title: Genome analyses of the sunflower pathogen Plasmopara halstedii provide insights into effector evolution in downy mildews and Phytophthora.
abstract: BACKGROUND
  Downy mildews are the most speciose group of oomycetes and affect crops of great economic importance. So far, there is only a single deeply-sequenced downy mildew genome available, from Hyaloperonospora arabidopsidis. Further genomic resources for downy mildews are required to study their evolution, including pathogenicity effector proteins, such as RxLR effectors. Plasmopara halstedii is a devastating pathogen of sunflower and a potential pathosystem model to study downy mildews, as several Avr-genes and R-genes have been predicted and unlike Arabidopsis downy mildew, large quantities of almost contamination-free material can be obtained easily.
  
  
  RESULTS
  Here a high-quality draft genome of Plasmopara halstedii is reported and analysed with respect to various aspects, including genome organisation, secondary metabolism, effector proteins and comparative genomics with other sequenced oomycetes. Interestingly, the present analyses revealed further variation of the RxLR motif, suggesting an important role of the conservation of the dEER-motif. Orthology analyses revealed the conservation of 28 RxLR-like core effectors among Phytophthora species. Only six putative RxLR-like effectors were shared by the two sequenced downy mildews, highlighting the fast and largely independent evolution of two of the three major downy mildew lineages. This is seemingly supported by phylogenomic results, in which downy mildews did not appear to be monophyletic.
  
  
  CONCLUSIONS
  The genome resource will be useful for developing markers for monitoring the pathogen population and might provide the basis for new approaches to fight Phytophthora and downy mildew pathogens by targeting core pathogenicity effectors.
authors.affiliation: Biodiversity and Climate Research Centre (BiK-F), Georg-Voigt-Str. 14-16, 60325, Frankfurt (Main), Germany. rahul.sharma@senckenberg.de.|Institute of Ecology, Evolution and Diversity, Goethe University, Max-von-Laue-Str. 9, 60323, Frankfurt (Main), Germany. rahul.sharma@senckenberg.de.|Senckenberg Gesellschaft für Naturforschung, Senckenberganlage 25, 60325, Frankfurt (Main), Germany. rahul.sharma@senckenberg.de.|Center for Integrative Fungal Research (IPF), Georg-Voigt-Str. 14-16, 60325, Frankfurt (Main), Germany. rahul.sharma@senckenberg.de.
authors.forename: Rahul
authors.initials: R
authors.lastname: Sharma
authors.affiliation: Biodiversity and Climate Research Centre (BiK-F), Georg-Voigt-Str. 14-16, 60325, Frankfurt (Main), Germany. Xiaojuan.Xia@senckenberg.de.|Institute of Ecology, Evolution and Diversity, Goethe University, Max-von-Laue-Str. 9, 60323, Frankfurt (Main), Germany. Xiaojuan.Xia@senckenberg.de.|Senckenberg Gesellschaft für Naturforschung, Senckenberganlage 25, 60325, Frankfurt (Main), Germany. Xiaojuan.Xia@senckenberg.de.
authors.forename: Xiaojuan
authors.initials: X
authors.lastname: Xia
authors.affiliation: The Sainsbury Laboratory, Norwich Research Park, Norwich, NR4 7UH, UK. lcanomo@ncsu.edu.|Present address: Department of Plant Pathology, North Carolina State University Raleigh, Raleigh, NC, 27695, USA. lcanomo@ncsu.edu.
authors.forename: Liliana M
authors.initials: LM
authors.lastname: Cano
authors.affiliation: Sainsbury Laboratory, University of Cambridge, Cambridge, CB2 1LR, UK. edouard.evangelisti@slcu.cam.ac.uk.
authors.forename: Edouard
authors.initials: E
authors.lastname: Evangelisti
authors.affiliation: Max Planck Institute for Plant Breeding Research, Carl von Linne´ Weg 10, Cologne, 50829, Germany. kemen@mpipz.mpg.de.
authors.forename: Eric
authors.initials: E
authors.lastname: Kemen
authors.affiliation: Department of Plant Pathology and Microbiology, University of California, Riverside, CA, 92521, USA. howard.judelson@ucr.edu.
authors.forename: Howard
authors.initials: H
authors.lastname: Judelson
authors.affiliation: Plant-Microbe Interactions, Department of Biology, Utrecht University, Padualaan 8, NL-3584 CH, Utrecht, The Netherlands. stan_oome@yahoo.com.
authors.forename: Stan
authors.initials: S
authors.lastname: Oome
authors.affiliation: Biosciences, University of Exeter, Stocker Road, Exeter, EX4 4QD, UK. C.M.Sambles@exeter.ac.uk.
authors.forename: Christine
authors.initials: C
authors.lastname: Sambles
authors.affiliation: Laboratory of Phytopathology, Wageningen University, Droevendaalsesteeg 1, NL-6708PB, Wageningen, The Netherlands. johan.vandenhoogen@wur.nl.
authors.forename: D Johan
authors.initials: DJ
authors.lastname: van den Hoogen
authors.affiliation: Department of Botany, Faculty of Science, Palacký University Olomouc, Šlechtitelů 11, 78371, Olomouc, Czech Republic. miloslav.kitner@gmail.com.
