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https://www.readbyqxmd.com/read/29772116/bioassay-guided-isolation-of-antifungal-compounds-from-disporopsis-aspera-engl-against-pseudoperonospora-cubensis-and-phytophthora-infestans
#1
Feng Zhu, Chengshan Yuan, Fangli Gang, Chaofu Yang, Wenjun Wu, Jiwen Zhang
Oomycetes are one type of the most highly destructive of the diseases that cause damage to some important crop plants, such as potato late blight, cucumber downy mildew and grape downy mildew. As main approach of the ongoing search for new botanical fungicide from plant, the secondary metabolites of D. aspera were investigated. Through efficient bioassay-guided isolation, two new (1, 2), twelve known compounds (3-14) were isolated, and their structures were determined via extensive NMR, HR-ESI-MS, IR. They were isolated from this genus for the first time except for compounds 11, 12...
May 17, 2018: Chemistry & Biodiversity
https://www.readbyqxmd.com/read/29706990/inferring-variation-in-copy-number-using-high-throughput-sequencing-data-in-r
#2
Brian J Knaus, Niklaus J Grünwald
Inference of copy number variation presents a technical challenge because variant callers typically require the copy number of a genome or genomic region to be known a priori . Here we present a method to infer copy number that uses variant call format (VCF) data as input and is implemented in the R package vcfR . This method is based on the relative frequency of each allele (in both genic and non-genic regions) sequenced at heterozygous positions throughout a genome. These heterozygous positions are summarized by using arbitrarily sized windows of heterozygous positions, binning the allele frequencies, and selecting the bin with the greatest abundance of positions...
2018: Frontiers in Genetics
https://www.readbyqxmd.com/read/29704555/the-g-protein-%C3%AE-subunit-of-phytophthora-infestans-is-involved-in-sporangial-development
#3
Johan van den Hoogen, Natalie Verbeek-de Kruif, Francine Govers
The oomycete Phytophthora infestans is a notorious plant pathogen with potato and tomato as its primary hosts. Previous research showed that the heterotrimeric G-protein subunits Gα and Gβ have a role in zoospore motility and virulence, and sporangial development, respectively. Here, we present analyses of the gene encoding a Gγ subunit in P. infestans, Pigpg1. The overall similarity of PiGPG1 with non-oomycete Gγ subunits is low, with only the most conserved amino acids maintained, but similarity with its homologs in other oomycetes is high...
April 25, 2018: Fungal Genetics and Biology: FG & B
https://www.readbyqxmd.com/read/29695739/the-phytophthora-cactorum-genome-provides-insights-into-the-adaptation-to-host-defense-compounds-and-fungicides
#4
Min Yang, Shengchang Duan, Xinyue Mei, Huichuan Huang, Wei Chen, Yixiang Liu, Cunwu Guo, Ting Yang, Wei Wei, Xili Liu, Xiahong He, Yang Dong, Shusheng Zhu
Phytophthora cactorum is a homothallic oomycete pathogen, which has a wide host range and high capability to adapt to host defense compounds and fungicides. Here we report the 121.5 Mb genome assembly of the P. cactorum using the third-generation single-molecule real-time (SMRT) sequencing technology. It is the second largest genome sequenced so far in the Phytophthora genera, which contains 27,981 protein-coding genes. Comparison with other Phytophthora genomes showed that P. cactorum had a closer relationship with P...
April 25, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29694416/the-chloroplast-genome-sequence-of-bittersweet-solanum-dulcamara-plastid-genome-structure-evolution-in-solanaceae
#5
Ali Amiryousefi, Jaakko Hyvönen, Péter Poczai
Bittersweet (Solanum dulcamara) is a native Old World member of the nightshade family. This European diploid species can be found from marshlands to high mountainous regions and it is a common weed that serves as an alternative host and source of resistance genes against plant pathogens such as late blight (Phytophthora infestans). We sequenced the complete chloroplast genome of bittersweet, which is 155,580 bp in length and it is characterized by a typical quadripartite structure composed of a large (85,901 bp) and small (18,449 bp) single-copy region interspersed by two identical inverted repeats (25,615 bp)...
