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Mar. Drugs 2017, 15(6), 165; doi:10.3390/md15060165

Interpreting Microbial Biosynthesis in the Genomic Age: Biological and Practical Considerations

1
Pharmaceutical Sciences Division, School of Pharmacy, University of Wisconsin-Madison, Madison, WI 53705, USA
2
Department of Genetics, Department of Bacteriology, University of Wisconsin-Madison, Madison, WI 53706, USA
*
Author to whom correspondence should be addressed.
Academic Editors: Marcy J. Balunas, Amy L. Lane and Paul Long
Received: 28 April 2017 / Revised: 22 May 2017 / Accepted: 31 May 2017 / Published: 6 June 2017
(This article belongs to the Special Issue Connecting Marine Microbial Natural Products to Biosynthetic Pathways)
View Full-Text   |   Download PDF [2576 KB, uploaded 6 June 2017]   |  

Abstract

Genome mining has become an increasingly powerful, scalable, and economically accessible tool for the study of natural product biosynthesis and drug discovery. However, there remain important biological and practical problems that can complicate or obscure biosynthetic analysis in genomic and metagenomic sequencing projects. Here, we focus on limitations of available technology as well as computational and experimental strategies to overcome them. We review the unique challenges and approaches in the study of symbiotic and uncultured systems, as well as those associated with biosynthetic gene cluster (BGC) assembly and product prediction. Finally, to explore sequencing parameters that affect the recovery and contiguity of large and repetitive BGCs assembled de novo, we simulate Illumina and PacBio sequencing of the Salinispora tropica genome focusing on assembly of the salinilactam (slm) BGC. View Full-Text
Keywords: genome mining; genome sequencing; metagenomics; binning; biosynthesis; bioinformatics; biosynthetic gene clusters; secondary metabolism genome mining; genome sequencing; metagenomics; binning; biosynthesis; bioinformatics; biosynthetic gene clusters; secondary metabolism
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Miller, I.J.; Chevrette, M.G.; Kwan, J.C. Interpreting Microbial Biosynthesis in the Genomic Age: Biological and Practical Considerations. Mar. Drugs 2017, 15, 165.

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