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ARS Home » Midwest Area » Peoria, Illinois » National Center for Agricultural Utilization Research » Mycotoxin Prevention and Applied Microbiology Research » Research » Publications at this Location » Publication #291828
Title: Comparative analysis of 35 basidiomycete genomes reveals diversity and uniqueness of the phylum

Author
item RILEY, ROBERT - Department Of Energy Joint Genome
item SALAMOV, ASAF - Department Of Energy Joint Genome
item OTILLAR, ROBERT - Department Of Energy Joint Genome
item FAGNAN, KIRSTEN - University Of California
item BOUSSAU, BASTIEN - University Of California
item Brown, Daren
item HENRISSAT, BERNARD - Aix-Marseille University
item LEVASSEUR, ANTHONY - Institut National De La Recherche Agronomique (INRA)
item BLANCHETTE, ROBERT - University Of Minnesota
item MORIN, EMMANUELLE - Institut National De La Recherche Agronomique (INRA)

Submitted to: Fungal Genetics Conference
Publication Type: Abstract Only
Publication Acceptance Date: 3/17/2013
Publication Date: 3/17/2013
Citation: Riley, R., Salamov, A., Otillar, R., Fagnan, K., Boussau, B., Brown, D.W., Henrissat, B., Levasseur, A., Blanchette, R.A., Morin, E. 2013. Comparative analysis of 35 basidiomycete genomes reveals diversity and uniqueness of the phylum. Fungal Genetics Conference/Asilomar.

Interpretive Summary:

Technical Abstract: Fungi of the phylum Basidiomycota (basidiomycetes), make up some 37% of the described fungi, and are important in forestry, agriculture, medicine, and bioenergy. This diverse phylum includes symbionts, pathogens, and saprobes including wood decaying fungi. To better understand the diversity of this phylum we compared the genomes of 35 basidiomycete fungi including 6 newly sequenced genomes. The genomes of basidiomycetes span extremes of genome size, gene number, and repeat content. A phylogenetic tree of Basidiomycota was generated using the Phyldog method, which uses all available protein sequence data to simultaneously infer gene and species trees. Analysis of core genes reveals that some 48% of basidiomycete proteins are unique to the phylum with nearly half of those (22%) comprised of proteins found in only one organism. Phylogenetic patterns of plant biomass-degrading genes suggest a continuum rather than a sharp dichotomy between the white rot and brown rot modes of wood decay among the members of Agaricomycotina subphylum. There is a correlation of the profile of certain gene families to nutritional mode in Agaricomycotina. Based on phylogenetically-informed principal component analysis (PCA) of such profiles, we predict Botryobasidium botryosum and Jaapia argillacea as white rots, and find the predictions to be supported by experiment. Analysis of the rate of discovery of proteins with no, or few, homologs suggests the high value of continued sequencing of basidiomycete fungi.