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38 results for “Phytophthora infestans”
Raw data for "Host-interactor screens of Phytophthora infestans RXLR proteins reveal vesicle trafficking as a major effector-targeted process"
<p>This dataset contains raw and original images, phylogenetic tree files, sequence alignment files used for phylogenetic tree construction and unprocessed data for figures presented in the manuscript titled "Host-interactor screens of <em>Phytophthora infestans</em> RXLR proteins reveal vesicle trafficking as a major effector-targeted process". Each zip file contains raw data for each figure in the manuscript. A version of the manuscript is available on bioRxiv with doi.org/10.1101/2020.09.24.308585.</p>
The effector secretome of the Irish potato famine pathogen Phytophthora infestans
<p>Phytophthora infestans is the most destructive pathogen of potato and a model organism for the oomycetes. Haas et al. (2009) reported the sequence of the 240 megabases (Mb) genome of P. infestans. In this dataset we provide an annotated list of candidate effectors that we identified in the proteome of P. infestans T30-4 (Haas et al. 2009). We have frozen this list since 2015 and we reference all the effectors with “PITG_xxxxx” numbers from this list. The proteins can be cross-referenced to the GenBank sequences using these PITG_xxxxx numbers. The matching GenBank accession for the genome assembly is GCA_000142945.1. We also provide here the assembly and gtf files.</p> <p>Reference:</p> <p><a href="https://kamounlab.dreamhosters.com/pdfs/Nature_09.pdf">Haas, B.J., Kamoun, S., Zody, M.C., Jiang, R.H.Y., Handsaker, R.E., Cano, L.M., Grabherr, M., Kodira, C.D., Raffaele, S., Torto-Alalibo, T., Bozkurt, T.O., Ah-Fong, A.M.V., Alvarado, L., Anderson, V.L., Armstrong, M.R., Avrova, A., Baxter, L., Beynon, J., Boevink, P.C., Bollmann, S.R., Bos, J.I.B., Bulone, V., Cai, G., Cakir, C., Carrington, J.C., Chawner, M., Conti, L., Costanzo, S., Ewan, R., Fahlgren, N., Fischbach, M.A., Fugelstad, J., Gilroy, E.M., Gnerre, S., Green, P.J., Grenville-Briggs, L.J., Griffith, J., Grunwald, N.J., Horn, K., Horner, N.R., Hu, C.-H., Huitema, E., Jeong, D.-H., Jones, A.M.E., Jones, J.D.G., Jones, R.W., Karlsson, E.K., Kunjeti, S.G., Lamour, K., Liu, Z., Ma, L., MacLean, D., Chibucos, M.C., McDonald, H., McWalters, J., Meijer, H.J.G., Morgan, W., Morris, P.F., Munro, C.A., O'Neill, K., Ospina-Giraldo, M., Pinzon, A., Pritchard, L., Ramsahoye, B., Ren, Q., Restrepo, S., Roy, S., Sadanandom, A., Savidor, A., Schornack, S., Schwartz, D.C., Schumann, U.D., Schwessinger, B., Seyer, L., Sharpe, T., Silvar, C., Song, J., Studholme, D.J., Sykes, S., Thines, M., van de Vondervoort, P.J.I., Phuntumart, V., Wawra, S., Weide, R., Win, J., Young, C., Zhou, S., Fry, W., Meyers, B.C., van West, P., Ristaino, J., Govers, F., Birch, P.R.J., Whisson, S.C., Judelson, H.S., and Nusbaum, C. 2009. Genome sequence and analysis of the Irish potato famine pathogen Phytophthora infestans. Nature 461:393-398.</a></p>
Data from: Tolerance and overcompensation to infection by Phytophthora infestans in the wild perennial climber Solanum dulcamara
Studies of infection by Phytophthora infestans—the causal agent of potato late blight—in wild species can provide novel insights into plant defense responses, and indicate how wild plants might be influenced by recurrent epidemics in agricultural fields. In the present study, our aim was to investigate if different clones of Solanum dulcamara (a relative of potato) collected in the wild differ in resistance and tolerance to infection by a common European isolate of P. infestans. We performed infection experiments with six S. dulcamara genotypes (clones) both in the laboratory and in the field and measured the degree of infection and plant performance traits. In the laboratory, the six evaluated genotypes varied from resistant to susceptible, as measured by degree of infection 20 days post infection. Two of the four genotypes susceptible to infection showed a quadratic (concave downward) relationship between the degree of infection and shoot length, with maximum shoot length at intermediate values of infection. This result suggests overcompensation, that is, an increase in growth in infected individuals. The number of leaves decreased with increasing degree of infection, but at different rates in the four susceptible genotypes, indicating genetic variation for tolerance. In the field, the inoculated genotypes did not show any disease symptoms, but plant biomass at the end of the growing season was higher for inoculated plants than for controls, in‐line with the overcompensation detected in the laboratory. We conclude that in S. dulcamara there are indications of genetic variation for both resistance and tolerance to P. infestans infection. Moreover, some genotypes displayed overcompensation. Learning about plant tolerance and overcompensation to infection by pathogens can help broaden our understanding of plant defense in natural populations and help develop more sustainable plant protection strategies for economically important crop diseases.
