title: The genome of the basal agaricomycete Xanthophyllomyces dendrorhous provides insights into the organization of its acetyl-CoA derived pathways and the evolution of Agaricomycotina.
abstract: BACKGROUND
  Xanthophyllomyces dendrorhous is a basal agaricomycete with uncertain taxonomic placement, known for its unique ability to produce astaxanthin, a carotenoid with antioxidant properties. It was the aim of this study to elucidate the organization of its CoA-derived pathways and to use the genomic information of X. dendrorhous for a phylogenomic investigation of the Basidiomycota.
  
  
  RESULTS
  The genome assembly of a haploid strain of Xanthophyllomyces dendrorhous revealed a genome of 19.50 Megabases with 6385 protein coding genes. Phylogenetic analyses were conducted including 48 fungal genomes. These revealed Ustilaginomycotina and Agaricomycotina as sister groups. In the latter a well-supported sister-group relationship of two major orders, Polyporales and Russulales, was inferred. Wallemia occupies a basal position within the Agaricomycotina and X. dendrorhous represents the basal lineage of the Tremellomycetes, highlighting that the typical tremelloid parenthesomes have either convergently evolved in Wallemia and the Tremellomycetes, or were lost in the Cystofilobasidiales lineage. A detailed characterization of the CoA-related pathways was done and all genes for fatty acid, sterol and carotenoid synthesis have been assigned.
  
  
  CONCLUSIONS
  The current study ascertains that Wallemia with tremelloid parenthesomes is the most basal agaricomycotinous lineage and that Cystofilobasidiales without tremelloid parenthesomes are deeply rooted within Tremellomycetes, suggesting that parenthesomes at septal pores might be the core synapomorphy for the Agaricomycotina. Apart from evolutionary insights the genome sequence of X. dendrorhous will facilitate genetic pathway engineering for optimized astaxanthin or oxidative alcohol production.
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: Department of Molecular Bioscience, J.W. Goethe University, Max-von-Laue-Str. 9, 60323, Frankfurt (Main), Germany. gassel@bio.uni-frankfurt.de.
authors.forename: Sören
authors.initials: S
authors.lastname: Gassel
authors.affiliation: Department of Molecular Bioscience, J.W. Goethe University, Max-von-Laue-Str. 9, 60323, Frankfurt (Main), Germany. s.steiger@em.uni-frankfurt.de.
authors.forename: Sabine
authors.initials: S
authors.lastname: Steiger
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: Institute of Evolution and Ecology, University of Tübingen, Auf der Morgenstelle 28, 72076, Tübingen, Germany. robert.bauer@uni-tuebingen.de.
authors.forename: Robert
authors.initials: R
authors.lastname: Bauer
authors.affiliation: Department of Molecular Bioscience, J.W. Goethe University, Max-von-Laue-Str. 9, 60323, Frankfurt (Main), Germany. sandmann@bio.uni-frankfurt.de.
authors.forename: Gerhard
authors.initials: G
authors.lastname: Sandmann
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.
authors.forename: Marco
authors.initials: M
authors.lastname: Thines
mesh_terms: D000105:Acetyl Coenzyme A / Q000378:metabolism*; D000363:Agaricales / Q000235:genetics* / Q000378:metabolism; D001487:Basidiomycota / Q000235:genetics* / Q000378:metabolism*; D019143:Evolution, Molecular; D005656:Fungal Proteins / Q000235:genetics / Q000378:metabolism; D016681:Genome, Fungal; D053858:Metabolic Networks and Pathways; D010802:Phylogeny; D064210:Secondary Metabolism / Q000235:genetics
chemical_list: D005656:Fungal Proteins; D000105:Acetyl Coenzyme A