title: Sex and parasites: genomic and transcriptomic analysis of Microbotryum lychnidis-dioicae, the biotrophic and plant-castrating anther smut fungus.
abstract: BACKGROUND
  The genus Microbotryum includes plant pathogenic fungi afflicting a wide variety of hosts with anther smut disease. Microbotryum lychnidis-dioicae infects Silene latifolia and replaces host pollen with fungal spores, exhibiting biotrophy and necrosis associated with altering plant development.
  
  
  RESULTS
  We determined the haploid genome sequence for M. lychnidis-dioicae and analyzed whole transcriptome data from plant infections and other stages of the fungal lifecycle, revealing the inventory and expression level of genes that facilitate pathogenic growth. Compared to related fungi, an expanded number of major facilitator superfamily transporters and secretory lipases were detected; lipase gene expression was found to be altered by exposure to lipid compounds, which signaled a switch to dikaryotic, pathogenic growth. In addition, while enzymes to digest cellulose, xylan, xyloglucan, and highly substituted forms of pectin were absent, along with depletion of peroxidases and superoxide dismutases that protect the fungus from oxidative stress, the repertoire of glycosyltransferases and of enzymes that could manipulate host development has expanded. A total of 14% of the genome was categorized as repetitive sequences. Transposable elements have accumulated in mating-type chromosomal regions and were also associated across the genome with gene clusters of small secreted proteins, which may mediate host interactions.
  
  
  CONCLUSIONS
  The unique absence of enzyme classes for plant cell wall degradation and maintenance of enzymes that break down components of pollen tubes and flowers provides a striking example of biotrophic host adaptation.
authors.affiliation: Department of Biology, Program on Disease Evolution, University of Louisville, Louisville, KY, 40292, USA. michael.perlin@louisville.edu.
authors.forename: Michael H
authors.initials: MH
authors.lastname: Perlin
authors.affiliation: Institut National de la Recherche Agronomique (INRA), Unité de Recherche Génomique Info (URGI), Versailles, France. joelle.amselem@versailles.inra.fr.|Institut National de la Recherche Agronomique (INRA), Biologie et gestion des risques en agriculture (BIOGER), Thiverval-Grignon, France. joelle.amselem@versailles.inra.fr.
authors.forename: Joelle
authors.initials: J
authors.lastname: Amselem
authors.affiliation: Ecologie, Systématique et Evolution, Bâtiment 360, Université Paris-Sud, F-91405, Orsay, France. eric.fonta@gmail.com.|CNRS, F-91405, Orsay, France. eric.fonta@gmail.com.
authors.forename: Eric
authors.initials: E
authors.lastname: Fontanillas
authors.affiliation: Department of Biology, Program on Disease Evolution, University of Louisville, Louisville, KY, 40292, USA. susan.toh@louisville.edu.
authors.forename: Su San
authors.initials: SS
authors.lastname: Toh
authors.affiliation: Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA. zchen@broadinstitute.org.
authors.forename: Zehua
authors.initials: Z
authors.lastname: Chen
authors.affiliation: Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA. goldberg@hsph.harvard.edu.
authors.forename: Jonathan
authors.initials: J
authors.lastname: Goldberg
authors.affiliation: INRA, UMR 1136, Interactions Arbres-Microorganismes, Champenoux, France. duplessi@nancy.inra.fr.|UMR 1136, Université de Lorraine, Interactions Arbres-Microorganismes, Vandoeuvre-lès-Nancy, France. duplessi@nancy.inra.fr.
authors.forename: Sebastien
authors.initials: S
authors.lastname: Duplessis
authors.affiliation: Centre National de la Recherche Scientifique (CNRS), UMR7257, Université Aix-Marseille, 13288, Marseille, France. bernard.henrissat@afmb.univ-mrs.fr.|Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia. bernard.henrissat@afmb.univ-mrs.fr.
authors.forename: Bernard
authors.initials: B
authors.lastname: Henrissat
authors.affiliation: Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA. stowey@broadinstitute.org.
authors.forename: Sarah
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authors.lastname: Young
authors.affiliation: Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA. qiandong_zeng@hotmail.com.