2018: PloS One
https://www.readbyqxmd.com/read/29671919/a-conserved-rxlr-effector-interacts-with-host-raba-type-gtpases-to-inhibit-vesicle-mediated-secretion-of-antimicrobial-proteins
#6
Iga Tomczynska, Michael Stumpe, Felix Mauch
Plant pathogens of the oomycete genus Phytophthora produce virulence factors, known as RxLR effector proteins that are transferred into host cells to suppress disease resistance. Here, we analyse the function of the highly conserved RxLR24 effector of Phytophthora brassicae. RxLR24 was expressed early in the interaction with Arabidopsis plants and ectopic expression in the host enhanced leaf colonization and zoosporangia formation. Co-immunoprecipitation experiments followed by mass spectrometry identified different members of the RABA GTPase family as putative RxLR24 targets...
April 19, 2018: Plant Journal: for Cell and Molecular Biology
https://www.readbyqxmd.com/read/29618319/nquire-a-statistical-framework-for-ploidy-estimation-using-next-generation-sequencing
#7
Clemens L Weiß, Marina Pais, Liliana M Cano, Sophien Kamoun, Hernán A Burbano
BACKGROUND: Intraspecific variation in ploidy occurs in a wide range of species including pathogenic and nonpathogenic eukaryotes such as yeasts and oomycetes. Ploidy can be inferred indirectly - without measuring DNA content - from experiments using next-generation sequencing (NGS). We present nQuire, a statistical framework that distinguishes between diploids, triploids and tetraploids using NGS. The command-line tool models the distribution of base frequencies at variable sites using a Gaussian Mixture Model, and uses maximum likelihood to select the most plausible ploidy model...
April 4, 2018: BMC Bioinformatics
https://www.readbyqxmd.com/read/29595084/a-tomato-nbs-lrr-gene-is-positively-involved-in-plant-resistance-to-phytophthora-infestans
#8
Ning Jiang, Jun Cui, Jun Meng, Yushi Luan
The nucleotide binding sites-leucine-rich repeat (NBS-LRR) genes are key regulatory components of plant to pathogens. Phytophthora infestans-inducible CDS encoding a NBS-LRR (SpNBS-LRR) protein in tomato (Solanum pimpinellifolium L3708) was cloned and characterized based on our RNA-Seq data and tomato genome. After sequence analysis, SpNBS-LRR was identified as a hydrophilic protein with no trans-membrane topological structure and no signal peptide. SpNBS-LRR had a close genetic relationship to RPS2 of Arabidopsis thaliana by phylogenetic analysis...
March 29, 2018: Phytopathology
https://www.readbyqxmd.com/read/29588335/the-potato-map3k-stvik-is-required-for-the-phytophthora-infestans-rxlr-effector-pi17316-to-promote-disease
#9
Fraser Murphy, Qin He, Miles Armstrong, Licida M Giuliani, Petra C Boevink, Wei Zhang, Zhendong Tian, Paul R J Birch, Eleanor M Gilroy
Plant pathogens deliver effectors to manipulate processes in their hosts, creating a suitable environment for invasion and proliferation. Yet, little is known about the host proteins that are targeted by effectors from filamentous pathogens. Here, we show that stable transgenic expression in potato ( Solanum tuberosum ) and transient expression in Nicotiana benthamiana of the arginine-any amino acid-leucine-arginine effector Pi17316 enhances leaf colonization by the late blight pathogen Phytophthora infestans Expression of Pi17316 also attenuates cell death triggered by the pathogen-associated molecular pattern Infestin1 (INF1), indicating that the effector suppresses pattern-triggered immunity...
May 2018: Plant Physiology
https://www.readbyqxmd.com/read/29578005/antifungal-antioxidant-and-cytotoxic-activities-of-chitosan-nanoparticles-and-its-use-as-an-edible-coating-on-vegetables
#10
K Divya, Smitha Vijayan, M S Jisha
Chitosan is an abundant non-toxic, biodegradable polymer with versatile applications. It is a linear amino polysaccharide obtained from crustacean shells. The chitosan nanoparticles (ChNP) prepared by ionic gelation of chitosan has greater activity owing to its small size. ChNP has been proved to be effective in controlling plants diseases. In this work, we have endeavoured to study the antifungal and antioxidant activity of ChNP and use of ChNP as a vegetable coating material. The activity of ChNP against selected plant pathogens Rhizoctonia solani, Fusarium oxysporum, Collectotrichum acutatum, and Phytophthora infestans were studied along with a brief account of its mechanism of action...
