Category Archives: Wiley: Plant Pathology

The genetic architecture of the adaptive potential of Arabidopsis thaliana in response to Pseudomonas syringae strains isolated from south‐west France

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The genetic architecture of the adaptive potential of Arabidopsis thaliana in response to Pseudomonas syringae strains isolated from south-west France

By conducting a GWAS on an ecologically relevant pathosystem, we identified a polygenic architecture underlying the adaptive potential of the response of Arabidopsis thaliana to a non-native Pseudomonas syringae pathogenic strain.


Abstract

Phytopathogens are a threat for global food production and security. Emergence or re-emergence of plant pathogens is highly dependent on the environmental conditions affecting pathogen spread and survival. Under climate change, a geographic expansion of pathogen distribution poleward has been observed, potentially resulting in disease outbreaks on crops and wild plants. Therefore, estimating the adaptive potential of plants to novel epidemics and describing the underlying genetic architecture is a primary need to propose agricultural management strategies reducing pathogen outbreaks and to breed novel plant cultivars adapted to pathogens that might spread under climate change. To address this challenge, we inoculated Pseudomonas syringae strains isolated from Arabidopsis thaliana populations from south-west of France on the highly genetically polymorphic TOU-A A. thaliana population from north-east France. While no adaptive potential was identified in response to most P. syringae strains, the TOU-A population displayed a variable disease response to the JACO-CL strain belonging to the P. syringae phylogroup 7 (PG7). This strain carried a reduced type III secretion system (T3SS) characteristic of the PG7 as well as flexible genomic traits and potential novel effectors. Genome-wide association mapping on 192 TOU-A accessions revealed a polygenic architecture of disease response to JACO-CL. The main quantitative trait locus (QTL) region encompasses two R genes and the AT5G18310 gene encoding ubiquitin hydrolase, a target of the AvrRpt2 P. syringae effector. Altogether, our results pave the way for a better understanding of the genetic and molecular basis of the adaptive potential in an ecologically relevant A. thaliana–P. syringae pathosystem.

Draft genome sequence of Colletotrichum fructicola causing leaf spot on tea plants (Camellia sinensis)

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Draft genome sequence of Colletotrichum fructicola causing leaf spot on tea plants (Camellia sinensis)

Draft whole-genome sequence of Colletotrichum fructicola SX-6 annotated 15,243 predicted protein-coding genes; four gene families whose genes were significantly more abundant were identified by comparative genome analyses.


Abstract

Colletotrichum fructicola, one of the dominant pathogens isolated from the main tea region in China, causes leaf spot in mature leaves of tea plants, affecting their growth and yield. Here, we present the draft whole-genome sequence of the C. fructicola strain SX-6 previously used for morphological and transcriptomic analyses. The assembly consists of 510 contigs with an estimated genome size of 56.8 Mb. A total of 15,243 predicted protein-coding genes in the SX-6 genome were annotated using NR, Swiss-Prot, KEGG, KOG, TCDB, GO, PHI, DFVF, P450, SignalP and CAZy databases. We identified 833 carbohydrate-active enzymes, 1803 secreted proteins, 79 secondary metabolite gene clusters and 576 fungal virulence factors that may be involved in the pathogenicity of this fungus. Comparative genome analyses with 25 Colletotrichum species revealed their evolutionary relationships via a constructed phylogenetic tree and identified four gene families whose genes were significantly more abundant in strain SX-6. The resulting assembly will provide a valuable resource for further research on the gene functions of C. fructicola.

Identification and characterization of Entyloma eschscholziae, a recently introduced pathogen in Europe, and its segregate Entyloma dendromeconis sp. nov.

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Identification and characterization of Entyloma eschscholziae, a recently introduced pathogen in Europe, and its segregate Entyloma dendromeconis sp. nov.

The morphology, phylogeny and species boundaries of Entyloma eschscholziae are revisited, and a new species Entyloma dendromeconis is described.


