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82 results for “Alternaria”
Ultra-high-resolution modified RGB UAV-imaging of Alternaria solani
<p>This dataset is collected from both symptomatic and non-symptomatic plants during the growing seasons of 2019 and 2022, on 40x20 m experimental fields in Lemberge (Merelbeke), Belgium (50.986544°N, 3.774066°E) using a DJI M600 PRO unmanned aerial vehicle equiped with a modified Sony Alpha 7III camera with 135 mm lens. The field trial is conducted in analogy to the method described by Van De Vijver et al. (2020, 2022), using two different cultivers, Spunta (2019) and Fontane (2022) respectively. The dataset of 2019 comprises data from three different flights (3, 6 and 9 days after inoculation) and the dataset of 2022 from four different flights (5,7, 9 and 13 days after inoculation). </p> <p>This dataset consists out of 7660 patches of 256x256 pixels, cropped out of the original images, labeled and sorted in two categories (1: Alternaria, 0: no Alternaria), accompagned by a csv file containing the following information:</p> <ul> <li>Original patch name</li> <li>Random patch name (used during the labeling process)</li> <li>Row patch number</li> <li>Column patch number</li> <li>Block number, column block number and row block number</li> <li>Original mage name</li> <li>Coordinates of original image: latitude, longitude, altitude</li> <li>Date of flight</li> <li>Label (0: no Alternaria, 1: Alternaria)</li> </ul> <p>More detailed information about this dataset (both the collection and the preprocessing) can be found in the corresponding article 'Ultra-high-resolution UAV-Imaging and Supervised Deep Learning for Accurate Detection of Alternaria Solani in Potato Fields.' </p> <p> </p> <p>If you use this dataset, please refer to the related journal paper as follows: "Wieme J, Leroux S, Cool SR, Van Beek J, Pieters JG and Maes WH (2024) Ultra-highresolution UAV-imaging and supervised deep learning for accurate detection of Alternaria solani in potato fields. Front. Plant Sci. 15:1206998. doi: 10.3389/fpls.2024.1206998"</p> <p> </p> <p>This dataset was gathered within the Proeftuin Smart Farming 4.0 project (180503) within the Industry 4.0 Living Labs with funding from Flanders innovation & entrepreneurship (VLAIO, Belgium) and in the Horizon 2020 project SmartAgriHubs - Connecting the dots to unleash the innovation potential for digital transformation of the European agrifood sector with funding from the European Union under grant agreement No. 818182. Jana Wieme is funded by grant 1SE3921N of Research Foundation Flanders (FWO).</p> <p> </p>
Supplementary Data for: ONT-based draft genome for Alternaria atra
<p>Species of <em>Alternaria</em> (phylum <em>Ascomycota</em>, family <em>Pleosporaceae</em>) are known as serious plant pathogens, causing major losses on a wide range of crops. <em>Alternaria atra</em><em> (Preuss) Woudenb. & Crous </em>(previously known as <em>Ulocladium atrum</em><em>) </em>can grow as a saprophyte on many hosts and causes<em> </em>Ulocladium blight on potato. It has been reported that it can also be used as a biocontrol agent against a.o. <em>Botrytis cinerea.</em></p> <p>Here we present a scaffold-level reference genome assembly for<em> A. atra.</em> The assembly contains 43 scaffolds with a total length of 39.62 Mbp, with scaffold N50 of 3,893,166 bp , L50 of 4 and the longest 10 scaffolds containing 89.9% of the assembled data. RNA Seq-guided, gene prediction using BRAKER resulted in 12,173 protein-coding genes with their functional annotation.</p>
Dataset on Alternaria disease on rocket under simulated climate change conditions
<p>This dataset is related to disease severity caused by the Alternaria spp. isolates tested in different temperature and CO2 combinations on cultivated rocket and published in https://doi.org/10.3920/WMJ2016.2108<em> </em>(Figure 1) and in https://doi.org/10.1007/s42161-018-0125-8,</p>
Fig. 1 in First record of Liriomyza huidobrensis (Diptera: Agromyzidae) disseminating Alternaria solani (Pleosporaceae) in potato crops in Brazil
Fig. 1. (a) Presence of Liriomyza huidobrensis mines on a Solanum tuberosum leaf infected with Alternaria solani; (b) diagram showing representative distribution of mines and fungal lesions.
