly alleviated downy mildew development in the greenhouses. These findings indicate that cucumber may have a complex physiological change to resist short-term heat shock, and suppress the development of the downy mildew disease.

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