Abstract

Entyloma includes pathogenic and saprobic species that infect or colonize dicotyledonous host plants. Although most Entyloma species are known only from native areas of occurrence, some species were introduced with their host plants and spread outside their natural areas. The identification of introduced species is important for detection and management of invasive species. In this study, the morphology, phylogeny and species boundaries of Entyloma eschscholziae, recently introduced from North America to Europe, are revisited. Morphology was similar among the type and other specimens of E. eschscholziae analysed on Eschscholzia californica. Both asexual and sexual morphs were observed. The rDNA ITS1-5.8S-ITS2 sequences of the E. eschscholziae specimens from Europe and New Zealand and the environmental sequence obtained from grassland soil in California, United States, were identical. Morphological and molecular analyses confirm that the causative agents of white smut on E. californica in native (North America) and introduced (Europe, New Zealand) areas belong to the same species. DNA barcodes obtained in this study (especially ITS sequence from the designated epitype specimen) could be used to facilitate its molecular identification. Specimens on Dendromecon rigida, previously assigned to E. eschscholziae, are morphologically distinct. An attempt to obtain DNA barcode data from degraded holotype material was not successful and no more recent material is available. However, based on the morphological differences and high host specificity found in Entyloma spp., it is appropriate to describe a new species, Entyloma dendromeconis, for this smut pathogen.

Cucurbit chlorotic yellows virus, a crinivirus infecting Cannabis sativa plants

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Cucurbit chlorotic yellows virus, a crinivirus infecting Cannabis sativa plants

Cucurbit chlorotic yellows virus (CCYV-Can), a crinivirus, was transmitted by the whitefly Bemisia tabaci to Cannabis sativa plants causing interveinal chlorosis and leaf yellowing in high-CBD plants.


Abstract

High cannabidiol-containing plants of Cannabis sativa (high-CBD) growing in farms in Israel displayed foliar symptoms of interveinal chlorosis and yellowing, brittleness and occasionally necrosis. These symptoms, which were more apparent in older leaves, resembled those caused by the crinivirus lettuce chlorosis virus (LCV). However, this virus was not detected by reverse transcription (RT)-PCR using specific primer sets. High-throughput sequencing of viral RNA extracted from symptomatic leaves revealed the presence of cucurbit chlorotic yellows virus (CCYV), a crinivirus in the Closteroviridae family. The complete viral genome sequence was obtained using RT-PCR followed by Sanger sequencing. The two CCYV RNA genomic segments shared 99.5%–99.85% nucleotide sequence identity with CCYV isolates from the GenBank. The virus was transmitted from symptomatic cannabis leaves to healthy plants of cannabis and Cucumis sativus ‘King Star’ (cucumber) by the whitefly Bemisia tabaci Middle Eastern Asia Minor 1 (MEAM1) species, causing disease symptoms identical to those of the donor plants. Cannabis-CCYV was also transmitted between infected cucumber plants and cannabis seedlings of unknown genotype. Severe disease symptoms of yellowing and leaf-edge necrosis were observed on high-CBD and high Δ9-tetrahydrocannabinol-containing (high-THC) flowering cannabis plants and were associated with mixed infections of LCV and CCYV. To the best of our knowledge, this is the first report of CCYV infecting C. sativa plants.

A new set of international Leptosphaeria maculans isolates as a resource for elucidation of the basis and evolution of blackleg disease on Brassica napus

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A new set of international Leptosphaeria maculans isolates as a resource for elucidation of the basis and evolution of blackleg disease on Brassica napus

An international collection of Leptosphaeria maculans isolates has been established as a key resource to help understand the interaction between this fungal pathogen and its host, canola (Brassica napus).


Abstract

A collection of isolates of the fungi Leptosphaeria maculans and L. biglobosa, which cause blackleg disease on Brassica napus (canola/oilseed rape) and other Brassicaceae species, was assembled to represent the global diversity of these pathogens and a resource for international research. The collection consists of 226 isolates (205 L. maculans and 21 L. biglobosa) from 11 countries. The genomes of all 205 L. maculans isolates were sequenced, and the distribution and identity of avirulence gene alleles were determined based on genotypic information and phenotypic reactions on B. napus lines that hosted specific resistance genes. Whilst the frequencies of some avirulence alleles were consistent across each of the regions, others differed dramatically, potentially reflecting the canola/oilseed rape cultivars grown in those countries. Analyses of the single-nucleotide polymorphism (SNP) diversity within these L. maculans isolates revealed geographical separation of the populations. This "open access" resource provides a standardized set of isolates that can be used to define the basis for how these fungal pathogens cause disease, and as a tool for discovery of new resistance traits in Brassica species.

