4.7 Article

Genome-wide analysis of Claviceps paspali: insights into the secretome of the main species causing ergot disease in Paspalum spp

Related references

Note: Only part of the references are listed.
Article Evolutionary Biology

Whole-Genome Comparisons of Ergot Fungi Reveals the Divergence and Evolution of Species within the Genus Claviceps Are the Result of Varying Mechanisms Driving Genome Evolution and Host Range Expansion

Stephen A. Wyka et al.

Summary: The genus Claviceps has been known for its economic importance in pharmacology and agricultural research. Recent studies have revealed its evolutionary history through sequencing and annotating 50 Claviceps genomes representing 21 species, shedding light on the factors influencing adaptability and providing valuable genomic resources for future research in the field.

GENOME BIOLOGY AND EVOLUTION (2021)

Article Biochemistry & Molecular Biology

PHI-base: the pathogen-host interactions database

Martin Urban et al.

NUCLEIC ACIDS RESEARCH (2020)

Review Microbiology

Chloroplasts and Plant Immunity: Where Are the Fungal Effectors?

Matthias Kretschmer et al.

PATHOGENS (2020)

Review Plant Sciences

The Multiple Facets of Plant-Fungal Interactions Revealed Through Plant and Fungal Secretomics

Delphine Vincent et al.

FRONTIERS IN PLANT SCIENCE (2020)

Article Microbiology

New Draft Genome Sequence of the Ergot Disease Fungus Claviceps paspali

H. Oberti et al.

MICROBIOLOGY RESOURCE ANNOUNCEMENTS (2020)

Article Biotechnology & Applied Microbiology

Comparative genomics of plant pathogenic Botrytis species with distinct host specificity

Claudio A. Valero-Jimenez et al.

BMC GENOMICS (2019)

Article Biotechnology & Applied Microbiology

SignalP 5.0 improves signal peptide predictions using deep neural networks

Jose Juan Almagro Armenteros et al.

NATURE BIOTECHNOLOGY (2019)

Article Biotechnology & Applied Microbiology

OrthoFinder: phylogenetic orthology inference for comparative genomics

David M. Emms et al.

GENOME BIOLOGY (2019)

Article Biology

Detecting sequence signals in targeting peptides using deep learning

Jose Juan Almagro Armenteros et al.

LIFE SCIENCE ALLIANCE (2019)

Article Plant Sciences

Host preference and network properties in biotrophic plant-fungal associations

Sergei Polme et al.

NEW PHYTOLOGIST (2018)

Article Biotechnology & Applied Microbiology

Inactivation of the indole-diterpene biosynthetic gene cluster of Claviceps paspali by Agrobacterium-mediated gene replacement

Laszlo Kozak et al.

APPLIED MICROBIOLOGY AND BIOTECHNOLOGY (2018)

Article Biochemistry & Molecular Biology

Evolutionary history of ergot with a new infrageneric classification (Hypocreales: Clavicipitaceae: Claviceps)

Kamila Pichova et al.

MOLECULAR PHYLOGENETICS AND EVOLUTION (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 Plant Sciences

Tools of the crook- infection strategies of fungal plant pathogens

Luis Rodriguez-Moreno et al.

PLANT JOURNAL (2018)

Review Biotechnology & Applied Microbiology

Plant-pathogen interactions: toward development of next-generation disease-resistant plants

Naghmeh Nejat et al.

CRITICAL REVIEWS IN BIOTECHNOLOGY (2017)

Review Microbiology

Effectors of Filamentous Plant Pathogens: Commonalities amid Diversity

Marina Franceschetti et al.

MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS (2017)

Article Mycology

A plant pathology perspective of fungal genome sequencing

Janneke Aylward et al.

IMA FUNGUS (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)

Article Biochemical Research Methods

FunGAP: Fungal Genome Annotation Pipeline using evidence-based gene model evaluation

Byoungnam Min et al.

BIOINFORMATICS (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 Biotechnology & Applied Microbiology

Cross-talk of the biotrophic pathogen Claviceps purpurea and its host Secale cereale

Birgitt Oeser et al.

BMC GENOMICS (2017)

Article Biochemical Research Methods

Homology to peptide pattern for annotation of carbohydrate-active enzymes and prediction of function

P. K. Busk et al.

BMC BIOINFORMATICS (2017)

Article Biochemical Research Methods

BRAKER1: Unsupervised RNA-Seq-Based Genome Annotation with GeneMark-ET and AUGUSTUS

Katharina J. Hoff et al.

