Wang, J.Y., Pausch, P. & Doudna, J.A. Structural biology of CRISPR–Cas immunity and genome editing enzymes. Nat. Rev. Microbiol. 20, 641–656 (2022).
Xu, X. & Qi, L. S. A CRISPR–dCas toolbox for genetic engineering and synthetic biology. J. Mol. Biol. 431, 34–47 (2019).
Google Scholar
Adli, M. The CRISPR tool kit for genome editing and beyond. Nat. Commun. 9, 1911 (2018).
Google Scholar
Jinek, M. et al. A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity. Science 337, 816–821 (2012).
Google Scholar
Bikard, D. et al. Programmable repression and activation of bacterial gene expression using an engineered CRISPR–Cas system. Nucleic Acids Res. 41, 7429–7437 (2013).
Google Scholar
Schultzhaus, Z., Wang, Z. & Stenger, D. CRISPR-based enrichment strategies for targeted sequencing. Biotechnol. Adv. 46, 107672 (2021).
Google Scholar
Feldman, D. et al. CloneSifter: enrichment of rare clones from heterogeneous cell populations. BMC Biol. 18, 177 (2020).
Google Scholar
Li, S. et al. CRISPRi chemical genetics and comparative genomics identify genes mediating drug potency in Mycobacterium tuberculosis. Nat. Microbiol. 7, 766–779 (2022).
Google Scholar
Jost, M. et al. Combined CRISPRi/a-based chemical genetic screens reveal that rigosertib is a microtubule-destabilizing agent. Mol. Cell 68, 210–223 (2017).
Google Scholar
Owen, J. G. et al. Multiplexed metagenome mining using short DNA sequence tags facilitates targeted discovery of epoxyketone proteasome inhibitors. Proc. Natl Acad. Sci. USA 112, 4221–4226 (2015).
Google Scholar
Jiang, W. et al. Cas9-Assisted Targeting of CHromosome segments CATCH enables one-step targeted cloning of large gene clusters. Nat. Commun. 6, 8101 (2015).
Google Scholar
Lee, N. C., Larionov, V. & Kouprina, N. Highly efficient CRISPR/Cas9-mediated TAR cloning of genes and chromosomal loci from complex genomes in yeast. Nucleic Acids Res. 43, e55 (2015).
Google Scholar
Wang, H. et al. ExoCET: exonuclease in vitro assembly combined with RecET recombination for highly efficient direct DNA cloning from complex genomes. Nucleic Acids Res. 46, e28 (2018).
Google Scholar
Eid, J. et al. Real-time DNA sequencing from single polymerase molecules. Science 323, 133–138 (2009).
Google Scholar
Burian, J. & Thompson, C. J. Regulatory genes coordinating antibiotic-induced changes in promoter activity and early transcriptional termination of the mycobacterial intrinsic resistance gene whiB7. Mol. Microbiol. 107, 402–415 (2018).
Google Scholar
Pierce, J. C., Sauer, B. & Sternberg, N. A positive selection vector for cloning high molecular weight DNA by the bacteriophage P1 system: improved cloning efficacy. Proc. Natl Acad. Sci. USA 89, 2056–2060 (1992).
Google Scholar
Gay, P., Le Coq, D., Steinmetz, M., Berkelman, T. & Kado, C. I. Positive selection procedure for entrapment of insertion sequence elements in gram-negative bacteria. J. Bacteriol. 164, 918–921 (1985).
Google Scholar
Brady, S. F. Construction of soil environmental DNA cosmid libraries and screening for clones that produce biologically active small molecules. Nat. Protoc. 2, 1297–1305 (2007).
Google Scholar
Haley, J. D. in New Nucleic Acid Techniques (ed Walker, J. M.) 257–283 (Humana Press, 1988).
Blin, K. et al. antiSMASH 6.0: improving cluster detection and comparison capabilities. Nucleic Acids Res. 49, W29–W35 (2021).
Google Scholar
Tesson, F. et al. Systematic and quantitative view of the antiviral arsenal of prokaryotes. Nat. Commun. 13, 2561 (2022).