Trichoderma atroviride suppresses Fusarium graminearum by altering primary and secondary metabolite biosynthesis profiling

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Trichoderma atroviride suppresses Fusarium graminearum by altering primary and secondary metabolite biosynthesis profiling

Trichoderma atroviride seems to be a potential biocontrol agent against Fusarium graminearum by altering the expression of genes related to vital processes in fungal life cycle.


Abstract

The use of Trichoderma spp. offers an ecologically friendly tool for the struggle with mycotoxigenic Fusarium spp. Here, the alterations in transcriptome level were investigated in 6-day-old Fusarium graminearum cultures treated with Trichoderma atroviride and nontreated with T. atroviride (FGc), using whole transcriptome sequencing to better understand the associated biological processes. Transcriptome analysis indicated a total of 55 up-regulated genes and 728 down-regulated genes with p adj < 0.05. Enrichment analysis revealed that the up-regulated genes were related to fatty acid biosynthesis, AMP-dependent biosynthesis, amino acid recognition/activation processes and secondary metabolite production, whereas down-regulated genes were involved in amino acid synthesis, oxidation–reduction processes, metal ion-binding and metabolic/catalytic activities. Among the down-regulated genes, the expression of pigmentation-related genes such as aurO, gip1 and aurR2 was remarkable. Similarly, the expression levels of key enzyme-coding genes involved in deoxynivalenol mycotoxin production were significantly decreased in the range of −1.77 and −2.94. For up-regulated genes, nonribosomal peptide synthetase and polyketide synthase genes were notably distinguished from the remaining down-regulated genes as these genes can be involved in biosynthesis of common secondary metabolites. The results clearly emphasize that T. atroviride repressed the biosynthesis of primary metabolites in F. graminearum while simultaneously up-regulating the expression of genes involved in the synthesis of secondary metabolites. This is the first report showing how T. atroviride leads to transcriptome alterations and the findings suggest that T. atroviride could serve as an effective fungus by employing a wide variety of strategies against phytopathogenic fungi.

Analysis of genetic diversity and population structure of Puccinia striiformis f. sp. tritici infers inoculum relationships from Yunnan to the middle and lower reaches of the Yangtze River

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Analysis of genetic diversity and population structure of Puccinia striiformis f. sp. tritici infers inoculum relationships from Yunnan to the middle and lower reaches of the Yangtze River

Puccinia striiformis f. sp. tritici uredinia from the middle/lower Yangtze River area in 2019 were analysed with SSR markers; the autumn inoculum probably came from south-western over-summering areas by long-distance migration.


Abstract

Wheat stripe rust, caused by Puccinia striiformis f. sp. tritici (Pst), is an important cereal fungal disease worldwide, including in the major wheat-producing areas in China. In 2019, there was a widespread epidemic of the disease in the middle and lower reaches of the Yangtze River (MLRYR) area, including Zhejiang, Jiangsu, Anhui and Guangxi. However, in north-western China, the postulated inoculum source of MLRYR, disease occurred mildly. Therefore, the origin of the Pst inoculum source for the MLRYR epidemic is still an open question. To address it, we collected 210 Pst uredinium samples from the Yangtze River basin and analysed their genetic structure with 13 pairs of simple-sequence repeat (SSR) markers that we coupled with an upper airflow trajectory analysis. Our results suggest that the autumn inoculum sources of wheat stripe rust in MLRYR in 2019 probably came from south-western over-summering areas of Pst through long-distance migration. We also found that Jingzhou and adjacent areas in Hubei Province function as an important bridge or stopover for inoculum sources.

Watermelon mosaic virus in the Czech Republic, its recent and historical origins

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Watermelon mosaic virus in the Czech Republic, its recent and historical origins

Watermelon mosaic virus probably moved from non-cucurbit hosts (Ailanthus altissima, Alcea rosea, Panax ginseng, etc.) to watermelon around 1000 years ago. (Pictures from Wikimedia)