BIOINFORMATICS (2016)

Review Plant Sciences

Plant-Pathogen Effectors: Cellular Probes Interfering with Plant Defenses in Spatial and Temporal Manners

Tania Y. Toruno et al.

ANNUAL REVIEW OF PHYTOPATHOLOGY, VOL 54 (2016)

Review Plant Sciences

Computational Prediction of Effector Proteins in Fungi: Opportunities and Challenges

Humira Sonah et al.

FRONTIERS IN PLANT SCIENCE (2016)

Article Veterinary Sciences

Impacts of Cereal Ergot in Food Animal Production

Stephanie Coufal-Majewski et al.

FRONTIERS IN VETERINARY SCIENCE (2016)

Review Plant Sciences

Fungal Effectors and Plant Susceptibility

Libera Lo Presti et al.

ANNUAL REVIEW OF PLANT BIOLOGY, VOL 66 (2015)

Article Biochemical Research Methods

BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs

Felipe A. Simao et al.

BIOINFORMATICS (2015)

Review Microbiology

How eukaryotic filamentous pathogens evade plant recognition

Ely Oliveira-Garcia et al.

CURRENT OPINION IN MICROBIOLOGY (2015)

Article Microbiology

De novo biosynthesis of cytokinins in the biotrophic fungus Claviceps purpurea

Janine Hinsch et al.

ENVIRONMENTAL MICROBIOLOGY (2015)

Article Mycology

Delimitation of cryptic species inside Claviceps purpurea

Sylvie Pazoutova et al.

FUNGAL BIOLOGY (2015)

Article Biochemical Research Methods

Fast and sensitive protein alignment using DIAMOND

Benjamin Buchfink et al.

NATURE METHODS (2015)

Review Microbiology

The battle for chitin recognition in plant-microbe interactions

Andrea Sanchez-Vallet et al.

FEMS MICROBIOLOGY REVIEWS (2015)

Review Plant Sciences

Plant Cell Wall-Degrading Enzymes and Their Secretion in Plant-Pathogenic Fungi

Christian P. Kubicek et al.

ANNUAL REVIEW OF PHYTOPATHOLOGY, VOL 52 (2014)

Article Biochemical Research Methods

Trimmomatic: a flexible trimmer for Illumina sequence data

Anthony M. Bolger et al.

BIOINFORMATICS (2014)

Article Biochemical Research Methods

InterProScan 5: genome-scale protein function classification

Philip Jones et al.

BIOINFORMATICS (2014)

Article Biotechnology & Applied Microbiology

Compositions of fungal secretomes indicate a greater impact of phylogenetic history than lifestyle adaptation

Jorrit-Jan Krijger et al.

BMC GENOMICS (2014)

Article Biochemical Research Methods

Quantitative assessment of single-cell RNRNA-sequencing methods

Angela R. Wu et al.

NATURE METHODS (2014)

Review Biochemistry & Molecular Biology

Intervention of Phytohormone Pathways by Pathogen Effectors

Kemal Kazan et al.

PLANT CELL (2014)

Review Plant Sciences

Effector-triggered defence against apoplastic fungal pathogens

Henrik U. Stotz et al.

TRENDS IN PLANT SCIENCE (2014)

Review Microbiology

Plant Cell Wall Deconstruction by Ascomycete Fungi

N. Louise Glass et al.

ANNUAL REVIEW OF MICROBIOLOGY, VOL 67 (2013)

Article Biochemical Research Methods

QUAST: quality assessment tool for genome assemblies

Alexey Gurevich et al.

BIOINFORMATICS (2013)

Article Biochemistry & Molecular Biology

WebAUGUSTUS-a web service for training AUGUSTUS and predicting genes in eukaryotes

Katharina J. Hoff et al.

NUCLEIC ACIDS RESEARCH (2013)

Article Biochemical Research Methods

SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing

Anton Bankevich et al.

JOURNAL OF COMPUTATIONAL BIOLOGY (2012)

Article Microbiology

Indifferent, Affectionate, or Deceitful: Lifestyles and Secretomes of Fungi

Rohan G. T. Lowe et al.

