Iwai, S., B. Chai, E. D. Jesus, C. R. Penton, T. K. Lee, J. R. Cole, and J. M. Tiedje. 2011. Gene-targeted-metagenomics (GT-metagenomics) to explore the extensive diversity of genes of interest in microbial communities. Pages 235-244 in F. J. Bruijin, ed. Handbook of Molecular Microbial Ecology I: Metagenomics and Complementary Approaches . Wiley/Blackwell Press.
Due to extensive genetic diversity in most microbial communities, it is currently impossible to sequence any gene with sufficient coverage by shotgun metagenomic sequencing for meaningful conclusions about the gene’s diversity or population characteristics. Functional screens is one means to recover more versions of targeted genes, but even this approach is not efficient for covering the extant diversity and is not feasible for genes whose functions depend on assembly of active protein com- plexes. In order to overcome this limitation, targeted gene sequencing approaches are needed. One approach is the use of polymerase chain reaction (PCR)-based targeting in concert with high-throughput sequencing technologies; i.e. amplicon sequencing. This approach, which we term gene-targeted metagenomics (GT metagenomics), can not only provide extensive insight into microbial gene diversity, but can also reveal functional, ecological, and evolutionary patterns of the targeted genes.
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