4.5 Article

EffectorP 3.0: Prediction of Apoplastic and Cytoplasmic Effectors in Fungi and Oomycetes

Related references

Note: Only part of the references are listed.
Article Mycology

Cell wall-associated effectors of plant-colonizing fungi

Shigeyuki Tanaka et al.

Summary: Plant-colonizing fungi secrete effector proteins that can directly affect plant immune system or redirect host processes, while some function in the apoplastic space and others are bound to the fungal cell wall. Little is known about the molecular function of these cell wall-bound effectors.

MYCOLOGIA (2021)

Article Multidisciplinary Sciences

An automated and combinative method for the predictive ranking of candidate effector proteins of fungal plant pathogens

Darcy A. B. Jones et al.

Summary: This study introduces a novel tool and pipeline, Predector, for ranking predicted effector candidates, which outperforms traditional methods in ranking performance. Predector aggregates and reports additional supporting information relevant to effector and secretome prediction in a simple, efficient, and reproducible manner.

SCIENTIFIC REPORTS (2021)

Article Microbiology

A cell surface-exposed protein complex with an essential virulence function in Ustilago maydis

Nicole Ludwig et al.

Summary: The study reveals that five effectors and two transmembrane proteins from the plant pathogenic fungus Ustilago maydis form a stable cell surface-exposed protein complex required for virulence. This complex is anchored in the fungal membrane, protrudes into host cells, and likely contacts channel-forming plant plasma membrane proteins. The findings suggest that the complex may be a potential target for fungicides due to its conservation in smut fungi.

NATURE MICROBIOLOGY (2021)

Article Biochemical Research Methods

Accurate plant pathogen effector protein classification ab initio with deepredeff: an ensemble of convolutional neural networks

Ruth Kristianingsih et al.

Summary: Effector proteins of plant pathogens cause significant crop losses annually. Deep learning models based on Convolutional Neural Networks were developed to accurately identify these effectors, outperforming traditional detection software. The study found distinct N-terminal regions in various taxonomic groups that may serve as indicators for effector proteins, providing biological insights for classification.

BMC BIOINFORMATICS (2021)

Article Biotechnology & Applied Microbiology

Chromosome-level genome assembly and manually-curated proteome of model necrotroph Parastagonospora nodorum Sn15 reveals a genome-wide trove of candidate effector homologs, and redundancy of virulence-related functions within an accessory chromosome

Stefania Bertazzoni et al.

Summary: This study presents a chromosome-scale genome assembly of the P. nodorum Australian reference isolate Sn15 using a combination of long read sequencing, optical mapping, and manual curation. Effector prediction identified 257 candidates, with 98 higher-ranked candidates revealing a wealth of functions related to pathogenicity. Analysis of the pan-genome indicated the presence of an accessory chromosome (AC23) with unique characteristics and pathogenicity-related genes.

BMC GENOMICS (2021)

Article Plant Sciences

A new avirulence gene of Leptosphaeria maculans, AvrLm14, identifies a resistance source in American broccoli (Brassica oleracea) genotypes

Alexandre Degrave et al.

Summary: Resistance to diseases in cultivated crops often comes from introgression of genes from wild relatives. A new resistance source in B. oleracea genotypes from America has been identified as potentially effective against French L. maculans isolates. Genetic analysis identified a new avirulence gene, AvrLm14, and suggested a typical gene-for-gene interaction with the Rlm14 gene.

MOLECULAR PLANT PATHOLOGY (2021)

Article Plant Sciences

Genomics accelerated isolation of a new stem rust avirulence gene-wheat resistance gene pair

Narayana M. Upadhyaya et al.

Summary: Stem rust caused by the fungus Puccinia graminis f. sp. tritici (Pgt) is a devastating disease of wheat globally. Breeding for disease resistance is the most cost-effective control method, but new virulent strains of Pgt pose a threat to global wheat production.

NATURE PLANTS (2021)

Article Biochemistry & Molecular Biology

Prediction and Characterization of RXLR Effectors in Pythium Species

Gan Ai et al.

MOLECULAR PLANT-MICROBE INTERACTIONS (2020)

Article Biochemistry & Molecular Biology

Blast Fungal Genomes Show Frequent Chromosomal Changes, Gene Gains and Losses, and Effector Gene Turnover

Luis B. Gomez Luciano et al.

MOLECULAR BIOLOGY AND EVOLUTION (2019)

Article Ecology

The global burden of pathogens and pests on major food crops

Serge Savary et al.

NATURE ECOLOGY & EVOLUTION (2019)

Article Evolutionary Biology

Genomic Plasticity Mediated by Transposable Elements in the Plant Pathogenic Fungus Colletotrichum higginsianum

Ayako Tsushima et al.

GENOME BIOLOGY AND EVOLUTION (2019)

Editorial Material Plant Sciences

Nature's genetic screens: using genome-wide association studies for effector discovery

Andrea Sanchez-Vallet et al.

MOLECULAR PLANT PATHOLOGY (2018)

Article Plant Sciences

Improved prediction of fungal effector proteins from secretomes with EffectorP 2.0

Jana Sperschneider et al.

MOLECULAR PLANT PATHOLOGY (2018)

Article Biochemistry & Molecular Biology

Specific Hypersensitive Response-Associated Recognition of New Apoplastic Effectors from Cladosporium fulvum in Wild Tomato

Carl H. Mesarich et al.

MOLECULAR PLANT-MICROBE INTERACTIONS (2018)

Article Biochemistry & Molecular Biology

Comparative Transcriptome Analyses in Zymoseptoria tritici Reveal Significant Differences in Gene Expression Among Strains During Plant Infection

Javier Palma-Guerrero et al.

