Comparative Genomics and Functional Studies of Wheat BED-NLR Loci

Nucleotide-binding leucine-rich-repeat (LRR) receptors (NLRs) with non-canonical integrated domains (NLR-IDs) are widespread in plant genomes. Zinc-finger BED (named after the Drosophila proteins Boundary Element-Associated Factor and DNA Replication-related Element binding Factor, named BED hereafter) are among the most frequently found IDs. Five BED-NLRs conferring resistance against bacterial and fungal pathogens have been characterized. However, it is unknown whether BED-NLRs function in a manner similar to other NLR-IDs. Here, we used chromosome-level assemblies of wheat to explore the Yr7 and Yr5a genomic regions and show that, unlike known NLR-ID loci, there is no evidence for a NLR-partner in their vicinity. Using neighbor-network analyses, we observed that BED domains from BED-NLRs share more similarities with BED domains from single-BED proteins and from BED-containing proteins harboring domains that are conserved in transposases. We identified a nuclear localization signal (NLS) in Yr7, Yr5, and the other characterized BED-NLRs. We thus propose that this is a feature of BED-NLRs that confer resistance to plant pathogens. We show that the NLS was functional in truncated versions of the Yr7 protein when expressed in N. benthamiana. We did not observe cell-death upon the overexpression of Yr7 full-length, truncated, and ‘MHD’ variants in N. benthamiana. This suggests that either this system is not suitable to study BED-NLR signaling or that BED-NLRs require additional components to trigger cell death. These results define novel future directions to further understand the role of BED domains in BED-NLR mediated resistance.

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The Ustilago hordei–Barley Interaction is a Versatile System for Characterization of Fungal Effectors

Journal of Fungi ◽

10.3390/jof7020086 ◽

2021 ◽

Vol 7 (2) ◽

pp. 86

Author(s):

Bilal Ökmen ◽

Daniela Schwammbach ◽

Guus Bakkeren ◽

Ulla Neumann ◽

Gunther Doehlemann

Keyword(s):

Fungal Pathogens ◽

Plant Pathogens ◽

Expression System ◽

Pathogenic Fungi ◽

Effector Proteins ◽

Mating Partner ◽

Fungal Virulence ◽

Functional Studies ◽

Infection Structures ◽

Ustilago Hordei

Obligate biotrophic fungal pathogens, such as Blumeria graminis and Puccinia graminis, are amongst the most devastating plant pathogens, causing dramatic yield losses in many economically important crops worldwide. However, a lack of reliable tools for the efficient genetic transformation has hampered studies into the molecular basis of their virulence or pathogenicity. In this study, we present the Ustilago hordei–barley pathosystem as a model to characterize effectors from different plant pathogenic fungi. We generate U. hordei solopathogenic strains, which form infectious filaments without the presence of a compatible mating partner. Solopathogenic strains are suitable for heterologous expression system for fungal virulence factors. A highly efficient Crispr/Cas9 gene editing system is made available for U. hordei. In addition, U. hordei infection structures during barley colonization are analyzed using transmission electron microscopy, showing that U. hordei forms intracellular infection structures sharing high similarity to haustoria formed by obligate rust and powdery mildew fungi. Thus, U. hordei has high potential as a fungal expression platform for functional studies of heterologous effector proteins in barley.

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Analysis of Fox genes in Schmidtea mediterranea reveals new families and a conserved role of Smed-foxO in controlling cell death

Scientific Reports ◽

10.1038/s41598-020-80627-0 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Eudald Pascual-Carreras ◽

Carlos Herrera-Úbeda ◽

Maria Rosselló ◽

Pablo Coronel-Córdoba ◽

Jordi Garcia-Fernàndez ◽

...

