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Original molecular cloning vectors were plasmids such as the pBR232, were meant to clone single genes, and were based in multicopy plasmids that have low stringency control of the copy number. Later on with the development of genomics, larger insert vectors were required for the assembly of repeated regions and in general to pair-end the individual shotgun reads. Bacterial artificial chromosomes (BAC) were developed based in the large single-copy plasmids of the F group (Shizuya et al. 1992). These can be propagated in Escherichia coli with inserts larger than 300 Kbp. BACs were used by Beja and coworkers in one of the first and more influential papers of the early development of metagenomics in which the existence of an energy-generating rhodopsin was found in a proteobacterial BAC clone (Beja et al. 2000). However, BACs are laborious to generate and do not work well with the limited amount of DNA that normally is available for...
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References
Beja O, Suzuki MT, et al. Construction and analysis of bacterial artificial chromosome libraries from a marine microbial assemblage. Environ Microbiol. 2000;2(5):516–29.
DeLong EF, Preston CM, et al. Community genomics among stratified microbial assemblages in the ocean’s interior. Science. 2006;311(5760):496–503.
Feingersch R, Beja O. Bias in assessments of marine SAR11 biodiversity in environmental fosmid and BAC libraries? ISME J. 2009;J3(10):1117–9.
Garcia-Heredia I, Martin-Cuadrado AB, et al. Reconstructing viral genomes from the environment using fosmid clones: the case of haloviruses. PLoS One. 2012;7(3):30.
Ghai R, Martin-Cuadrado A, et al. Metagenome of the Mediterranean deep chlorophyll maximum studied by direct and fosmid library 454 pyrosequencing. ISME J. 2010;9:1154–1166.
Huang Y, Lai X, et al. Characterization of a deep-sea sediment metagenomic clone that produces water-soluble melanin in Escherichia coli. Mar Biotechnol. 2009;11(1):124–31.
Iverson V, Morris RM, et al. Untangling genomes from metagenomes: revealing an uncultured class of marine Euryarchaeota. Science. 2012;335(6068):587–90.
Kim UJ, Shizuya H, et al. Stable propagation of cosmid sized human DNA inserts in an F factor based vector. Nucleic Acids Res. 1992;20(5):1083–5.
Manrao EA, Derrington IM, et al. Reading DNA at single-nucleotide resolution with a mutant MspA nanopore and phi29 DNA polymerase. Nat Biotechnol. 2012;30(4):349–53.
Martin-Cuadrado AB, Lopez-Garcia P, et al. Metagenomics of the deep Mediterranean, a warm bathypelagic habitat. PLoS One. 2007;2(9):e914.
Martin-Cuadrado AB, Rodriguez-Valera F, et al. Hindsight in the relative abundance, metabolic potential and genome dynamics of uncultivated marine archaea from comparative metagenomic analyses of bathypelagic plankton of different oceanic regions. ISME J. 2008;2(8):865–86.
Martin-Cuadrado AB, Ghai R, et al. CO dehydrogenase genes found in metagenomic fosmid clones from the deep Mediterranean sea. Appl Environ Microbiol. 2009;75(23):7436–44.
Munroe DJ, Harris TJ. Third-generation sequencing fireworks at Marco Island. Nat Biotechnol. 2010;28(5):426–8.
Parsley LC, Linneman J, et al. Polyketide synthase pathways identified from a metagenomic library are derived from soil Acidobacteria. FEMS Microbiol Ecol. 2011;78(1):176–87.
Quaiser A, Lopez-Garcia P, et al. Comparative analysis of genome fragments of Acidobacteria from deep Mediterranean plankton. Environ Microbiol. 2008;10(10):2704–17.
Riaz K, Elmerich C, et al. A metagenomic analysis of soil bacteria extends the diversity of quorum-quenching lactonases. Environ Microbiol. 2008;10(3):560–70.
Selvin J, Kennedy J, et al. Isolation identification and biochemical characterization of a novel halo-tolerant lipase from the metagenome of the marine sponge Haliclona simulans. Microb Cell Fact. 2012;11(1):72.
Shizuya H, Birren B, et al. Cloning and stable maintenance of 300-kilobase-pair fragments of human DNA in Escherichia coli using an F-factor-based vector. Proc Natl Acad Sci USA. 1992;89(18):8794–7.
Venter JC, Remington K, et al. Environmental genome shotgun sequencing of the Sargasso Sea. Science. 2004;304(5667):66–74.
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Rodriguez-Valera, F. (2013). Fosmid System. In: Nelson, K. (eds) Encyclopedia of Metagenomics. Springer, New York, NY. https://doi.org/10.1007/978-1-4614-6418-1_115-3
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DOI: https://doi.org/10.1007/978-1-4614-6418-1_115-3
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