title: Signatures of adaptation to obligate biotrophy in the Hyaloperonospora arabidopsidis genome.
abstract: Many oomycete and fungal plant pathogens are obligate biotrophs, which extract nutrients only from living plant tissue and cannot grow apart from their hosts. Although these pathogens cause substantial crop losses, little is known about the molecular basis or evolution of obligate biotrophy. Here, we report the genome sequence of the oomycete Hyaloperonospora arabidopsidis (Hpa), an obligate biotroph and natural pathogen of Arabidopsis thaliana. In comparison with genomes of related, hemibiotrophic Phytophthora species, the Hpa genome exhibits dramatic reductions in genes encoding (i) RXLR effectors and other secreted pathogenicity proteins, (ii) enzymes for assimilation of inorganic nitrogen and sulfur, and (iii) proteins associated with zoospore formation and motility. These attributes comprise a genomic signature of evolution toward obligate biotrophy.
authors.affiliation: School of Life Sciences, Warwick University, Wellesbourne, CV35 9EF, UK.
authors.forename: Laura
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authors.lastname: Baxter
authors.affiliation: Virginia Bioinformatics Institute, Virginia Tech, Blacksburg, VA, 24061, USA.
authors.forename: Sucheta
authors.initials: S
authors.lastname: Tripathy
authors.affiliation: Sainsbury Laboratory, University of East Anglia, John Innes Centre, Norwich NR4 7UH, UK.
authors.forename: Naveed
authors.initials: N
authors.lastname: Ishaque
authors.affiliation: Centre for Biosystems Genomics, P.O. Box 98,6700 AB Wageningen, The Netherlands.
authors.forename: Nico
authors.initials: N
authors.lastname: Boot
authors.affiliation: Centre for Biosystems Genomics, P.O. Box 98,6700 AB Wageningen, The Netherlands.
authors.forename: Adriana
authors.initials: A
authors.lastname: Cabral
authors.affiliation: Sainsbury Laboratory, University of East Anglia, John Innes Centre, Norwich NR4 7UH, UK.
authors.forename: Eric
authors.initials: E
authors.lastname: Kemen
authors.affiliation: Sainsbury Laboratory, University of East Anglia, John Innes Centre, Norwich NR4 7UH, UK.|Biodiversity and Climate Research Centre (BiK-F), Senckenberganlage 25, D-60325 Frankfurt (Main), Germany.|Johann Wolfgang Goethe University, Department of Biological Sciences, Institute of Ecology, Evolution and Diversity, Siesmayerstr. 70, D-60323 Frankfurt (Main), Germany.
authors.forename: Marco
authors.initials: M
authors.lastname: Thines
authors.affiliation: Department of Plant Pathology and Microbiology, University of California, Riverside, CA 92521, USA.
authors.forename: Audrey
authors.initials: A
authors.lastname: Ah-Fong
authors.affiliation: Department of Plant Pathology, Physiology and Weed Science, Virginia Tech, Blacksburg, VA 24061, USA.
authors.forename: Ryan
authors.initials: R
authors.lastname: Anderson
authors.affiliation: School of Life Sciences, Warwick University, Wellesbourne, CV35 9EF, UK.
authors.forename: Wole
authors.initials: W
authors.lastname: Badejoko
authors.affiliation: School of Life Sciences, Warwick University, Wellesbourne, CV35 9EF, UK.
authors.forename: Peter
authors.initials: P
authors.lastname: Bittner-Eddy
authors.affiliation: Department of Integrative Biology, University of California, Berkeley, USA.
authors.forename: Jeffrey L
authors.initials: JL
authors.lastname: Boore
authors.affiliation: Virginia Bioinformatics Institute, Virginia Tech, Blacksburg, VA, 24061, USA.
authors.forename: Marcus C
authors.initials: MC
authors.lastname: Chibucos
authors.affiliation: School of Life Sciences, Warwick University, Wellesbourne, CV35 9EF, UK.
authors.forename: Mary
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authors.lastname: Coates
authors.affiliation: Lawrence Berkeley National Laboratories, Berkeley, CA, 94720, USA.
authors.forename: Paramvir
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authors.lastname: Dehal
authors.affiliation: Genome Sequencing Centre, Washington University School of Medicine, St Louis, MO63110, USA.
