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Amplification Methods Bias Metagenomic Libraries of Uncultured Single-Stranded and Double-Stranded DNA Viruses.
Appl Environ Microbiol. 2011 Sep 16;
Authors: Kim KH, Bae JW
Abstract
Investigation of viruses in the environment often requires the amplification of viral DNA before sequencing of viral metagenomes. In this study, two of the most widely-used amplification methods, the linker amplified shotgun library (LASL) and multiple displacement amplification (MDA), were applied to a sample from the seawater surface. Viral DNA was extracted from viruses concentrated by tangential flow filtration and amplified by these two methods. 454 pyrosequencing was used to read the metagenomic sequences from different libraries. The resulting taxonomic classification of the viruses, their functional assignment, and assembly pattern differed substantially depending on the amplification method. Only double-stranded DNA viruses were retrieved from the LASL, whereas most sequences in the MDA library were from single-stranded DNA viruses and double-stranded DNA viral sequences were minorities. Thus, the two amplification methods reveal different aspects of viral diversity.
PMID: 21926223 [PubMed - as supplied by publisher]
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Amplification Methods Bias Metagenomic Libraries of Uncultured Single-Stranded and Double-Stranded DNA Viruses.
Appl Environ Microbiol. 2011 Sep 16;
Authors: Kim KH, Bae JW
Abstract
Investigation of viruses in the environment often requires the amplification of viral DNA before sequencing of viral metagenomes. In this study, two of the most widely-used amplification methods, the linker amplified shotgun library (LASL) and multiple displacement amplification (MDA), were applied to a sample from the seawater surface. Viral DNA was extracted from viruses concentrated by tangential flow filtration and amplified by these two methods. 454 pyrosequencing was used to read the metagenomic sequences from different libraries. The resulting taxonomic classification of the viruses, their functional assignment, and assembly pattern differed substantially depending on the amplification method. Only double-stranded DNA viruses were retrieved from the LASL, whereas most sequences in the MDA library were from single-stranded DNA viruses and double-stranded DNA viral sequences were minorities. Thus, the two amplification methods reveal different aspects of viral diversity.
PMID: 21926223 [PubMed - as supplied by publisher]
More...