authors.forename: Miloslav
authors.initials: M
authors.lastname: Kitner
authors.affiliation: Plant-Microbe Interactions, Department of Biology, Utrecht University, Padualaan 8, NL-3584 CH, Utrecht, The Netherlands. J.Klein@uu.nl.
authors.forename: Joël
authors.initials: J
authors.lastname: Klein
authors.affiliation: Laboratory of Phytopathology, Wageningen University, Droevendaalsesteeg 1, NL-6708PB, Wageningen, The Netherlands. harold.meijer@wur.nl.
authors.forename: Harold J G
authors.initials: HJ
authors.lastname: Meijer
authors.affiliation: University of Hohenheim, Institute of Botany 210, D-70593, Stuttgart, Germany. spring@uni-hohenheim.de.
authors.forename: Otmar
authors.initials: O
authors.lastname: Spring
authors.affiliation: The Sainsbury Laboratory, Norwich Research Park, Norwich, NR4 7UH, UK. Joe.Win@sainsbury-laboratory.ac.uk.
authors.forename: Joe
authors.initials: J
authors.lastname: Win
authors.affiliation: University of Hohenheim, Institute of Botany 210, D-70593, Stuttgart, Germany. zipper@uni-hohenheim.de.
authors.forename: Reinhard
authors.initials: R
authors.lastname: Zipper
authors.affiliation: Merck-Stiftungsprofessur für Molekulare Biotechnologie, Fachbereich Biowissenschaften and Buchmann Institute for Molecular Life Sciences (BMLS), Goethe Universität Frankfurt, Max-von-Laue-Str. 9, 60438, Frankfurt am Main, Germany. h.bode@bio.uni-frankfurt.de.
authors.forename: Helge B
authors.initials: HB
authors.lastname: Bode
authors.affiliation: Laboratory of Phytopathology, Wageningen University, Droevendaalsesteeg 1, NL-6708PB, Wageningen, The Netherlands. francine.govers@wur.nl.
authors.forename: Francine
authors.initials: F
authors.lastname: Govers
authors.affiliation: The Sainsbury Laboratory, Norwich Research Park, Norwich, NR4 7UH, UK. sophien.kamoun@sainsbury-laboratory.ac.uk.
authors.forename: Sophien
authors.initials: S
authors.lastname: Kamoun
authors.affiliation: Sainsbury Laboratory, University of Cambridge, Cambridge, CB2 1LR, UK. Sebastian.Schornack@slcu.cam.ac.uk.
authors.forename: Sebastian
authors.initials: S
authors.lastname: Schornack
authors.affiliation: Biosciences, University of Exeter, Stocker Road, Exeter, EX4 4QD, UK. D.J.Studholme@exeter.ac.uk.
authors.forename: David J
authors.initials: DJ
authors.lastname: Studholme
authors.affiliation: Plant-Microbe Interactions, Department of Biology, Utrecht University, Padualaan 8, NL-3584 CH, Utrecht, The Netherlands. g.vandenackerveken@uu.nl.
authors.forename: Guido
authors.initials: G
authors.lastname: Van den Ackerveken
authors.affiliation: Biodiversity and Climate Research Centre (BiK-F), Georg-Voigt-Str. 14-16, 60325, Frankfurt (Main), Germany. marco.thines@senckenberg.de.|Institute of Ecology, Evolution and Diversity, Goethe University, Max-von-Laue-Str. 9, 60323, Frankfurt (Main), Germany. marco.thines@senckenberg.de.|Senckenberg Gesellschaft für Naturforschung, Senckenberganlage 25, 60325, Frankfurt (Main), Germany. marco.thines@senckenberg.de.|Center for Integrative Fungal Research (IPF), Georg-Voigt-Str. 14-16, 60325, Frankfurt (Main), Germany. marco.thines@senckenberg.de.|Integrative Fungal Research (IPF), Biodiversity and Climate Research Centre (BiK-F), Senckenberganlage 25, D-60325, Frankfurt am Main, Germany. marco.thines@senckenberg.de.
authors.forename: Marco
authors.initials: M
authors.lastname: Thines
mesh_terms: D005075:Biological Evolution; D005656:Fungal Proteins; D020869:Gene Expression Profiling; D016681:Genome, Fungal; D023281:Genomics / Q000379:methods; D006368:Helianthus / Q000382:microbiology*; D006579:Heterozygote; D018895:Microsatellite Repeats; D009868:Oomycetes / Q000145:classification / Q000235:genetics* / Q000378:metabolism; D010743:Phospholipids / Q000378:metabolism; D010802:Phylogeny; D010838:Phytophthora / Q000235:genetics; D011401:Promoter Regions, Genetic; D012091:Repetitive Sequences, Nucleic Acid; D064210:Secondary Metabolism; D015398:Signal Transduction; D037521:Virulence Factors / Q000235:genetics
chemical_list: D005656:Fungal Proteins; D010743:Phospholipids; D037521:Virulence Factors