authors.forename: Kim
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authors.lastname: Delehaunty
authors.affiliation: Agriculture and Agri-Food Canada, London, Ontario, N5V 4T3, Canada.|Department of Plant Pathology, Nanjing Agricultural University, China.
authors.forename: Suomeng
authors.initials: S
authors.lastname: Dong
authors.affiliation: School of Life Sciences, Warwick University, Wellesbourne, CV35 9EF, UK.
authors.forename: Polly
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authors.lastname: Downton
authors.affiliation: Université de Toulouse, UPS, Surfaces Cellulaires et Signalisation chez les Végétaux, 24 chemin de Borde Rouge, BP42617, Auzeville, F-31326, Castanet-Tolosan, France.|CNRS, Surfaces Cellulaires et Signalisation chez les Végétaux, 24 chemin de Borde Rouge, BP42617, Auzeville, F-31326, Castanet-Tolosan, France.
authors.forename: Bernard
authors.initials: B
authors.lastname: Dumas
authors.affiliation: Sainsbury Laboratory, University of East Anglia, John Innes Centre, Norwich NR4 7UH, UK.
authors.forename: Georgina
authors.initials: G
authors.lastname: Fabro
authors.affiliation: Genome Sequencing Centre, Washington University School of Medicine, St Louis, MO63110, USA.
authors.forename: Catrina
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authors.lastname: Fronick
authors.affiliation: Department of Integrative Biology, University of California, Berkeley, USA.
authors.forename: Susan I
authors.initials: SI
authors.lastname: Fuerstenberg
authors.affiliation: Genome Sequencing Centre, Washington University School of Medicine, St Louis, MO63110, USA.
authors.forename: Lucinda
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authors.lastname: Fulton
authors.affiliation: Université de Toulouse, UPS, Surfaces Cellulaires et Signalisation chez les Végétaux, 24 chemin de Borde Rouge, BP42617, Auzeville, F-31326, Castanet-Tolosan, France.|CNRS, Surfaces Cellulaires et Signalisation chez les Végétaux, 24 chemin de Borde Rouge, BP42617, Auzeville, F-31326, Castanet-Tolosan, France.
authors.forename: Elodie
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authors.lastname: Gaulin
authors.affiliation: Laboratory of Phytopathology, Wageningen University, and Centre for BioSystems Genomics, NL-1-6708 PB Wageningen, The Netherlands.
authors.forename: Francine
authors.initials: F
authors.lastname: Govers
authors.affiliation: School of Life Sciences, Warwick University, Wellesbourne, CV35 9EF, UK.
authors.forename: Linda
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authors.lastname: Hughes
authors.affiliation: Sanger, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK.
authors.forename: Sean
authors.initials: S
authors.lastname: Humphray
authors.affiliation: Laboratory of Phytopathology, Wageningen University, and Centre for BioSystems Genomics, NL-1-6708 PB Wageningen, The Netherlands.|The Broad Institute of MIT and Harvard, Cambridge, MA 02141-2023, USA.
authors.forename: Rays H Y
authors.initials: RHY
authors.lastname: Jiang
authors.affiliation: Department of Plant Pathology and Microbiology, University of California, Riverside, CA 92521, USA.
authors.forename: Howard
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authors.lastname: Judelson
authors.affiliation: Sainsbury Laboratory, University of East Anglia, John Innes Centre, Norwich NR4 7UH, UK.
authors.forename: Sophien
authors.initials: S
authors.lastname: Kamoun
authors.affiliation: Genome Sequencing Centre, Washington University School of Medicine, St Louis, MO63110, USA.
authors.forename: Kim
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authors.affiliation: Laboratory of Phytopathology, Wageningen University, and Centre for BioSystems Genomics, NL-1-6708 PB Wageningen, The Netherlands.
authors.forename: Harold
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authors.lastname: Meijer
authors.affiliation: Genome Sequencing Centre, Washington University School of Medicine, St Louis, MO63110, USA.
authors.forename: Patrick
authors.initials: P
authors.lastname: Minx
authors.affiliation: Department of Biological Sciences, Bowling Green State University, Bowling Green, Ohio 43403-0212, USA.