Google Scholar
Calvo-Villamanan, A. et al. On-target activity predictions enable improved CRISPR–dCas9 screens in bacteria. Nucleic Acids Res. 48, e64 (2020).
Google Scholar
Wang, W., Zheng, G. & Lu, Y. Recent advances in strategies for the cloning of natural product biosynthetic gene clusters. Front. Bioeng. Biotechnol. 9, 692797 (2021).
Google Scholar
Picelli, S. et al. Tn5 transposase and tagmentation procedures for massively scaled sequencing projects. Genome Res. 24, 2033–2040 (2014).
Google Scholar
Athanasopoulou, K., Boti, M. A., Adamopoulos, P. G., Skourou, P. C. & Scorilas, A. Third-generation sequencing: the spearhead towards the radical transformation of modern genomics. Life (Basel) 12, 30 (2021).
Sternberg, N., Ruether, J. & deRiel, K. Generation of a 50,000-member human DNA library with an average DNA insert size of 75-100 kbp in a bacteriophage P1 cloning vector. New Biol. 2, 151–162 (1990).
Google Scholar
Zaburannyi, N., Rabyk, M., Ostash, B., Fedorenko, V. & Luzhetskyy, A. Insights into naturally minimised Streptomyces albus J1074 genome. BMC Genomics 15, 97 (2014).
Google Scholar
Wu, C., Shang, Z., Lemetre, C., Ternei, M. A. & Brady, S. F. Cadasides, Calcium-dependent acidic lipopeptides from the soil metagenome that are active against multidrug-resistant bacteria. J. Am. Chem. Soc. 141, 3910–3919 (2019).
Google Scholar
Jiang, Y. et al. Multigene editing in the Escherichia coli genome via the CRISPR–Cas9 system. Appl. Environ. Microbiol. 81, 2506–2514 (2015).
Google Scholar
Chang, A. C. & Cohen, S. N. Construction and characterization of amplifiable multicopy DNA cloning vehicles derived from the P15A cryptic miniplasmid. J. Bacteriol. 134, 1141–1156 (1978).
Google Scholar
Qi, L. S. et al. Repurposing CRISPR as an RNA-guided platform for sequence-specific control of gene expression. Cell 152, 1173–1183 (2013).
Google Scholar
Cohen, S. N., Chang, A. C., Boyer, H. W. & Helling, R. B. Construction of biologically functional bacterial plasmids in vitro. Proc. Natl Acad. Sci. USA 70, 3240–3244 (1973).
Google Scholar
Doench, J. G. et al. Rational design of highly active sgRNAs for CRISPR–Cas9-mediated gene inactivation. Nat. Biotechnol. 32, 1262–1267 (2014).
Google Scholar
Chan, W. T., Verma, C. S., Lane, D. P. & Gan, S. K. A comparison and optimization of methods and factors affecting the transformation of Escherichia coli. Biosci. Rep. 33, e00086 (2013).
Google Scholar
Kolmogorov, M. et al. metaFlye: scalable long-read metagenome assembly using repeat graphs. Nat. Methods 17, 1103–1110 (2020).
Google Scholar
Blin, K. et al. antiSMASH 5.0: updates to the secondary metabolite genome mining pipeline. Nucleic Acids Res. 47, W81–W87 (2019).
Google Scholar
Shen, W., Le, S., Li, Y. & Hu, F. SeqKit: a cross-platform and ultrafast toolkit for FASTA/Q file manipulation. PLoS ONE 11, e0163962 (2016).
Google Scholar
Rognes, T., Flouri, T., Nichols, B., Quince, C. & Mahe, F. VSEARCH: a versatile open source tool for metagenomics. PeerJ 4, e2584 (2016).
Google Scholar
Okonechnikov, K., Golosova, O., Fursov, M. & UGENE Team. Unipro UGENE: a unified bioinformatics toolkit. Bioinformatics 28, 1166–1167 (2012).
Google Scholar