March 22, 2018: International Journal of Biological Macromolecules
https://www.readbyqxmd.com/read/29576086/pamp-responsive-atl-gene-strfp1-and-its-orthologue-nbatl60-positively-regulate-phytophthora-infestans-resistance-in-potato-and-nicotiana-benthamiana
#11
Cheng Zhong, Yajuan Ren, Yetong Qi, Xiaoling Yu, Xintong Wu, Zhendong Tian
Ubiquitination is a post-translational modification that plays a crucial role during the regulation of plant immune signalling. The plant ATL family consists of a large number of putative RING type ubiquitin ligases. We show that potato ATL family gene StRFP1 and its orthologue NbATL60 from N. benthamiana both respond to Phytophthora infestans culture filtrate (CF) and flg22 induction. StRFP1 positively regulates immunity against P. infestans in potato. Ectopic transient expression of StRFP1 or expression of NbATL60 in N...
May 2018: Plant Science: An International Journal of Experimental Plant Biology
https://www.readbyqxmd.com/read/29563919/prospects-and-potential-uses-of-genomic-prediction-of-key-performance-traits-in-tetraploid-potato
#12
Benjamin Stich, Delphine Van Inghelandt
Genomic prediction is a routine tool in breeding programs of most major animal and plant species. However, its usefulness for potato breeding has not yet been evaluated in detail. The objectives of this study were to (i) examine the prospects of genomic prediction of key performance traits in a diversity panel of tetraploid potato modeling additive, dominance, and epistatic effects, (ii) investigate the effects of size and make up of training set, number of test environments and molecular markers on prediction accuracy, and (iii) assess the effect of including markers from candidate genes on the prediction accuracy...
2018: Frontiers in Plant Science
https://www.readbyqxmd.com/read/29560514/identification-and-rapid-mapping-of-a-gene-conferring-broad-spectrum-late-blight-resistance-in-the-diploid-potato-species-solanum-verrucosum-through-dna-capture-technologies
#13
Xinwei Chen, Dominika Lewandowska, Miles R Armstrong, Katie Baker, Tze-Yin Lim, Micha Bayer, Brian Harrower, Karen McLean, Florian Jupe, Kamil Witek, Alison K Lees, Jonathan D Jones, Glenn J Bryan, Ingo Hein
A broad-spectrum late blight disease-resistance gene from Solanum verrucosum has been mapped to potato chromosome 9. The gene is distinct from previously identified-resistance genes. We have identified and characterised a broad-spectrum resistance to Phytophthora infestans from the wild Mexican species Solanum verrucosum. Diagnostic resistance gene enrichment (dRenSeq) revealed that the resistance is not conferred by previously identified nucleotide-binding, leucine-rich repeat genes. Utilising the sequenced potato genome as a reference, two complementary enrichment strategies that target resistance genes (RenSeq) and single/low-copy number genes (Generic-mapping enrichment Sequencing; GenSeq), respectively, were deployed for the rapid, SNP-based mapping of the resistance through bulked-segregant analysis...
March 20, 2018: TAG. Theoretical and Applied Genetics. Theoretische und Angewandte Genetik
https://www.readbyqxmd.com/read/29535313/large-sub-clonal-variation-in-phytophthora-infestans-from-recent-severe-late-blight-epidemics-in-india
#14
Tanmoy Dey, Amanda Saville, Kevin Myers, Susanta Tewari, David E L Cooke, Sucheta Tripathy, William E Fry, Jean B Ristaino, Sanjoy Guha Roy
The population structure of the Phytophthora infestans populations that caused the recent 2013-14 late blight epidemic in eastern India (EI) and northeastern India (NEI) was examined. The data provide new baseline information for populations of P. infestans in India. A migrant European 13_A2 genotype was responsible for the 2013-14 epidemic, replacing the existing populations. Mutations have generated substantial sub-clonal variation with 24 multi-locus genotypes (MLGs) found, of which 19 were unique variants not yet reported elsewhere globally...
March 13, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29530614/food-safety-evaluation-for-r-proteins-introduced-by-biotechnology-a-case-study-of-vnt1-in-late-blight-protected-potatoes
#15
REVIEW
Jeffrey W Habig, Aaron Rowland, Matthew G Pence, Cathy X Zhong
Resistance genes (R-genes) from wild potato species confer protection against disease and can be introduced into cultivated potato varieties using breeding or biotechnology. The R-gene, Rpi-vnt1, which encodes the VNT1 protein, protects against late blight, caused by Phytophthora infestans. Heterologous expression and purification of active VNT1 in quantities sufficient for regulatory biosafety studies was problematic, making it impractical to generate hazard characterization data. As a case study for R-proteins, a weight-of-evidence, tiered approach was used to evaluate the safety of VNT1...