authors.forename: Paul
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authors.lastname: Morris
authors.affiliation: Genome Sequencing Centre, Washington University School of Medicine, St Louis, MO63110, USA.
authors.forename: Joanne
authors.initials: J
authors.lastname: Nelson
authors.affiliation: Department of Biological Sciences, Bowling Green State University, Bowling Green, Ohio 43403-0212, USA.
authors.forename: Vipa
authors.initials: V
authors.lastname: Phuntumart
authors.affiliation: Agriculture and Agri-Food Canada, London, Ontario, N5V 4T3, Canada.
authors.forename: Dinah
authors.initials: D
authors.lastname: Qutob
authors.affiliation: School of Life Sciences, Warwick University, Wellesbourne, CV35 9EF, UK.
authors.forename: Anne
authors.initials: A
authors.lastname: Rehmany
authors.affiliation: Sainsbury Laboratory, University of East Anglia, John Innes Centre, Norwich NR4 7UH, UK.
authors.forename: Alejandra
authors.initials: A
authors.lastname: Rougon-Cardoso
authors.affiliation: School of Life Sciences, Warwick University, Wellesbourne, CV35 9EF, UK.
authors.forename: Peter
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authors.lastname: Ryden
authors.affiliation: Virginia Bioinformatics Institute, Virginia Tech, Blacksburg, VA, 24061, USA.
authors.forename: Trudy
authors.initials: T
authors.lastname: Torto-Alalibo
authors.affiliation: Sainsbury Laboratory, University of East Anglia, John Innes Centre, Norwich NR4 7UH, UK.
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authors.affiliation: Department of Plant Pathology, Nanjing Agricultural University, China.
authors.forename: Yuanchao
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authors.affiliation: Sainsbury Laboratory, University of East Anglia, John Innes Centre, Norwich NR4 7UH, UK.
authors.forename: Joe
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authors.lastname: Win
authors.affiliation: Sanger, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK.
authors.forename: Jo
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authors.affiliation: Genome Sequencing Centre, Washington University School of Medicine, St Louis, MO63110, USA.
authors.forename: Sandra W
authors.initials: SW
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authors.affiliation: Sanger, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK.
authors.forename: Jane
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authors.lastname: Rogers
authors.affiliation: Johann Wolfgang Goethe University, Department of Biological Sciences, Institute of Ecology, Evolution and Diversity, Siesmayerstr. 70, D-60323 Frankfurt (Main), Germany.
authors.forename: Guido
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authors.lastname: Van den Ackerveken
authors.affiliation: Sainsbury Laboratory, University of East Anglia, John Innes Centre, Norwich NR4 7UH, UK.
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authors.initials: JDG
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authors.affiliation: Department of Plant Pathology, Physiology and Weed Science, Virginia Tech, Blacksburg, VA 24061, USA.
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authors.initials: JM
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authors.affiliation: School of Life Sciences, Warwick University, Wellesbourne, CV35 9EF, UK.
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authors.affiliation: Virginia Bioinformatics Institute, Virginia Tech, Blacksburg, VA, 24061, USA.|Department of Plant Pathology, Physiology and Weed Science, Virginia Tech, Blacksburg, VA 24061, USA.
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authors.initials: BM
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mesh_terms: D000222:Adaptation, Physiological; D000595:Amino Acid Sequence; D017360:Arabidopsis / Q000469:parasitology*; D004798:Enzymes / Q000235:genetics; D019143:Evolution, Molecular; D018628:Gene Dosage; D005796:Genes; D016678:Genome; D054884:Host-Pathogen Interactions; D053858:Metabolic Networks and Pathways / Q000235:genetics; D008969:Molecular Sequence Data; D009868:Oomycetes / Q000235:genetics* / Q000254:growth & development* / Q000472:pathogenicity / Q000502:physiology; D010838:Phytophthora / Q000235:genetics; D010935:Plant Diseases / Q000469:parasitology*; D020641:Polymorphism, Single Nucleotide; D011506:Proteins / Q000235:genetics; D012641:Selection, Genetic; D017422:Sequence Analysis, DNA; D013170:Spores / Q000502:physiology; D026801:Synteny; D037521:Virulence Factors / Q000235:genetics
chemical_list: D004798:Enzymes; D011506:Proteins; D037521:Virulence Factors