title: SMURF: Genomic mapping of fungal secondary metabolite clusters.
abstract: Fungi produce an impressive array of secondary metabolites (SMs) including mycotoxins, antibiotics and pharmaceuticals. The genes responsible for their biosynthesis, export, and transcriptional regulation are often found in contiguous gene clusters. To facilitate annotation of these clusters in sequenced fungal genomes, we developed the web-based software SMURF (www.jcvi.org/smurf/) to systematically predict clustered SM genes based on their genomic context and domain content. We applied SMURF to catalog putative clusters in 27 publicly available fungal genomes. Comparison with genetically characterized clusters from six fungal species showed that SMURF accurately recovered all clusters and detected additional potential clusters. Subsequent comparative analysis revealed the striking biosynthetic capacity and variability of the fungal SM pathways and the correlation between unicellularity and the absence of SMs. Further genetics studies are needed to experimentally confirm these clusters.
authors.affiliation: Smurfit Institute of Genetics, Trinity College, Dublin, Ireland.
authors.forename: Nora
authors.initials: N
authors.lastname: Khaldi
authors.forename: Fayaz T
authors.initials: FT
authors.lastname: Seifuddin
authors.forename: Geoff
authors.initials: G
authors.lastname: Turner
authors.forename: Daniel
authors.initials: D
authors.lastname: Haft
authors.forename: William C
authors.initials: WC
authors.lastname: Nierman
authors.forename: Kenneth H
authors.initials: KH
authors.lastname: Wolfe
authors.forename: Natalie D
authors.initials: ND
authors.lastname: Fedorova
mesh_terms: D002874:Chromosome Mapping / Q000379:methods*; D016000:Cluster Analysis; D005656:Fungal Proteins / Q000235:genetics / Q000378:metabolism; D005658:Fungi / Q000737:chemistry / Q000201:enzymology / Q000235:genetics* / Q000378:metabolism*; D023281:Genomics; D020407:Internet; D012680:Sensitivity and Specificity; D012984:Software
chemical_list: D005656:Fungal Proteins