authors.forename: Qiandong
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authors.lastname: Zeng
authors.affiliation: Centre for Genomic Regulation (CRG), Barcelona, Spain. gabriela.aguileta@crg.eu.
authors.forename: Gabriela
authors.initials: G
authors.lastname: Aguileta
authors.affiliation: Ecologie, Systématique et Evolution, Bâtiment 360, Université Paris-Sud, F-91405, Orsay, France. elsa.petit@u-psud.fr.|CNRS, F-91405, Orsay, France. elsa.petit@u-psud.fr.|Centre National de la Recherche Scientifique (CNRS), UMR7257, Université Aix-Marseille, 13288, Marseille, France. elsa.petit@u-psud.fr.
authors.forename: Elsa
authors.initials: E
authors.lastname: Petit
authors.affiliation: Ecologie, Systématique et Evolution, Bâtiment 360, Université Paris-Sud, F-91405, Orsay, France. helene.badouin@u-psud.fr.|CNRS, F-91405, Orsay, France. helene.badouin@u-psud.fr.
authors.forename: Helene
authors.initials: H
authors.lastname: Badouin
authors.affiliation: Department of Biology, Program on Disease Evolution, University of Louisville, Louisville, KY, 40292, USA. jared.andrews07@gmail.com.
authors.forename: Jared
authors.initials: J
authors.lastname: Andrews
authors.affiliation: Department of Biology, Program on Disease Evolution, University of Louisville, Louisville, KY, 40292, USA. dominique.razeeq@louisville.edu.
authors.forename: Dominique
authors.initials: D
authors.lastname: Razeeq
authors.affiliation: Centre for Genomic Regulation (CRG), Barcelona, Spain. toni.gabaldon@crg.eu.|Universitat Pompeu Fabra (UPF), Barcelona, Spain. toni.gabaldon@crg.eu.|Institució Catalana d'Estudis Avançats (ICREA), Barcelona, Spain. toni.gabaldon@crg.eu.
authors.forename: Toni
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authors.lastname: Gabaldón
authors.affiliation: Institut National de la Recherche Agronomique (INRA), Unité de Recherche Génomique Info (URGI), Versailles, France. Hadi.Quesneville@versailles.inra.fr.
authors.forename: Hadi
authors.initials: H
authors.lastname: Quesneville
authors.affiliation: Ecologie, Systématique et Evolution, Bâtiment 360, Université Paris-Sud, F-91405, Orsay, France. tatiana.giraud@u-psud.fr.|CNRS, F-91405, Orsay, France. tatiana.giraud@u-psud.fr.
authors.forename: Tatiana
authors.initials: T
authors.lastname: Giraud
authors.affiliation: Department of Biology, Amherst College, Amherst, MA, 01002, USA. mhood@amherst.edu.
authors.forename: Michael E
authors.initials: ME
authors.lastname: Hood
authors.affiliation: Department of Biology, Program on Disease Evolution, University of Louisville, Louisville, KY, 40292, USA. david.schultz@louisville.edu.
authors.forename: David J
authors.initials: DJ
authors.lastname: Schultz
authors.affiliation: Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA. cuomo@broadinstitute.org.
authors.forename: Christina A
authors.initials: CA
authors.lastname: Cuomo
mesh_terms: D000818:Animals; D002874:Chromosome Mapping / Q000379:methods; D005658:Fungi / Q000235:genetics*; D020869:Gene Expression Profiling / Q000379:methods; D016681:Genome, Fungal / Q000235:genetics*; D006790:Host-Parasite Interactions / Q000235:genetics; D008049:Lipase / Q000235:genetics; D010271:Parasites / Q000235:genetics*; D010544:Peroxidases / Q000235:genetics; D010935:Plant Diseases / Q000382:microbiology*; D010944:Plants / Q000382:microbiology*; D029751:Silene / Q000382:microbiology*; D013482:Superoxide Dismutase / Q000235:genetics; D059467:Transcriptome / Q000235:genetics*
chemical_list: D010544:Peroxidases; D013482:Superoxide Dismutase; D008049:Lipase