SMURF: Genomic mapping of fungal secondary metabolite clusters

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 sequ...

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Bibliographic Details
Published in:Fungal genetics and biology 2010-09, Vol.47 (9), p.736-741
Main Authors: Khaldi, Nora, Seifuddin, Fayaz T., Turner, Geoff, Haft, Daniel, Nierman, William C., Wolfe, Kenneth H., Fedorova, Natalie D.
Format: Article
Language:English
Subjects:
Antibiotics
Aspergillus
Chromosome Mapping - methods
Cluster Analysis
Filamentous fungi
Fungal Proteins - genetics
Fungal Proteins - metabolism
Fungi - chemistry
Fungi - enzymology
Fungi - genetics
Fungi - metabolism
Genome annotation
Genomics
Internet
NRPS
PKS
Polyketides
Prenyltransferases
Secondary metabolism
Sensitivity and Specificity
Software
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Summary: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.
ISSN:1087-1845
1096-0937
DOI:10.1016/j.fgb.2010.06.003