Dynamics and Innovations within Oomycete Genomes: Insights into Biology, Pathology, and Evolution

Oomycetes, effectors, and all that jazz

(2012) Tolga O Bozkurt et al.   CURRENT OPINION IN PLANT BIOLOGY

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

Natural antisense transcripts in fungi

(2012) Michael E. Donaldson et al.   MOLECULAR MICROBIOLOGY

Genome Sequencing and Mapping Reveal Loss of Heterozygosity as a Mechanism for Rapid Adaptation in the Vegetable Pathogen Phytophthora capsici

(2012) Kurt H. Lamour et al.   MOLECULAR PLANT-MICROBE INTERACTIONS

The NLP Toxin Family in Phytophthora sojae Includes Rapidly Evolving Groups That Lack Necrosis-Inducing Activity

(2012) Suomeng Dong et al.   MOLECULAR PLANT-MICROBE INTERACTIONS

Alternative Splicing of a Multi-Drug Transporter from Pseudoperonospora cubensis Generates an RXLR Effector Protein That Elicits a Rapid Cell Death

(2012) Elizabeth A. Savory et al.   PLoS One

Phenotypic Diversification Is Associated with Host-Induced Transposon Derepression in the Sudden Oak Death Pathogen Phytophthora ramorum

(2012) Takao Kasuga et al.   PLoS One

mRNA-Seq Analysis of the Pseudoperonospora cubensis Transcriptome During Cucumber (Cucumis sativus L.) Infection

(2012) Elizabeth A. Savory et al.   PLoS One

Emergence of the sudden oak death pathogen Phytophthora ramorum

(2012) Niklaus J. Grünwald et al.   TRENDS IN MICROBIOLOGY

Transcriptomic analysis of the interaction between Helianthus annuus and its obligate parasite Plasmopara halstedii shows single nucleotide polymorphisms in CRN sequences

(2011) Falah As-sadi et al.   BMC GENOMICS

The aspartic proteinase family of three Phytophthora species

(2011) John Kay et al.   BMC GENOMICS

Characterization of intronic structures and alternative splicing in Phytophthora sojae by comparative analysis of expressed sequence tags and genomic sequences

(2011) Danyu Shen et al.   CANADIAN JOURNAL OF MICROBIOLOGY

How do oomycete effectors interfere with plant life?

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

Transposable element origins of epigenetic gene regulation

(2011) Damon Lisch et al.   CURRENT OPINION IN PLANT BIOLOGY

Silencing of the PiAvr3a effector-encoding gene from Phytophthora infestans by transcriptional fusion to a short interspersed element

(2011) Ramesh R. Vetukuri et al.   Fungal Biology

The oomycete Pythium oligandrum expresses putative effectors during mycoparasitism of Phytophthora infestans and is amenable to transformation

(2011) Neil R. Horner et al.   Fungal Biology

RNA-Seq reveals infection-related global gene changes in Phytophthora phaseoli, the causal agent of lima bean downy mildew

(2011) SRIDHARA G. KUNJETI et al.   MOLECULAR PLANT PATHOLOGY

454 Genome Sequencing ofPseudoperonospora cubensisReveals Effector Proteins with a QXLR Translocation Motif

(2011) Miaoying Tian et al.   MOLECULAR PLANT-MICROBE INTERACTIONS

Presence/absence, differential expression and sequence polymorphisms between PiAVR2 and PiAVR2-like in Phytophthora infestans determine virulence on R2 plants

(2011) Eleanor M. Gilroy et al.   NEW PHYTOLOGIST

The Genus Phytophthora Anno 2012

(2011) Laurens P. N. M. Kroon et al.   PHYTOPATHOLOGY

A Molecular Insight into Algal-Oomycete Warfare: cDNA Analysis of Ectocarpus siliculosus Infected with the Basal Oomycete Eurychasma dicksonii

(2011) Laura Grenville-Briggs et al.   PLoS One

Sequence Variants of the Phytophthora sojae RXLR Effector Avr3a/5 Are Differentially Recognized by Rps3a and Rps5 in Soybean

(2011) Suomeng Dong et al.   PLoS One

Red and Green Algal Origin of Diatom Membrane Transporters: Insights into Environmental Adaptation and Cell Evolution

(2011) Cheong Xin Chan et al.   PLoS One

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

Gene Gain and Loss during Evolution of Obligate Parasitism in the White Rust Pathogen of Arabidopsis thaliana

(2011) Eric Kemen et al.   PLOS BIOLOGY

Crypton transposons: identification of new diverse families and ancient domestication events