MOLECULAR PLANT-MICROBE INTERACTIONS (2017)

Article Biochemical Research Methods

Salmon provides fast and bias-aware quantification of transcript expression

Rob Patro et al.

NATURE METHODS (2017)

Article Multidisciplinary Sciences

LOCALIZER: subcellular localization prediction of both plant and effector proteins in the plant cell

Jana Sperschneider et al.

SCIENTIFIC REPORTS (2017)

Review Plant Sciences

How filamentous plant pathogen effectors are translocated to host cells

Libera Lo Presti et al.

CURRENT OPINION IN PLANT BIOLOGY (2017)

Article Plant Sciences

EffectorP: predicting fungal effector proteins from secretomes using machine learning

Jana Sperschneider et al.

NEW PHYTOLOGIST (2016)

Article Plant Sciences

Apoplastic fungal effectors in historic perspective; a personal view

Pierre J. G. M. De Wit

NEW PHYTOLOGIST (2016)

Review Plant Sciences

Fungal Effectors and Plant Susceptibility

Libera Lo Presti et al.

ANNUAL REVIEW OF PLANT BIOLOGY, VOL 66 (2015)

Article Plant Sciences

Evaluation of Secretion Prediction Highlights Differing Approaches Needed for Oomycete and Fungal Effectors

Jana Sperschneider et al.

FRONTIERS IN PLANT SCIENCE (2015)

Review Microbiology

Bacterial Type III Secretion Systems: Specialized Nanomachines for Protein Delivery into Target Cells

Jorge E. Galan et al.

ANNUAL REVIEW OF MICROBIOLOGY, VOL 68 (2014)

Review Biochemistry & Molecular Biology

Effectors as Tools in Disease Resistance Breeding Against Biotrophic, Hemibiotrophic, and Necrotrophic Plant Pathogens

Vivianne G. A. A. Vleeshouwers et al.

MOLECULAR PLANT-MICROBE INTERACTIONS (2014)

Article Biotechnology & Applied Microbiology

Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2

Michael I. Love et al.

GENOME BIOLOGY (2014)

Article Biochemical Research Methods

In-depth insight into in vivo apoplastic secretome of rice-Magnaporthe oryzae interaction

Sang Gon Kim et al.

JOURNAL OF PROTEOMICS (2013)

Review Plant Sciences

Nematode effector proteins: an emerging paradigm of parasitism

Melissa G. Mitchum et al.

NEW PHYTOLOGIST (2013)

Review Biochemistry & Molecular Biology

Toward Understanding the Role of Aphid Effectors in Plant Infestation

Patricia A. Rodriguez et al.

MOLECULAR PLANT-MICROBE INTERACTIONS (2013)

Article Multidisciplinary Sciences

Two distinct secretion systems facilitate tissue invasion by the rice blast fungus Magnaporthe oryzae

Martha C. Giraldo et al.

NATURE COMMUNICATIONS (2013)

Article Biochemical Research Methods

CD-HIT: accelerated for clustering the next-generation sequencing data

Limin Fu et al.

BIOINFORMATICS (2012)

Article Biotechnology & Applied Microbiology

Structure and evolution of barley powdery mildew effector candidates

Carsten Pedersen et al.

BMC GENOMICS (2012)

Article Biochemistry & Molecular Biology

A Secreted Effector Protein of Laccaria bicolor Is Required for Symbiosis Development

Jonathan M. Plett et al.

CURRENT BIOLOGY (2011)

Article Biochemistry & Molecular Biology

A Secreted Fungal Effector of Glomus intraradices Promotes Symbiotic Biotrophy

Silke Kloppholz et al.

CURRENT BIOLOGY (2011)

Letter Biochemical Research Methods

SignalP 4.0: discriminating signal peptides from transmembrane regions

Thomas Nordahl Petersen et al.

NATURE METHODS (2011)

Editorial Material Multidisciplinary Sciences

Showdown at the RXLR motif: Serious differences of opinion in how effector proteins from filamentous eukaryotic pathogens enter plant cells

Jeffrey G. Ellis et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2011)

Article Biochemistry & Molecular Biology

Translocation of Magnaporthe oryzae Effectors into Rice Cells and Their Subsequent Cell-to-Cell Movement

Chang Hyun Khang et al.

PLANT CELL (2010)

Article Multidisciplinary Sciences

Ancient class of translocated oomycete effectors targets the host nucleus

Sebastian Schornack et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2010)

Article Biochemical Research Methods

2-DE proteome maps for the leaf apoplast of Nicotiana benthamiana

Charles Goulet et al.

PROTEOMICS (2010)

Article Plant Sciences

Fungal Effector Proteins

Ioannis Stergiopoulos et al.

Annual Review of Phytopathology (2009)

Article Multidisciplinary Sciences

The genome of Laccaria bicolor provides insights into mycorrhizal symbiosis

F. Martin et al.

NATURE (2008)

Article Multidisciplinary Sciences

A translocation signal for delivery of oomycete effector proteins into host plant cells

Stephen C. Whisson et al.

NATURE (2007)

Article Biochemistry & Molecular Biology

Predicting transmembrane protein topology with a hidden Markov model: Application to complete genomes

A Krogh et al.

JOURNAL OF MOLECULAR BIOLOGY (2001)

Article Biochemical Research Methods

Intrinsically disordered protein

AK Dunker et al.

JOURNAL OF MOLECULAR GRAPHICS & MODELLING (2001)