Keyword(s):

Cell Death ◽

Phylogenetic Reconstruction ◽

Single Copy ◽

Schmidtea Mediterranea ◽

Functional Studies ◽

New Family ◽

Gene Diversification ◽

Fox Genes ◽

Key Aspects

AbstractThe forkhead box (Fox) genes encode transcription factors that control several key aspects of development. Present in the ancestor of all eukaryotes, Fox genes underwent several duplications followed by loss and diversification events that gave rise to the current 25 families. However, few Fox members have been identified from the Lophotrochozoa clade, and specifically from planarians, which are a unique model for understanding development, due to the striking plasticity of the adult. The aim of this study was to identify and perform evolutionary and functional studies of the Fox genes of lophotrochozoan species and, specifically, of the planarian Schmidtea mediterranea. Generating a pipeline for identifying Forkhead domains and using phylogenetics allowed us the phylogenetic reconstruction of Fox genes. We corrected the annotation for misannotated genes and uncovered a new family, the QD, present in all metazoans. According to the new phylogeny, the 27 Fox genes found in Schmidtea mediterranea were classified into 12 families. In Platyhelminthes, family losses were accompanied by extensive gene diversification and the appearance of specific families, the A(P) and N(P). Among the newly identified planarian Fox genes, we found a single copy of foxO, which shows an evolutionary conserved role in controlling cell death.

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Biodiversity of pathogenic wood fungi isolated from Xylotrechus arvicola (Olivier) galleries in vine shoots

OENO One ◽

10.20870/oeno-one.2013.47.2.1540 ◽

2013 ◽

Vol 47 (2) ◽

pp. 73 ◽

Cited By ~ 2

Author(s):

Pablo García Benavides ◽

Pedro Martin Zamorano ◽

Carlos Alvar Ocete ◽

Lara Maistrello ◽

Rafael Ocete

Keyword(s):

Fungal Pathogens ◽

Plant Pathogens ◽

Pathogenic Fungi ◽

Fungal Species ◽

Its2 Sequence ◽

Plant Diseases ◽

Northern Spain ◽

Grapevine Decline ◽

La Rioja

Aim: Grapevine decline caused by wood fungi seriously threatens viticulture worldwide. In Spain, the polyphagous borer Xylotrechus arvicola (Coleoptera, Cerambycidae) is becoming a serious pest in different Qualified Designation of Origin (DOC) wine regions. The aim of the present work was to identify the fungal species growing in the galleries excavated by X. arvicola larvae inside the vine branches and investigate the possible relationship between wood pathogenic fungi and this borer.Methods and results: Wood samples from branches of Tempranillo vines and Prunus pisardi trees affected by the borer X. arvicola were collected in La Rioja DOC vineyards (Northern Spain) and analyzed for the presence of fungi using both morphological techniques and genetic tools based on Internal Transcribed Spacer 2 (ITS2) sequence. Among the 20 different fungal species/isolates identified, 7 belonged to fungi associated with grapevine decline (esca, Petri disease, and Eutypa dieback), 6 were plant pathogens, 6 were saprophytic and one was entomopathogenic (Beauveria bassiana).Conclusion: The fact that 65 % of the fungi detected inside X. arvicola galleries belong to species recognized as plant pathogens suggests that this borer, in addition to causing a progressive decay of the branches, could facilitate the transmission of plant diseases, further threatening the vineyards by spreading grapevine decline pathogens.Significance and impact of the study: The present work represents a first step in recognizing the association between the fungal pathogens associated with grapevine decline and the borer X. arvicola, suggesting a possible role of this insect as a vector in the transmission of these fungi.

