The Secreted Proteins of Achlya hypogyna and Thraustotheca clavata Identify the Ancestral Oomycete Secretome and Reveal Gene Acquisitions by Horizontal Gene Transfer

Coevolution and Life Cycle Specialization of Plant Cell Wall Degrading Enzymes in a Hemibiotrophic Pathogen

(2013) Patrick C. Brunner et al.   MOLECULAR BIOLOGY AND EVOLUTION

Sequence Comparative Analysis Using Networks: Software for Evaluating De Novo Transcript Assembly from Next-Generation Sequencing

(2013) Ian Misner et al.   MOLECULAR BIOLOGY AND EVOLUTION

Horizontal gene transfer in osmotrophs: playing with public goods

(2013) Thomas A. Richards et al.   NATURE REVIEWS MICROBIOLOGY

Comparative Genomics Reveals Insight into Virulence Strategies of Plant Pathogenic Oomycetes

(2013) Bishwo N. Adhikari et al.   PLoS One

The evolution and pathogenic mechanisms of the rice sheath blight pathogen

(2013) Aiping Zheng et al.   Nature Communications

Distinctive Expansion of Potential Virulence Genes in the Genome of the Oomycete Fish Pathogen Saprolegnia parasitica

(2013) Rays H. Y. Jiang et al.   PLoS Genetics

Inferring duplications, losses, transfers and incomplete lineage sorting with nonbinary species trees

(2012) Maureen Stolzer et al.   BIOINFORMATICS

Reconstruction of Oomycete Genome Evolution Identifies Differences in Evolutionary Trajectories Leading to Present-Day Large Gene Families

(2012) Michael F. Seidl et al.   Genome Biology and Evolution

The Revised Classification of Eukaryotes

(2012) Sina M. Adl et al.   JOURNAL OF EUKARYOTIC MICROBIOLOGY

Lifestyle transitions in plant pathogenic Colletotrichum fungi deciphered by genome and transcriptome analyses

(2012) Richard J O'Connell et al.   NATURE GENETICS

dbCAN: a web resource for automated carbohydrate-active enzyme annotation

(2012) Yanbin Yin et al.   NUCLEIC ACIDS RESEARCH

The Predicted Secretome of the Plant Pathogenic Fungus Fusarium graminearum: A Refined Comparative Analysis

(2012) Neil A. Brown et al.   PLoS One

ProtTest 3: fast selection of best-fit models of protein evolution

(2011) Diego Darriba et al.   BIOINFORMATICS

De novo sequence assembly of Albugo candida reveals a small genome relative to other biotrophic oomycetes

(2011) Matthew G Links et al.   BMC GENOMICS

How do oomycete effectors interfere with plant life?

(2011) Joost HM Stassen et al.   CURRENT OPINION IN PLANT BIOLOGY

The Pfam protein families database

(2011) M. Punta et al.   NUCLEIC ACIDS RESEARCH

Potato and Tomato Late Blight Caused byPhytophthora infestans: An Overview of Pathology and Resistance Breeding

(2011) Marcin Nowicki et al.   PLANT DISEASE

Horizontal gene transfer facilitated the evolution of plant parasitic mechanisms in the oomycetes

(2011) T. A. Richards et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The evolutionary phylogeny of the oomycete “fungi”

(2011) Gordon W. Beakes et al.   PROTOPLASMA

The hidden duplication past of the plant pathogen Phytophthora and its consequences for infection

(2010) Cindy Martens et al.   BMC GENOMICS

Fungal Secretome Database: Integrated platform for annotation of fungal secretomes

(2010) Jaeyoung Choi et al.   BMC GENOMICS

The CAZyome of Phytophthora spp.: A comprehensive analysis of the gene complement coding for carbohydrate-active enzymes in species of the genus Phytophthora

(2010) Manuel D Ospina-Giraldo et al.   BMC GENOMICS

An inventory of the Aspergillus niger secretome by combining in silico predictions with shotgun proteomics data

(2010) Machtelt Braaksma et al.   BMC GENOMICS

Analyses of genome architecture and gene expression reveal novel candidate virulence factors in the secretome of Phytophthora infestans

(2010) Sylvain Raffaele et al.   BMC GENOMICS

Horizontal Transfer of a Large and Highly Toxic Secondary Metabolic Gene Cluster between Fungi

(2010) Jason C. Slot et al.   CURRENT BIOLOGY

Oomycetes RXLR Effectors Function as Both Activator and Suppressor of Plant Immunity