Data from: Rapid adaptation of the Irish potato famine pathogen Phytophthora infestans to changing temperature
<p>Temperature plays a multidimensional role in host-pathogen interactions. As an important element of climate change, elevated world temperature resulting from global warming presents new challenges to sustainable disease management. Knowledge of pathogen adaptation to global warming is needed to predict future disease epidemiology and formulate mitigating strategies. In this study, 21 <i>Phytophthora infestans</i> isolates originating from seven thermal environments were acclimated for 200 days under stepwise increase or decrease of experimental temperatures and evolutionary responses of the isolates to the thermal changes were evaluated. We found temperature acclimation significantly increased the fitness and genetic adaptation of <i>P. infestans </i>isolates at both low and high temperatures. Low temperature acclimation enforced the counter-gradient adaptation of the pathogen to its past selection and enhanced the positive association between the pathogen's intrinsic growth rate and aggressiveness. At high temperatures we found that pathogen growth collapsed near the maximum temperature for growth, suggesting a thermal niche boundary may exist in the evolutionary adaptation of <i>P. infestans.</i> These results indicate that pathogens can quickly adapt to temperature shifts in global warming. If this is associated with environmental conditions favouring pathogen spread it will threaten future food security and human health and require the establishment of mitigating actions.</p>
Data from: Persistence of the mitochondrial lineage responsible for the Irish potato famine in extant New World Phytophthora infestans
The plant pathogen Phytophthora infestans emerged in Europe in 1845, triggering the Irish potato famine and massive European potato crop losses that continued until effective fungicides were widely employed in the 20th century. Today the pathogen is ubiquitous, with more aggressive and virulent strains surfacing in recent decades. Recently, complete P. infestans mitogenome sequences from 19th-century herbarium specimens were shown to belong to a unique lineage (HERB-1) predicted to be rare or extinct in modern times. We report 44 additional P. infestans mitogenomes: four from 19th-century Europe, three from 1950s U.K. and 34 from modern populations across the New World. We use phylogenetic analyses to identify the HERB-1 lineage in modern populations from both Mexico and South America, and to demonstrate distinct mitochondrial haplotypes were present in 19th-century Europe, with this lineage initially diversifying 75 years before the first reports of potato late blight.
Data from: Long-distance gene flow outweighs a century of local selection and prevents local adaptation in the Irish famine pathogen Phytophthora infestans
Sustainably managing plant resistance to epidemic pathogens implies controlling the genetic and demographic changes in pathogen populations faced with resistant hosts. Resistance management thus depends upon the dynamics of local adaptation, mainly driven by the balance between selection and gene flow. This dynamics is best investigated with populations from locally dominant hosts in islands with long histories of local selection. We used the unique case of the potato late blight pathosystem on Jersey, where a monoculture of potato cultivar 'Jersey Royal' has been in place for over a century. We also sampled populations from the coasts of Brittany and Normandy, as likely sources for gene flow. The isolation by distance pattern and the absence of genetic differentiation between Jersey and the closest French sites revealed gene flow at that spatial scale. Microsatellite allele frequencies revealed no evidence of recombination in the populations, but admixture of two genotypic clusters. No local adaptation in Jersey was detected from pathogenicity tests on Jersey Royal and on French cultivars. These data suggest that long-distance gene flow (~ 50/100 km) prevents local adaptation in Jersey despite a century of local selection by a single host cultivar and emphasize the need for regional rather than local management of resistance gene deployment.