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Fungal plant pathogens and soil biodiversity

Canadian Journal of Soil Science ◽

10.4141/s01-068 ◽

2003 ◽

Vol 83 (Special Issue) ◽

pp. 331-336 ◽

Cited By ~ 17

Author(s):

R. D. Reeleder

Keyword(s):

Disease Control ◽

Management Strategy ◽

Fungal Pathogens ◽

Plant Pathogens ◽

Molecular Techniques ◽

Control Measures ◽

Soil Biodiversity ◽

Naturally Occurring ◽

Fungal Plant Pathogens

The role of biodiversity as it affects the control of soil-borne fungal pathogens is discussed. Soil-borne fungal plant pathogens have often proven difficult to manage with conventional methods of disease control. Nonetheless, researchers have characterized several naturally occurring “disease-suppressive” soils where crop loss from disease is less than would otherwise be expected. Suppressive soils can also result from the incorporation of various amendments into soil. In most cases, disease control in such soils has been shown to be biological in nature; that is, soil organisms appear to directly or indirectly inhibit the development of disease. Increased knowledge of the identity and functioning of these organisms may support the development of techniques that can be used to develop suppressiveness in soils that are otherwise disease-conducive. Populations of pathogens themselves have been shown to exhibit considerable genetic diversity; the ability of populations to respond to disease control measures should be considered when developing a management strategy. New molecular techniques can be exploited to better characterize soil communities, including the pathogens themselves, as well as community responses to various disease control options. The contributions of Canadian researchers to these areas are discussed and models for further study are proposed. Key words: Biocontrol, molecular technologies, functional diversity, integrated pest management

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The Arabidopsis SENESCENCE-ASSOCIATED GENE 13 Regulates Dark-Induced Senescence and Plays Contrasting Roles in Defense Against Bacterial and Fungal Pathogens

Molecular Plant-Microbe Interactions ◽

10.1094/mpmi-11-19-0329-r ◽

2020 ◽

Vol 33 (5) ◽

pp. 754-766 ◽

Cited By ~ 7

Author(s):

Nikhilesh Dhar ◽

Julie Caruana ◽

Irmak Erdem ◽

Krishna V. Subbarao ◽

Steven J. Klosterman ◽

...

Keyword(s):

Oxidative Stress ◽

Cell Death ◽

Seed Germination ◽

Stress Responses ◽

Fungal Pathogens ◽

Crop Improvement ◽

Anthocyanin Accumulation ◽

Normal Seed ◽

Conserved Gene

SENESCENCE-ASSOCIATED GENE 13 (SAG13) of Arabidopsis is a widely conserved gene of unknown function that has been extensively used as a marker of plant senescence. SAG13 induction occurs during plant cell death processes, including senescence and hypersensitive response, a type of programmed cell death that occurs in response to pathogens. This implies that SAG13 expression is regulated through at least two different signaling pathways affecting these two different processes. Our work highlights a contrasting role for SAG13 in regulating resistance against disease-causing biotrophic bacterial and necrotrophic fungal pathogens with contrasting infection strategies. We provide further evidence that SAG13 is not only induced during oxidative stress but also plays a role in protecting the plant against other stresses. SAG13 is also required for normal seed germination, seedling growth, and anthocyanin accumulation. The work presented here provides evidence for the role of SAG13 in regulating multiple plant processes including senescence, defense, seed germination, and abiotic stress responses. SAG13 is a valuable molecular marker for these processes and is conserved in multiple plant species, and this knowledge has important implications for crop improvement.

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Taxonomy of fruitrotting fungal pathogens whats really out there

New Zealand Plant Protection ◽

10.30843/nzpp.2005.58.4252 ◽

2005 ◽

Vol 58 ◽

pp. 42-46 ◽

Cited By ~ 11

Author(s):

P.R. Johnston ◽

S.R. Pennycook ◽

M.A. Manning

Keyword(s):

