TY  - JOUR
TI  - A Rapid and Cost-Effective Pipeline to Identify and Capture BGCs From Bacterial Draft Genomes
AU  - Campos-Magaña, Marco A.
AU  - Martins dos Santos, Vitor A. P.
AU  - Garcia-Morales, Luis 
VL  - 15
IS  - 24
PY  - 2025
DA  - 2025/12/20
SP  - e5549
C1  - Bio-protocol 2025;15:e5549
DO  - 10.21769/BioProtoc.5549
UR  - https://doi.org/10.21769/BioProtoc.5549
AB  - The exploration of microbial genomes through next-generation sequencing (NGS) and genome mining has transformed the discovery of natural products, revealing an immense reservoir of previously untapped chemical diversity. Bacteria remain a prolific source of specialized metabolites with potential applications in medicine and biotechnology. Here, we present a protocol to access novel biosynthetic gene clusters (BGCs) that encode natural products from soil bacteria. The protocol uses a combination of Oxford Nanopore Technology (ONT) sequencing, de novo genome assembly, antiSMASH for BGC identification, and transformation-associated recombination (TAR) for cloning the BGCs. We used this protocol to allow the detection of large BGCs at a relatively fast and low-cost DNA sequencing. The protocol can be applied to diverse bacteria, provided that sufficient high-molecular-weight DNA can be obtained for long-read sequencing. Moreover, this protocol enables subsequent cloning of uncharacterized BGCs into a genome engineering-ready vector, illustrating the capabilities of this powerful and cost-effective strategy.
KW  - Biosynthetic gene clusters
KW  - Genome mining
KW  - Transformation-associated recombination cloning
KW  - Myxobacteria
KW  - Microbial genomics
KW  - Oxford nanopore sequencing
KW  - AntiSMASH
JF  - Bio-protocol
SN  - 2331-8325
PB  - Bio-protocol LLC.
BIO101  - False