Dataset for "Species diversity and molecular characterization of Alternaria section Alternaria isolates collected mainly from cereal crops in Canada" by Jeremy R. Dettman, Quinn Eggertson, and Natalie E. Kim
<p>Dataset consists of three files, each containing aligned nucleotide sequences from 559 Alternaria strains. The three sequenced loci are ASA-10, ASA-19, and rpb2. Strain names are stated in the header of each sequence.</p>
The critical role of MetR/MetB/MetC/MetX in cysteine and methionine metabolism, fungal development and virulence of Alternaria alternata
<p>Methionine is a unique sulfur-containing amino acid, which plays an important role in biological protein synthesis and various cellular processes. Here, we characterize the biological functions of <em>AaMetB</em>, <em>AaMetC</em>, and <em>AaMetX</em> in the tangerine pathotype of <em>Alternaria alternata</em>. Morphological analysis showed that mutants lacking <em>AaMetB</em>, <em>AaMetC</em>, or <em>AaMetX</em> resulted in less aerial hypha and fewer conidia in artificial media. The virulence assays revealed that <em>AaMetB</em>, <em>AaMetC</em>, and <em>AaMetX </em>are required for full virulence. The defects of <em></em><em>MetB</em>, <em></em><em>MetC</em>, and <em></em><em>MetX</em> in vegetative growth, conidiation and virulence can be restored by exogenous methionine and homocysteine, indicating that <em>AaMetB</em>, <em>AaMetC</em>, and <em>AaMetX </em>are required for methionine biosynthesis. The defects of <em></em><em>MetR </em>in vegetative growth and virulence can be restored by exogenous cysteine, indicating that <em>AaMetR</em> is essential for cysteine biosynthesis. The oxidant sensitivity assay showed that only <em></em><em>MetR</em> is sensitivity to H<sub>2</sub>O<sub>2</sub> and many ROS-generating compounds, which indicates that <em>AaMetR</em> is essential for oxidative tolerance. Interestingly, indoor bioassays of these mutants on fungicides showed that only the <em></em><em>MetR </em>mutants<em> </em>are susceptive to chlorothalonil, which can interact with the cysteine of glyceraldehyde-3-phosphate dehydrogenase. Comparative transcriptome analysis showed that the inactivation of <em>MetB</em>, <em>MetC</em>, <em>MetX</em>, or <em>MetR</em> significantly affected the expression of many genes related to methionine metabolism. Moreover, the inactivation of Aa<em>MetR</em> significantly affected the expression of many genes related to glutathione metabolism, which is required for ROS tolerance. In conclusion, our study provides genetic evidence to define the critical roles of <em>AaMetB</em>, <em>AaMetC</em>, <em>AaMetX</em>, and <em>AaMetR</em> in the metabolism of cysteine and methionine, fungal development and virulence of <em>Alternaria alternata.</em></p>
Transcription regulator ACTR contributes pathogenicity through mediating ACT toxin synthesis gene ACTS4 in Alternaria alternata
<p>Host-selective ACT toxin are critical for the pathogenesis of the citrus fungal pathogen <em>Alternaria alternata</em>. The biosynthesis of ACT toxin is mainly regulated by multiple ACT toxin genes located in the secondary metabolite gene cluster. However, the regulatory hierarchy of ACT toxin synthesis by these ACT genes have not been explored. In this study, we reported a transcription regulator <em>ACTR</em> contributes ACT toxin biosynthesis through mediating ACT toxin synthesis gene ACTS4 in <em>Alternaria alternata.</em> We generated <em>ACTR</em>-disrupted and -silenced mutants in the tangerine pathotype of <em>A. alternata.</em> Phenotype analysis showed that the <em>ACTR</em> mutants displayed a significant loss of ACT toxin production and a decreased virulence on citrus leaves whereas the vegetative growth and sporulation were not affected, indicating an essential role of <em>ACTR</em> in both ACT toxin biosynthesis and pathogenicity. To elucidate the transcription network of ACTR, we performed RNA-Seq experiments on wild-type and <em>ACTR</em> null mutant and identified genes that were differentially expressed between two genotypes. Transcriptome profiling and RT-qPCR analysis demonstrated that the ACT toxin biosynthetic gene <em>ACTS4</em> is down-regulated in<em> ACTR </em>mutant<em>.</em> We generated <em>ACTS4 </em>knock-down mutant and found that the pathogenicity of <em>ACTS4</em> mutant was severely impaired. Interestingly, both <em>ACTR</em> and <em>ACTS4</em> are not involved in the response to different abiotic stresses including oxidative stress, salt stress, cell-wall disrupting regents, and Cu<sup>2+</sup>, indicating the function of these two genes is highly specific. In conclusion, our results highlight the important regulatory role of <em>ACTR</em> in ACT toxin biosynthesis through mediating ACT toxin synthesis gene ACTS4 and underline the essential role of in the tangerine pathotype of <em>A. alternata</em>.</p>