Fungal Pathogens ◽

Plant Pathogens ◽

Management Practices ◽

Management Strategies ◽

Research Data ◽

Effective Control ◽

Accurate Identification ◽

Control And Management ◽

Plant Susceptibility

This paper discusses the role of taxonomy in understanding the epidemiology of fruit rotting diseases and in determining the biosecurity status of the fungi associated with those diseases The taxonomy of most highly specialised fruitrotting pathogens is well understood but some degree of uncertainty or confusion applies to the taxonomy of many less specialised pathogens The taxonomic lumping of morphologically similar but genetically and biologically distinct taxa often confounds our ability to understand diseases frustrates the interpretation of research data and can result in misinformation about biosecurity status Such unspecialised pathogens are widespread in New Zealand but whether they cause a problem in a specific orchard depends on environmental conditions management of the orchard and host plant susceptibility As management practices and preferred cultivars change so does the spectrum of these lowspecificity taxa that cause disease problems Five examples illustrate the need for unambiguous taxonomy to facilitate more effective control and management strategies of plant pathogens Accurate identification allows a clear understand the biology of the pathogens and subsequently the epidemiology of their associated diseases

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Comparative secretomics identifies conserved WAxR motif-containing effectors in rust fungi that suppress cell death in plants

10.1101/2021.08.18.456800 ◽

2021 ◽

Author(s):

Rajdeep Jaswal ◽

Himanshu Dubey ◽

Kanti Kiran ◽

Hukam Rawal ◽

Sivasubramanian Rajarammohan ◽

...

Keyword(s):

Cell Death ◽

Plant Pathogen ◽

Fungal Pathogens ◽

Plant Pathogens ◽

Rust Fungi ◽

Cell Wall Degrading Enzymes ◽

Conserved Motifs ◽

Large Numbers ◽

Biotrophic Pathogens ◽

Plant Pathogen Interaction

Identification of novel effectors with conserved features has always remained a challenge in plant-pathogen interaction studies. The introduction of the genomics era in plant-pathogen studies has led to the identification of significant candidate effectors with novel motifs such as RxLR and dEER motifs. However, in the case of fungal pathogens, limited conserved motifs associated with effectors have been discovered yet. In the present study, we have performed comparative secretome analysis for major plant pathogens of diverse nutrition mechanisms with the aim of dissecting the features underlying their corresponding secretome and conserved motifs. We showed that rust fungi possess the lowest Cell wall degrading enzymes (CWDEs) consortium lower than other biotrophic pathogens. We also showed rust fungi possess the highest secretory superoxide dismutase (SOD) than other studied plant pathogens. Further, we prioritized the candidate secretory effectors proteins (CSEPs) of all the studied pathogens by combining various effector mining parameters to highlight the candidates with potential effector features. A novel WAxR motif in conjugation with the Y/F/WxC (FGC) motif was identified in the effectors of various P. striiformis races present globally. The WAxR/WAxR like motifs ( WxxR, WAxx, xAxR) containing effectors were also found in the secretome of other rust fungi. Further, the functional validation of two candidate effectors with WAxR motif from P. striiformis Yr9 showed that these effectors localize to the nucleus as well as cytoplasm, and are able to suppress BAX induced cell death in Nicotiana benthamiana. The mutation analysis of individual residues of the WAxR motif (W, A, R ) however did not affect the cell death suppression nor subcellular localization of these effectors. Overall, the current study reports the presence of novel motifs in large numbers of effectors of rust fungi with cell death suppression features.

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Identification of Novel PHD-Finger Genes in Pepper by Genomic Re-Annotation and Comparative Analyses

10.21203/rs.3.rs-914688/v1 ◽

2021 ◽

Author(s):

Ji Yoon Guk ◽

Min Jeong Jang ◽

Seungill Kim

Keyword(s):