Abstract

Watermelon mosaic virus (WMV) is a potyvirus and a member of the bean common mosaic virus (BCMV) lineage. It is one of the most economically important viral pathogens of cucurbits worldwide and was first reported in the Czech Republic in 2011 from serological surveys (2005–2011). In this study, we confirmed this identification by determining the complete coding regions of five Czech WMV isolates using high-throughput sequencing and Sanger sequencing (MW188031; OP585149–OP585152), together with the coat protein (CP) genes of 26 additional isolates. Phylogenies were made from these and more than 128 genomes or 128 CP genes from GenBank. They showed that the Czech isolates were most closely related to other European isolates, but, surprisingly, 96.2% of the genomes were recombinant. The nonrecombinant sequences mostly came from basal isolates, all originating from China, and some from unusual hosts (Ailanthus altissima, Alcea rosea and Panax ginseng). The complete WMV genomes form three phylogenetic clades, two of them small and basal, and the third includes all other isolates. Comparative dating suggests that the basal Chinese isolates are descendants of a potyvirus population infecting various dicotyledonous plant species in China at least 2000 years ago. WMV became a crop pathogen around 1000 years ago, a few years after watermelon was taken to northern China and first grown as a crop during the Five Dynasties (907–960 ce).

Banana bunchy top disease in Africa—Predicting continent‐wide disease risks by combining survey data and expert knowledge

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Banana bunchy top disease in Africa—Predicting continent-wide disease risks by combining survey data and expert knowledge

Visualizing and mitigating the growing risks of BBTD spread across Africa, leveraging a decade's worth of survey data and expert insights for strategic decision-making.


Abstract

Across Africa, banana bunchy top disease (BBTD) severely impacts banana production and livelihoods of millions of smallholder farmers. Mapping vulnerability of landscapes to monitor BBTD establishment and spread is crucial for proactive measures of disease exclusion. To highlight current and future risks of BBTD in Africa, the relationship between 1160 field observations from 14 BBTD surveys and environmental covariate maps was determined using logistic regression. From these relationships, we inferred the environmental suitability of the African landscape for the possible wider spread of BBTD. Using this information and expert knowledge, we generated a map highlighting the main banana production areas at risk of BBTD entry and establishment. We combined these maps to create a priority map that highlights the areas that need most attention in combating BBTD through surveillance and measures to prevent its spread. Our analysis shows that BBTD is widespread across tropical Africa, with dispersal over several hotspots. Central and Western Africa are most favourable for the development of BBTD. Central, West and South-East Africa are most at risk of BBTD entry and initial establishment. Areas in West and Central Africa, in the Great Lakes Region in Eastern Africa and in South-East Africa, particularly in Malawi and Mozambique, score high on the prioritization index for surveillance and mitigation efforts. Recent reports of BBTD presence in north-western Uganda and western Tanzania support these risk predictions. For these and other not-yet-infected areas, measures for close surveillance and proactive management of the disease are needed.

A review on common root rot of wheat and barley in Australia

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A review on common root rot of wheat and barley in Australia

This article comprehensively reviews common root rot (Bipolaris sorokiniana) in Australia, covering the disease cycle, economic loss, management, traditional and emerging detection methods and research focus in the last 50 years.


Abstract

Common root rot (CRR) caused by the soilborne pathogen Bipolaris sorokiniana (teleomorph Cochliobolus sativus) is becoming increasingly prevalent worldwide. Identification of CRR is difficult and time-consuming for human assessors due to the non-distinctive above-ground symptoms, with browning of subcrown internodes and roots the most distinguishing symptom of infection. CRR disease has been recognized as a significant disease for cereal crops in many countries. In 2009, CRR in Australia was estimated to cause $30 million average annual yield loss for wheat and $13 million for barley. Recent evidence indicates CRR may be more prevalent than expected in Australian wheat cropping areas due to lack of research on this disease. Low levels of B. sorokiniana survive in the soil for up to 10 years and attack plants at early stages of growth. Therefore, mitigating CRR in wheat and barley may not be practical at the late stages of infection due to lack of effective methods; however, early detection might be viable to alleviate the impact of this disease. A comprehensive overview of CRR caused by B. sorokiniana, including disease background, worldwide economic losses, management methods, potential CRR detection using multispectral and hyperspectral sensors and the research focus over the past 50 years is provided in this article. This review paper is expected to provide thorough supplemental information for current studies about CRR and proposes recommendations for whole-of-field disease scouting methods to farmers, enabling reduced time and cost for CRR management and increasing wheat and barley production worldwide.