Occurrence data on Alternaria toxins in food
<p>Alternaria toxins are mycotoxins produced by Alternaria species that cause plant diseases on many crops. They are the principal contaminating fungi in wheat, sorghum and barley, and have also been reported to occur in oilseeds such as sunflower and rapeseed, tomato, apples, citrus fruits, olives and several other fruits and vegetables. In addition, some Alternaria toxins are genotoxic in vitro and/or fetotoxic in rats. This published dataset contains data related to years 1995, 2002, 2003, 2004, 2008 and 2009. Occurrence data were received from two Member States, which provided 11,730 occurrence results in food, and complemented with data published in the scientific literature. This data has been used for the preparation of the Scientific Opinion on the risks for animal and public health related to the presence of Alternaria toxins in feed and food adopted by EFSA in 2011.</p> <p>Several chromatography-based techniques are suitable for Alternaria toxin quantification in foods and feeds, and liquid chromatography coupled to (tandem) mass spectrometry, compliant with the requirements as described by the Commission regulation No. 401/2006, has become the method of choice. In the dataset published the following analytical methods have been used: HPLC-RI; Chromatographic tests (Not Specified); HPLC-UV; Standard Chromatographic tests (paper- thin layer- and column chromatography); LC-MS-MS (QqQ); HPLC-HG-AFS.</p>
Distinct and essential roles of bZIP transcription factors in stress response and pathogenesis in Alternaria alternata
<p>The ability to cope with environmental abiotic stress and biotic stress is crucial for the survival of plants and microorganisms, which enable them to occupy multiple niches in the environment. Previous studies have shown that transcription factors play crucial roles in regulating various biological processes including multiple stress tolerance and response in eukaryotes. This work identified multiple critical transcription factor genes, metabolic pathways and gene ontology (GO) terms related to abiotic stress response were broadly activated by analyzing the transcriptome of phytopathogenic fungus Alternaria alternata un- der metal ions stresses, oxidative stress, salt stresses, and host-pathogen interaction. We determined the biological functions and regulatory roles of the bZIP transcriptional factor (TF) genes in the phytopathogenic fungus A. alternata by analyzing targeted gene deletion mutants. Morphological analysis provides evidence that bZIPs including Gcn4, MeaB, Atf1, Hac1 and Ada1 are required for morphogenesis as the colony morphology of these gene deletion mutants was significantly different from that of the wild-type. In addition, bZIPs are involved in the resistance to multiple stresses such as oxidative stress (Ada1, Yap1, MetR) and virulence (Hac1, MetR, Yap1, Ada1) at varying degrees. Transcriptome data demonstrated that the inactivation of bZIPs (Hac1, Atf1, Ada1 and Yap1) significantly affected many genes in multiple critical metabolism pathways and gene ontology (GO) terms. Moreover, the ΔHac1 mutants displayed reduced aerial hypha and are hypersensitivity to endoplasmic reticulum disruptors such as tunicamycin and dithiothreitol. Transcriptome analysis showed that inactivation of Hac1 significantly affected the proteasome process and its downstream unfolded protein binding, indicating that Hac1 participates in the endoplasmic reticulum stress response through the conserved unfolded protein response. Taken together, our findings identified many crucial transcription factor genes and pathways related to cell development, abiotic stress response and pathogenesis, and expand our understanding of how microbial pathogens utilize these genes to deal with environmental stresses and achieve successful infection in the host plant.</p>
RNA-Seq analysis to identify differentially expressed genes in top and bottom leaves under Alternaria brassicicola infection
<p>The broccoli plants were infected with Alternaria brassicicola and RNA samples were extracted for control and inoculated plants at 10 days post inoculation. </p>
Supplementary Data for: Whole genome sequencing elucidates the species-wide diversity and evolution of fungicide resistance in the early blight pathogen Alternaria solani
