title: Comparative Genomics Including the Early-Diverging Smut Fungus Ceraceosorus bombacis Reveals Signatures of Parallel Evolution within Plant and Animal Pathogens of Fungi and Oomycetes.
abstract: Ceraceosorus bombacis is an early-diverging lineage of smut fungi and a pathogen of cotton trees (Bombax ceiba). To study the evolutionary genomics of smut fungi in comparison with other fungal and oomycete pathogens, the genome of C. bombacis was sequenced and comparative genomic analyses were performed. The genome of 26.09 Mb encodes for 8,024 proteins, of which 576 are putative-secreted effector proteins (PSEPs). Orthology analysis revealed 30 ortholog PSEPs among six Ustilaginomycotina genomes, the largest groups of which are lytic enzymes, such as aspartic peptidase and glycoside hydrolase. Positive selection analyses revealed the highest percentage of positively selected PSEPs in C. bombacis compared with other Ustilaginomycotina genomes. Metabolic pathway analyses revealed the absence of genes encoding for nitrite and nitrate reductase in the genome of the human skin pathogen Malassezia globosa, but these enzymes are present in the sequenced plant pathogens in smut fungi. Interestingly, these genes are also absent in cultivable oomycete animal pathogens, while nitrate reductase has been lost in cultivable oomycete plant pathogens. Similar patterns were also observed for obligate biotrophic and hemi-biotrophic fungal and oomycete pathogens. Furthermore, it was found that both fungal and oomycete animal pathogen genomes are lacking cutinases and pectinesterases. Overall, these findings highlight the parallel evolution of certain genomic traits, revealing potential common evolutionary trajectories among fungal and oomycete pathogens, shaping the pathogen genomes according to their lifestyle.
authors: Biodiversity and Climate Research Centre (BiK-F), Frankfurt (Main), Germany Department for Biological Sciences, Institute of Ecology, Evolution and Diversity, Goethe University, Frankfurt (Main), Germany Senckenberg Gesellschaft für Naturforschung, Frankfurt (Main), Germany Cluster for Integrative Fungal Research (IPF), Frankfurt (Main), Germany.
authors: Rahul
authors: R
authors: Sharma
authors: Biodiversity and Climate Research Centre (BiK-F), Frankfurt (Main), Germany Department for Biological Sciences, Institute of Ecology, Evolution and Diversity, Goethe University, Frankfurt (Main), Germany Senckenberg Gesellschaft für Naturforschung, Frankfurt (Main), Germany.
authors: Xiaojuan
authors: X
authors: Xia
authors: Plant Evolutionary Ecology, Institute of Evolution and Ecology, University of Tübingen, Germany.
authors: Kai
authors: K
authors: Riess
authors: Plant Evolutionary Ecology, Institute of Evolution and Ecology, University of Tübingen, Germany.
authors: Robert
authors: R
authors: Bauer
authors: Biodiversity and Climate Research Centre (BiK-F), Frankfurt (Main), Germany Department for Biological Sciences, Institute of Ecology, Evolution and Diversity, Goethe University, Frankfurt (Main), Germany Senckenberg Gesellschaft für Naturforschung, Frankfurt (Main), Germany Cluster for Integrative Fungal Research (IPF), Frankfurt (Main), Germany marco.thines@senckenberg.de.
authors: Marco
authors: M
authors: Thines
mesh_terms: D001487:Basidiomycota / Q000145:classification / Q000235:genetics* / Q000254:growth & development / Q000378:metabolism; D019143:Evolution, Molecular; D005656:Fungal Proteins / Q000235:genetics; D005800:Genes, Fungal; D016681:Genome, Fungal; D023281:Genomics; D025301:Hyphae / Q000235:genetics; D053858:Metabolic Networks and Pathways / Q000235:genetics; D009868:Oomycetes / Q000235:genetics*; D010802:Phylogeny; D012641:Selection, Genetic
chemical_list: D005656:Fungal Proteins
keywords: Ustilaginomycotina; comparative genomics; convergent evolution; evolutionary biology; metabolic pathways; positive selection; smut fungi