March 9, 2018: Regulatory Toxicology and Pharmacology: RTP
https://www.readbyqxmd.com/read/29528408/broad-spectrum-inhibition-of-phytophthora-infestans-by-fungal-endophytes
#16
Sophie de Vries, Janina K von Dahlen, Anika Schnake, Sarah Ginschel, Barbara Schulz, Laura E Rose
Phytophthora infestans is a devastating pathogen of tomato and potato. It readily overcomes resistance genes and applied agrochemicals and hence even today causes large yield losses. Fungal endophytes provide a largely unexplored avenue of control of Phytophthora infestans. Not only do endophytes produce a wide array of bioactive metabolites, they may also directly compete with and defeat pathogens in planta. Here, we tested twelve fungal endophytes isolated from different plant species in vitro for their production of metabolites with anti- Phytophthora activity...
March 8, 2018: FEMS Microbiology Ecology
https://www.readbyqxmd.com/read/29507733/function-identification-of-mir482b-a-negative-regulator-during-tomato-resistance-to-phytophthora-infestans
#17
Ning Jiang, Jun Meng, Jun Cui, Guangxin Sun, Yushi Luan
Tomato is an important horticultural and economic crop cultivated worldwide. As Phytophthora infestans becomes a huge threat to tomato production, it is necessary to study the resistance mechanisms of tomato against P. infestans . Our previous research has found that miR482 might be involved in tomato- P . infestans interaction. In this study, miR482b precursor was cloned from Solanum pimpinellifolium "L3708" and miR482b was shown to decrease in abundance in tomato following P . infestans infection...
2018: Horticulture Research
https://www.readbyqxmd.com/read/29491170/expression-profiling-across-wild-and-cultivated-tomatoes-supports-the-relevance-of-early-mir482-2118-suppression-for-phytophthora-resistance
#18
Sophie de Vries, Andreas Kukuk, Janina K von Dahlen, Anika Schnake, Thorsten Kloesges, Laura E Rose
Plants possess a battery of specific pathogen resistance ( R- )genes. Precise R- gene regulation is important in the presence and absence of a pathogen. Recently, a microRNA family, miR482/2118, was shown to regulate the expression of a major class of R- genes , nucleotide-binding site leucine-rich repeats ( NBS-LRRs ). Furthermore, RNA silencing suppressor proteins, secreted by pathogens, prevent the accumulation of miR482/2118, leading to an upregulation of R- genes. Despite this transcriptional release of R -genes, RNA silencing suppressors positively contribute to the virulence of some pathogens ...
February 28, 2018: Proceedings. Biological Sciences
https://www.readbyqxmd.com/read/29487574/versatile-antagonistic-activities-of-soil-borne-bacillus-spp-and-pseudomonas-spp-against-phytophthora-infestans-and-other-potato-pathogens
#19
Simon Caulier, Annika Gillis, Gil Colau, Florent Licciardi, Maxime Liépin, Nicolas Desoignies, Pauline Modrie, Anne Legrève, Jacques Mahillon, Claude Bragard
The world potato is facing major economic losses due to disease pressure and environmental concerns regarding pesticides use. This work aims at addressing these two issues by isolating indigenous bacteria that can be integrated into pest management strategies. More than 2,800 strains of Bacillus -like and Pseudomonas -like were isolated from several soils and substrates associated with potato agro-systems in Belgium. Screenings for antagonistic activities against the potato pathogens Alternaria solani, Fusarium solani (BCCM-MUCL 5492), Pectobacterium carotovorum (ATCC 15713), Phytophthora infestans (CRA-W10022) and Rhizoctonia solani (BCCM-MUCL 51929) were performed, allowing the selection of 52 Bacillus spp...
2018: Frontiers in Microbiology
https://www.readbyqxmd.com/read/29458721/galleria-melonella-as-an-experimental-in-vivo-host-model-for-the-fish-pathogenic-oomycete-saprolegnia-parasitica
#20
Andreas Wuensch, Franziska Trusch, Nurul A Iberahim, Pieter van West
Oomycetes are eukaryotic pathogens infecting animals and plants. Amongst them Saprolegnia parasitica is a fish pathogenic oomycete causing devastating losses in the aquaculture industry. To secure fish supply, new drugs are in high demand and since fish experiments are time consuming, expensive and involve animal welfare issues the search for adequate model systems is essential. Galleria mellonella serves as a heterologous host model for bacterial and fungal infections. This study extends the use of G. mellonella for studying infections with oomycetes...
February 2018: Fungal Biology
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