title: The evolutionary history of cytochrome P450 genes in four filamentous Ascomycetes.
abstract: BACKGROUND
  The Cytochrome P450 system is important in fungal evolution for adapting to novel ecological niches. To elucidate the evolutionary process of cytochrome P450 genes in fungi with different life styles, we studied the patterns of gene gains and losses in the genomes of four filamentous Ascomycetes, including two saprotrophs (Aspergillus nidulans (AN) and Neurospora crassa (NC)) and two plant pathogens (Fusarium graminearum (FG) and Magnaporthe grisea (MG)).
  
  
  RESULTS
  A total of 376 P450 genes were assigned to 168 families according to standard nomenclature. On average, only 1 to 2 genes per family were in each genome. To resolve conflicting results between different clustering analyses and standard family designation, a higher order relationship was formulated. 376 genes were clustered into 115 clans. Subsequently a novel approach based on parsimony was developed to build the evolutionary models. Based on these analyses, a core of 30 distinct clans of P450s was defined. The core clans experienced contraction in all four fungal lineages while new clans expanded in all with exception of NC. MG experienced more genes and clans gains compared to the other fungi. Parsimonious analyses unanimously supported one species topology for the four fungi.
  
  
  CONCLUSIONS
  The four studied fungi exhibit unprecedented diversity in their P450omes in terms of coding sequence, intron-exon structures and genome locations, suggesting a complicated evolutionary history of P450s in filamentous Ascomycetes. Clan classification and a novel strategy were developed to study evolutionary history. Contraction of core clans and expansion of novel clans were identified. The exception was the NC lineage, which exhibited pure P450 gene loss.
authors.affiliation: Center for Integrated Fungal Research, North Carolina State University, Raleigh, NC 27695, USA. dengj@email.unc.edu <dengj@email.unc.edu>
authors.forename: Jixin
authors.initials: J
authors.lastname: Deng
authors.forename: Ignazio
authors.initials: I
authors.lastname: Carbone
authors.forename: Ralph A
authors.initials: RA
authors.lastname: Dean
mesh_terms: D020816:Amino Acid Motifs; D000595:Amino Acid Sequence; D001203:Ascomycota / Q000201:enzymology / Q000235:genetics*; D001233:Aspergillus nidulans / Q000201:enzymology / Q000235:genetics; D017124:Conserved Sequence; D003577:Cytochrome P-450 Enzyme System / Q000235:genetics*; D019143:Evolution, Molecular; D005091:Exons; D005670:Fusarium / Q000201:enzymology / Q000235:genetics; D020440:Gene Duplication; D005800:Genes, Fungal; D007438:Introns; D020082:Magnaporthe / Q000201:enzymology / Q000235:genetics; D005810:Multigene Family; D009492:Neurospora crassa / Q000201:enzymology / Q000235:genetics; D010802:Phylogeny
chemical_list: D003577:Cytochrome P-450 Enzyme System