(2010) Sang-Keun Oh et al.   Plant Pathology Journal

FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments

(2010) Morgan N. Price et al.   PLoS One

Chitin Synthases from Saprolegnia Are Involved in Tip Growth and Represent a Potential Target for Anti-Oomycete Drugs

(2010) Gea Guerriero et al.   PLoS Pathogens

Genome sequence of the necrotrophic plant pathogen Pythium ultimum reveals original pathogenicity mechanisms and effector repertoire

(2010) C André Lévesque et al.   GENOME BIOLOGY

trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses

(2009) S. Capella-Gutierrez et al.   BIOINFORMATICS

Towards understanding the virulence functions of RXLR effectors of the oomycete plant pathogen Phytophthora infestans

(2009) P. R. J. Birch et al.   JOURNAL OF EXPERIMENTAL BOTANY

SeaView Version 4: A Multiplatform Graphical User Interface for Sequence Alignment and Phylogenetic Tree Building

(2009) M. Gouy et al.   MOLECULAR BIOLOGY AND EVOLUTION

Induction of Distinct Defense-Associated Protein Patterns inAphanomyces euteiches(Oomycota)–Elicited and –InoculatedMedicago truncatulaCell-Suspension Cultures: A Proteome and Phosphoproteome Approach

(2009) Tom Trapphoff et al.   MOLECULAR PLANT-MICROBE INTERACTIONS

Genome sequence and analysis of the Irish potato famine pathogen Phytophthora infestans

(2009) Brian J. Haas et al.   NATURE

Sterol metabolism in the oomycete Aphanomyces euteiches, a legume root pathogen

(2009) Mohammed-Amine Madoui et al.   NEW PHYTOLOGIST

Multiple Horizontal Gene Transfer Events and Domain Fusions Have Created Novel Regulatory and Metabolic Networks in the Oomycete Genome

(2009) Paul Francis Morris et al.   PLoS One

Three-dimensional solution structure of β cryptogein, a β elicitin secreted by a phytopathogenic fungus phytophthora cryptogea

(2009) Sandrine Fefeu et al.   PROTEIN SCIENCE

Acquisition of prokaryotic genes by fungal genomes

(2009) Marina Marcet-Houben et al.   TRENDS IN GENETICS

Analysis of the Pythium ultimum transcriptome using Sanger and Pyrosequencing approaches

(2008) Foo Cheung et al.   BMC GENOMICS

Oomycete RXLR effectors: delivery, functional redundancy and durable disease resistance

(2008) Paul RJ Birch et al.   CURRENT OPINION IN PLANT BIOLOGY

Experimental infection and detection of Aphanomyces invadans in European catfish, rainbow trout and European eel

(2008) B Oidtmann et al.   DISEASES OF AQUATIC ORGANISMS

Reconciliation with Non-Binary Species Trees

(2008) Benjamin Vernot et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Saprolegnia brachydanis, A New Oomycete Isolated from Zebra Fish

(2008) Xiaoli Ke et al.   MYCOPATHOLOGIA

Accurate whole human genome sequencing using reversible terminator chemistry

(2008) David R. Bentley et al.   NATURE

Horizontal gene transfer in eukaryotic evolution

(2008) Patrick J. Keeling et al.   NATURE REVIEWS GENETICS

The Carbohydrate-Active EnZymes database (CAZy): an expert resource for Glycogenomics

(2008) B. L. Cantarel et al.   NUCLEIC ACIDS RESEARCH

Comparative Genome Analysis of Filamentous Fungi Reveals Gene Family Expansions Associated with Fungal Pathogenesis

(2008) Darren M. Soanes et al.   PLoS One

Evolution of malaria parasite plastid targeting sequences

(2008) C. J. Tonkin et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Whole-genome analysis reveals molecular innovations and evolutionary transitions in chromalveolate species

(2008) C. Martens et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

RXLR effector reservoir in two Phytophthora species is dominated by a single rapidly evolving superfamily with more than 700 members

(2008) R. H. Y. Jiang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Moving targets: rapid evolution of oomycete effectors

(2008) Darren M. Soanes et al.   TRENDS IN MICROBIOLOGY

Evolution of the cutinase gene family: Evidence for lateral gene transfer of a candidate Phytophthora virulence factor

(2007) Lassaad Belbahri et al.   GENE