(2011) Kenji K Kojima et al.   Mobile DNA

The inclusion of downy mildews in a multi-locus-dataset and its reanalysis reveals a high degree of paraphyly in Phytophthora

(2011) Fabian Runge et al.   IMA Fungus

The kinome of Phytophthora infestans reveals oomycete-specific innovations and links to other taxonomic groups

(2010) Howard S Judelson 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

Myb transcription factors in the oomycete Phytophthora with novel diversified DNA-binding domains and developmental stage-specific expression

(2010) Qijun Xiang et al.   GENE

Phylogenomic Evidence for Separate Acquisition of Plastids in Cryptophytes, Haptophytes, and Stramenopiles

(2010) D. Baurain et al.   MOLECULAR BIOLOGY AND EVOLUTION

A Domain-Centric Analysis of Oomycete Plant Pathogen Genomes Reveals Unique Protein Organization

(2010) M. F. Seidl et al.   PLANT PHYSIOLOGY

Ancient class of translocated oomycete effectors targets the host nucleus

(2010) S. Schornack et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Signatures of Adaptation to Obligate Biotrophy in the Hyaloperonospora arabidopsidis Genome

(2010) L. Baxter et al.   SCIENCE

Genome Evolution Following Host Jumps in the Irish Potato Famine Pathogen Lineage

(2010) S. Raffaele et al.   SCIENCE

Broadly Sampled Multigene Analyses Yield a Well-Resolved Eukaryotic Tree of Life

(2010) Laura Wegener Parfrey et al.   SYSTEMATIC BIOLOGY

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

(2010) C André Lévesque et al.   GENOME BIOLOGY

Cyanobacterial contribution to the genomes of the plastid-lacking protists

(2009) Shinichiro Maruyama et al.   BMC EVOLUTIONARY BIOLOGY

Are algal genes in nonphotosynthetic protists evidence of historical plastid endosymbioses?

(2009) John W Stiller et al.   BMC GENOMICS

A motif within a complex promoter from the oomycete Phytophthora infestans determines transcription during an intermediate stage of sporulation

(2009) Qijun Xiang et al.   FUNGAL GENETICS AND BIOLOGY

Co-Expression of Neighboring Genes in the Zebrafish (Danio rerio) Genome

(2009) Huai-Kuang Tsai et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Chromalveolates and the Evolution of Plastids by Secondary Endosymbiosis

(2009) PATRICK J. KEELING   JOURNAL OF EUKARYOTIC MICROBIOLOGY

Evolutionary Forces Act on Promoter Length: Identification of Enriched Cis-Regulatory Elements

(2009) E. Kristiansson et al.   MOLECULAR BIOLOGY AND EVOLUTION

Metabolic adaptation ofPhytophthora infestansduring growth on leaves, tubers and artificial media

(2009) HOWARD S. JUDELSON et al.   MOLECULAR PLANT PATHOLOGY

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

Genomic Footprints of a Cryptic Plastid Endosymbiosis in Diatoms

(2009) A. Moustafa et al.   SCIENCE

The transferome of metabolic genes explored: analysis of the horizontal transfer of enzyme encoding genes in unicellular eukaryotes

(2009) John W Whitaker et al.   GENOME BIOLOGY

FTFD: an informatics pipeline supporting phylogenomic analysis of fungal transcription factors

(2008) J. Park et al.   BIOINFORMATICS

Optimization of transgene-mediated silencing in Phytophthora infestans and its association with small-interfering RNAs

(2008) Audrey M.V. Ah-Fong et al.   FUNGAL GENETICS AND BIOLOGY

Internuclear gene silencing in Phytophthora infestans is established through chromatin remodelling

(2008) P. van West et al.   MICROBIOLOGY-SGM

Phytophthora infestans: the plant (and R gene) destroyer

(2008) WILLIAM FRY   MOLECULAR PLANT PATHOLOGY

Gene Expression Profiling During Asexual Development of the Late Blight Pathogen Phytophthora infestans Reveals a Highly Dynamic Transcriptome

(2008) Howard S. Judelson et al.   MOLECULAR PLANT-MICROBE INTERACTIONS

Structure of the Glucanase Inhibitor Protein (GIP) Family fromPhytophthoraSpecies Suggests Coevolution with Plant Endo-β-1,3-Glucanases

(2008) Cynthia M. B. Damasceno et al.   MOLECULAR PLANT-MICROBE INTERACTIONS

The Phaeodactylum genome reveals the evolutionary history of diatom genomes

(2008) Chris Bowler et al.   NATURE

Transcriptome of Aphanomyces euteiches: New Oomycete Putative Pathogenicity Factors and Metabolic Pathways

(2008) Elodie Gaulin et al.   PLoS One

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