The DOI matches its Crossref record; 6 of the 6 references it cites were found in a registry or an index.
SMURF: Genomic mapping of fungal secondary metabolite clusters
Open accessAbstract
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.
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Cites
Genomic sequence of the pathogenic and allergenic filamentous fungus Aspergillus fumigatus
Nierman, W. C., Pain, A., Anderson, M. J., Wortman, J. R., Kim, H. S., Arroyo, J., Berriman, M., Abe, K., Archer, D. B., Bermejo, C., et al. (2005) · Nature · doi:10.1038/nature04332 · Cited by 1,391
Self-citationGenomic Islands in the Pathogenic Filamentous Fungus Aspergillus fumigatus
Fedorova, N. D., Khaldi, N., Joardar, V. S., Maiti, R., Amedeo, P., Anderson, M. J., Crabtree, J., Silva, J. C., Badger, J. H., Albarraq, A., et al. (2008) · PLoS Genetics · doi:10.1371/journal.pgen.1000046 · Cited by 508 · cited 1×
“To answer this question, we further analyzed the genomes of the three closely related species A. fumigatus Af293, A. clavatus , and Neosartorya fischeri (Fedorova et al., 2008; Nierman et al., 2005).”
Self-citationSchrettl, M., Bignell, E., Kragl, C., Joechl, C., Rogers, T., Arst, H. N., Haynes, K., & Haas, H. (2004) · The Journal of Experimental Medicine · doi:10.1084/jem.20041242 · Cited by 493
Transcriptional Regulation of Chemical Diversity in Aspergillus fumigatus by LaeA
Perrin, R. M., Fedorova, N. D., Bok, J. W., Cramer, R. A., Wortman, J. R., Kim, H. S., Nierman, W. C., & Keller, N. P. (2007) · PLoS Pathogens · doi:10.1371/journal.ppat.0030050 · Cited by 352
Self-citationHydrolytic Polyketide Shortening by Ayg1p, a Novel Enzyme Involved in Fungal Melanin Biosynthesis
Fujii, I., Yasuoka, Y., Tsai, H.-F., Chang, Y. C., Kwon-Chung, K. J., & Ebizuka, Y. (2004) · Journal of Biological Chemistry · doi:10.1074/jbc.m406758200 · Cited by 105
Reeves, E. P., Reiber, K., Neville, C., Scheibner, O., Kavanagh, K., & Doyle, S. (2006) · The FEBS Journal · doi:10.1111/j.1742-4658.2006.05315.x · Cited by 70
Cited by
O'Connell, R. J., Thon, M. R., Hacquard, S., Amyotte, S. G., Kleemann, J., Torres, M. F., Damm, U., Buiate, E. A., Epstein, L., Alkan, N., et al. (2012) · Nature Genetics · doi:10.1038/ng.2372 · Cited by 1,047
Amaike, S., & Keller, N. P. (2011) · Annual Review of Phytopathology · doi:10.1146/annurev-phyto-072910-095221 · Cited by 668
Gan, P., Ikeda, K., Irieda, H., Narusaka, M., O'Connell, R. J., Narusaka, Y., Takano, Y., Kubo, Y., & Shirasu, K. (2013) · New Phytologist · doi:10.1111/nph.12085 · Cited by 379
A deep convolutional neural network approach for predicting phenotypes from genotypes
Ma, W., Qiu, Z., Song, J., Li, J., Cheng, Q., Zhai, J., & Ma, C. (2018) · Planta · doi:10.1007/s00425-018-2976-9 · Cited by 341
Inglis, D. O., Binkley, J., Skrzypek, M. S., Arnaud, M. B., Cerqueira, G. C., Shah, P., Wymore, F., Wortman, J. R., & Sherlock, G. (2013) · BMC Microbiology · doi:10.1186/1471-2180-13-91 · Cited by 293
Metadata
- Authors
- Khaldi, N., Seifuddin, F. T., Turner, G., Haft, D., Nierman, W. C., Wolfe, K. H., & Fedorova, N. D.
- Venue
- Fungal Genetics and Biology
- Publisher
- Elsevier BV
- Published
- 2010-09
- Volume
- 47
- Issue
- 9
- Pages
- 736-741
- ISSN
- 1087-1845 (ISSN-L)
- OpenAlex
- W2086953382
- Cited by
- 771
- References
- 6
- FWCI
- 19.68
- Type
- journal article
- Language
- en
- Open access
- green
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- Khaldi, N., Seifuddin, F. T., Turner, G., Haft, D., Nierman, W. C., Wolfe, K. H., & Fedorova, N. D. (2010). SMURF: Genomic mapping of fungal secondary metabolite clusters. Fungal Genetics and Biology. https://doi.org/10.1016/j.fgb.2010.06.003
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