Leaf necrosis of potato leaves infected with Phytophthora infestans
<p>This dataset contains observations on the development of necrosis and sporangia on potato leaves post-inoculation with <em>Phytophthora infestans</em>. It includes data on various potato genotypes (Capiro, Única, Suprema, Margarita) and tracks parameters such as the number of affected leaflets and leaves, the presence of necrotic spots of different sizes, and the extent of necrotic and sporangia-infected areas. The dataset is valuable for understanding the progression and impact of <em>Phytophthora infestans</em> on potato plants, aiding in the study of plant pathology and disease management.</p>
Data from: Trade-offs and evolution of thermal adaptation in the Irish potato famine pathogen Phytophthora infestans
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Data from: Persistence of the mitochondrial lineage responsible for the Irish potato famine in extant New World Phytophthora infestans
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Data from: Tolerance and overcompensation to infection by Phytophthora infestans in the wild perennial climber Solanum dulcamara
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Data from: Long-distance gene flow outweighs a century of local selection and prevents local adaptation in the Irish famine pathogen Phytophthora infestans
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Data from: Rapid adaptation of the Irish potato famine pathogen Phytophthora infestans to changing temperature
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Supplementary materials for "Effect of cesium ions on the mycelium growth and zoospores motility in the oomycete Phytophthora infestans" article
<p>This archive contains supplementary materials for Safonov et al. (2020) article.</p> <p>Each of the three subfolders (series a-c) contains data regarding the corresponding series of zoospore tracking experiments: “video fragments” subfolder with analyzed recordings and “excluded regions” subfolder with ROI-files. ROI-files contain ROIs needed to exclude certain parts of a video frame from analysis (for example, if they contain any debris that can be falsely recognized by the program as a zoospore). Each ROI-file corresponds to its video fragment: for example, “excluded regions control 3 mM a” is a ROI-file for “control 3 mM a”.</p>
Data from: The coexistence of generalist and specialist clonal lineages in natural populations of the Irish Famine pathogen Phytophthora infestans explains local adaptation to potato and tomato
Phytophthora infestans, causing late blight on Solanaceae, is a serious threat to potato and tomato crops worldwide. P. infestans populations sampled on either potato or tomato differ in genotypes and pathogenicity, suggesting niche exclusion in the field. We hypothesized that such niche separation can reflect differential host exploitation by different P. infestans genotypes. We thus compared genotypes and phenotypes in 21 isolates sampled on potato (n = 11) or tomato (n = 10). Typing at 12 microsatellite loci assigned potato isolates to the 13_A2, 6_A1 and 1_A1 lineages, and tomato isolates to the 23_A1, 2_A1 and unclassified multi-locus genotypes. Cross-inoculations on potato and tomato leaflets showed that all isolates were pathogenic on both hosts. However: tomato isolates performed much better on tomato than did potato isolates, which performed better on potato than did tomato isolates, thus revealing a clear pattern of local adaptation. Potato isolates were significantly fitter on potato than on tomato, and are best described as potato-specialists; tomato isolates appear to be generalists, with similar pathogenicity on both hosts. Niche separation in the field may thus result mainly from the large fitness gap on tomato between generalists and unadapted potato-specialists, while the small, but significant fitness difference on potato between both types of isolates may prevent population invasion by generalists. Extreme specialization to potato seems very costly relative to performance loss on the alternative host. This study therefore shows that local adaptation and niche separation, commonly expected to involve and generate specialists, can occur with generalists.
Data from: The coexistence of generalist and specialist clonal lineages in natural populations of the Irish Famine pathogen Phytophthora infestans explains local adaptation to potato and tomato
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Phytophthora infestans gene expression during potato infection 2-5 days post inoculation
GEO Series GSE14480. Solanum lycopersicum; Phytophthora infestans. 14 samples. Type: Expression profiling by array.
Phytophthora infestans Ago1 binds miRNA and sRNAs from effector genes and transposable elements (RNA-Seq)
GEO Series GSE75281. Phytophthora infestans. 2 samples. Type: Expression profiling by high throughput sequencing.
Studying the mating mechanisms in Phytophthora infestans
GEO Series GSE94137. Phytophthora infestans. 34 samples. Type: Expression profiling by high throughput sequencing.
Fragmentation of tRNA in Phytophthora infestans asexual life cycle stages and during host plant infection [host plant infection]
GEO Series GSE63292. Phytophthora infestans. 8 samples. Type: Non-coding RNA profiling by high throughput sequencing.
Identification of novel potato candidate genes for quantitative resistance to Phytophthora infestans by SuperSAGE transcriptome analysis
GEO Series GSE48071. Solanum tuberosum. 18 samples. Type: Expression profiling by high throughput sequencing.
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