Gene Family ◽

Phd Finger ◽

Functional Studies ◽

Qrt Pcr ◽

Genome Wide ◽

Zinc Finger Genes ◽

Plant Homeodomain ◽

Integrated Domains ◽

Functional Analyses

Abstract BackgroundThe plant homeodomain (PHD)-finger gene family that belongs to zinc-finger genes, plays important roles in epigenetics by regulating gene expression in eukaryotes. However, inaccurate annotation of PHD-finger genes hinders further downstream comparative, evolutionary, and functional studies.ResultsWe performed genome-wide re-annotation in Arabidopsis, rice, pepper, potato, and tomato to better understand the role of PHD-finger genes in these species. Our investigation identified 875 PHD-finger genes, of which 225 (26% of total) were newly identified, including 57 (54%) novel PHD-finger genes in pepper. The PHD-finger genes of the five plant species have various integrated domains that may be responsible for the diversification of structures and functions of these genes. Evolutionary analyses suggest that PHD-finger genes were expanded recently by lineage-specific duplication, especially in pepper and potato, resulting in diverse repertoires of PHD-finger genes among the species. We validated the expression of six newly identified PHD-finger genes in pepper with qRT-PCR. Transcriptome analyses suggest potential functions of PHD-finger genes in response to various abiotic stresses in pepper.ConclusionsOur data, including the updated annotation of PHD-finger genes, provide useful information for further evolutionary and functional analyses to better understand the roles of the PHD-finger gene family in pepper.

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Regulation and Dynamics of Gene Expression During the Life Cycle of Fusarium graminearum

Phytopathology ◽

10.1094/phyto-03-20-0080-ia ◽

2020 ◽

Vol 110 (8) ◽

pp. 1368-1374

Author(s):

Elizabeth K. Brauer ◽

Rajagopal Subramaniam ◽

Linda J. Harris

Keyword(s):

Gene Expression ◽

Fusarium Graminearum ◽

Fungal Pathogens ◽

Plant Pathogens ◽

Transcriptional Profiling ◽

Fungal Plant Pathogens ◽

Essential Components ◽

Host Infection

Fungal pathogens survive harsh environments and overcome physical, temporal, and chemical barriers to colonize their hosts and reproduce. Fusarium graminearum was one of the first fungal plant pathogens for which transcriptomic tools were developed, making analysis of gene expression a cornerstone approach in studying its biology. The analysis of gene expression in diverse in vitro conditions and during infection of different cereal crops has revealed subsets of both unique and shared transcriptionally regulated genes. Together with genetic studies, these approaches have enhanced our understanding of the development and infection cycle of this economically important pathogen. Here, we will outline recent advances in transcriptional profiling during sporogenesis, spore germination, vegetative growth, and host infection. Several transcriptional regulators have been identified as essential components in these responses and the role of select transcription factors will be highlighted. Finally, we describe some of the gaps in our understanding of F. graminearum biology and how expression analysis could help to address these gaps.

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The Ustilago hordei-barley interaction is a versatile system to characterize fungal effectors

10.1101/2020.12.10.419150 ◽

2020 ◽

Author(s):

Bilal Ökmen ◽

Daniela Schwammbach ◽

Guus Bakkeren ◽

Ulla Neumann ◽

Gunther Doehlemann

Keyword(s):

Fungal Pathogens ◽

Plant Pathogens ◽

Expression System ◽

Pathogenic Fungi ◽

Effector Proteins ◽

Mating Partner ◽

Fungal Virulence ◽

Functional Studies ◽

Infection Structures ◽

Expression Platform

AbstractObligate biotrophic fungal pathogens, such as Blumeria graminis and Puccinia graminis, are amongst the most devastating plant pathogens, causing dramatic yield losses in many economically important crops worldwide. However, a lack of reliable tools for the efficient genetic transformation has hampered studies into the molecular basis of their virulence/pathogenicity. In this study, we present the U. hordei-barley pathosystem as a model to characterize effectors from different plant pathogenic fungi. We have generated U. hordei solopathogenic strains, which form infectious filaments without presence of compatible mating partner. Solopathogenic strains are suitable as heterologous expression system for fungal virulence factors. A highly efficient Crispr/Cas9 gene editing system is made available for U. hordei. In addition, U. hordei infection structures during barley colonization were analyzed by transmission electron microscopy, which shows that U. hordei forms intracellular infection structures sharing high similarity to haustoria formed by obligate rust and powdery mildew fungi. Thus, U. hordei has high potential as a fungal expression platform for functional studies of heterologous effector proteins in barley.

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