PLOS PATHOGENS (2012)

Article Biochemical Research Methods

FIMO: scanning for occurrences of a given motif

Charles E. Grant et al.

BIOINFORMATICS (2011)

Article Biochemical Research Methods

MAKER2: an annotation pipeline and genome-database management tool for second-generation genome projects

Carson Holt et al.

BMC BIOINFORMATICS (2011)

Article Biochemical Research Methods

RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome

Bo Li et al.

BMC BIOINFORMATICS (2011)

Article Biochemistry & Molecular Biology

HMMER web server: interactive sequence similarity searching

Robert D. Finn et al.

NUCLEIC ACIDS RESEARCH (2011)

Article Biochemistry & Molecular Biology

Of PAMPs and Effectors: The Blurred PTI-ETI Dichotomy

Bart P. H. J. Thomma et al.

PLANT CELL (2011)

Article Multidisciplinary Sciences

Obligate biotrophy features unraveled by the genomic analysis of rust fungi

Sebastien Duplessis et al.

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

Article Biochemical Research Methods

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

Mark D. Robinson et al.

BIOINFORMATICS (2010)

Article Biochemical Research Methods

Search and clustering orders of magnitude faster than BLAST

Robert C. Edgar

BIOINFORMATICS (2010)

Article Biotechnology & Applied Microbiology

Powdery mildew fungal effector candidates share N-terminal Y/F/WxC-motif

Dale Godfrey et al.

BMC GENOMICS (2010)

Article Agronomy

Are more productive varieties of Paspalum dilatatum less tolerant to drought?

L. L. Couso et al.

GRASS AND FORAGE SCIENCE (2010)

Article Biochemical Research Methods

Alternative expression analysis by RNA sequencing

Malachi Griffith et al.

NATURE METHODS (2010)

Article Multidisciplinary Sciences

Conserved Fungal LysM Effector Ecp6 Prevents Chitin-Triggered Immunity in Plants

Ronnie de Jonge et al.

SCIENCE (2010)

Article Biochemical Research Methods

BLAST plus : architecture and applications

Christiam Camacho et al.

BMC BIOINFORMATICS (2009)

Article Biochemical Research Methods

LTRharvest, an efficient and flexible software for de novo detection of LTR retrotransposons

David Ellinghaus et al.

BMC BIOINFORMATICS (2008)

Article Biochemical Research Methods

PredGPI: a GPI-anchor predictor

Andrea Pierleoni et al.

BMC BIOINFORMATICS (2008)

Article Biochemistry & Molecular Biology

The expression of a bean PGIP in transgenic wheat confers increased resistance to the fungal pathogen Bipolaris sorokiniana

Michela Janni et al.

MOLECULAR PLANT-MICROBE INTERACTIONS (2008)

Article Biochemistry & Molecular Biology

High-throughput functional annotation and data mining with the Blast2GO suite

Stefan Gotz et al.

NUCLEIC ACIDS RESEARCH (2008)

Article Biotechnology & Applied Microbiology

Comparison of ergot alkaloid biosynthesis gene clusters in Claviceps species indicates loss of late pathway steps in evolution of C-fusiformis

Nicole Lorenz et al.

APPLIED AND ENVIRONMENTAL MICROBIOLOGY (2007)

Article Biochemistry & Molecular Biology

Advantages of combined transmembrane topology and signal peptide prediction -: the Phobius web server

Lukas Kaell et al.

NUCLEIC ACIDS RESEARCH (2007)

Article Biochemistry & Molecular Biology

WoLF PSORT: protein localization predictor

Paul Horton et al.

NUCLEIC ACIDS RESEARCH (2007)

Article Biochemistry & Molecular Biology

ScanProsite: detection of PROSITE signature matches and ProRule-associated functional and structural residues in proteins

Edouard de Castro et al.

NUCLEIC ACIDS RESEARCH (2006)

Article Plant Sciences

Claviceps purpurea:: molecular aspects of a unique pathogenic lifestyle

P Tudzynski et al.

MOLECULAR PLANT PATHOLOGY (2004)

Article Biochemistry & Molecular Biology

Disruption of Botrytis cinerea pectin methylesterase gene Bcpme1 reduces virulence on several host plants

O Valette-Collet et al.

MOLECULAR PLANT-MICROBE INTERACTIONS (2003)

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)