<p>Supplementary Data for: Whole genome sequencing elucidates the species-wide diversity and evolution of fungicide resistance in the early blight pathogen Alternaria solani</p> <p>This repository contains:</p> <p>SNP call data / VCF file</p> <p>Scripts for all processing steps from mapping up to PCA and phylogenetic analyses (script.ts)<br> Scripts for population genomic analyses with LEA and PopGenome (scripts.SE)<br> All script names are self explanatory.</p>
Fungicide-free management of Alternaria leaf blotch and fruit spot on apple indicates Alternaria spp. as secondary colonizer
<p>Raw data of the article: <strong>"Fungicide-free management of Alternaria leaf blotch and fruit spot on apple indicates <em>Alternaria spp</em>. as secondary colonizer"</strong>, DOI: 10.1038/s41598-023-35448-2</p> <p>-->see Read Me file</p>
Data from: Mapping resistance to Alternaria cucumerina in Cucumis melo
Infection with Alternaria cucumerina causes Alternaria leaf blight (ALB), a disease characterized by lesion formation on leaves, leading to substantial yield and quality losses in Cucumis melo (melon). While fungicides are effective against ALB, reduction in the frequency of application would be economically and environmentally beneficial. Resistant melon lines have been identified but the genetic basis of this resistance has not been determined. A saturated melon genetic map was constructed with markers developed through genotyping-by sequencing of an MR-1 (resistant) by Ananas Yokneum (susceptible Israeli cultivar) a recombinant inbred line (RIL) population (F6-F10; N=82) derived from single seed descent of a F2 population from a cross between the ALB resistant parent MR-1 and the ALB susceptible parent Ananas Yokneum. The population was evaluated for A. cucumerina resistance with an augmented block greenhouse study using inoculation with the wounded-leaf method. Multiple quantitative trait loci (QTL) mapping identified two QTL that explained 33.9% of variation in lesion area. Several candidate genes within range of these QTL were identified using the C. melo v3.5 genome. Markers linked to these QTL will be used to accelerate efforts to breed melon cultivars resistant to ALB.
FIGURE 2 in Alternaria vignae sp. nov. (Ascomycota: Pleosporaceae) from Vigna unguiculata in China
FIGURE 2. Alternaria vignae (YZU 171714, ex-type). a: samples; b: colony on PDA for 7 days at 25 ˚C; c–d: sporulation patterns on PCA; e–f: conidiophores; g–i: conidia on PCA; j–l: conidia on V8A. Scale bars: c-l=25 μm.
FIGURE 1 in Alternaria vignae sp. nov. (Ascomycota: Pleosporaceae) from Vigna unguiculata in China
FIGURE 1. Maximum likelihood phylogenetic tree based on the combined dataset of the ITS, GAPDH, RPB2 and TEF1 gene sequences. The Bayesian posterior probabilities (PP)>0.6 and maximum likelihood bootstrap (BS) support values>60% are given at the nodes (PP/ BS). Examined strains are in bold.
FIGURE 2 in A new section and a new species of Alternaria encountered from Oman
FIGURE 2. Alternaria omanensis (SQUCC 13580, ex-type). a–e, h, i. Conidia and conidiophores (Arrow indicates new emerging conidium). f, g Mature conidia. Scale bars: a, e, f = 20 μm. g, h = 10 μm. Scale bar of a applies to a-d. Scale bar of h applies to h-i.
FIGURE 2 in A new section and a new species of Alternaria encountered from Oman
FIGURE 2. Alternaria omanensis (SQU H-105, holotype) a–b. Ascomata on host substrate. c–d. Section of ascoma (TS). e. Close up of peridium. f–i. Asci with 8-spores. k–j. Muriform, brown ascospores. Scale bars: c, e = 100 μm. f = 25 μm. j, k = 10 μm. Scale bar of c applies to c-d. Scale bar of f applies to f-i.
FIGURE 2 in Multigene phylogeny and morphology of Alternaria reveal a novel species and a new record in China
FIGURE 2. Morphology of Alternaria carotiincultae YZU 151039 from Ligusticum chuanxiong. A: colony on PDA. B–D: sporulations on PCA. E: conidia. Scale bars = 20 mm.
FIGURE 1 in Multigene phylogeny and morphology of Alternaria reveal a novel species and a new record in China
FIGURE 1. ML phylogram of the present Alternaria strains (in bold) based on combined ITS, EF-1α, RPB2 and ATPase gene sequences. Bootstrap support values above 70 % from 1000 replicates are shown at the nodes. The bar indicates the number of substitutions per position.
FIGURE 3 in Multigene phylogeny and morphology of Alternaria reveal a novel species and a new record in China
FIGURE 3. Morphology of Alternaria glehniae YZU 161149 from Glehnia littoralis. A: colony on PDA. B, C: sporulations on PCA. D: conidia. Scale bars = 20 mm.
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