Amplification Methods Bias Metagenomic Libraries of Uncultured Single-Stranded and Double-Stranded DNA Viruses
Amplification Methods Bias Metagenomic Libraries of Uncultured Single-Stranded and Double-Stranded DNA Viruses
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DOI：
10.1128/aem.00289-11
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发表时间：
2011-11-01
影响因子：
4.4
通讯作者：
Bae, Jin-Woo
中科院分区：
文献类型：
--
作者：
Kim, Kyoung-Ho;Bae, Jin-Woo
环境中病毒的调查通常需要在病毒宏基因组测序之前扩增病毒DNA。在这项研究中，两个最广泛使用的扩增方法，接头扩增鸟枪文库（LASL）和多重置换扩增（MDA）的方法，适用于从海水表面的样品。从切向流过滤浓缩的病毒中提取病毒DNA，并通过这两种方法进行扩增。454焦磷酸测序用于读取来自不同文库的宏基因组序列。由此产生的病毒的分类学分类，其功能分配，和组装模式有很大的不同，这取决于扩增方法。从LASL中只检索到双链DNA病毒，而MDA文库中的大多数序列来自单链DNA病毒，双链DNA病毒序列是少数。因此，两种扩增方法揭示了病毒多样性的不同方面。
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) methods, 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 classifications of the viruses, their functional assignments, and assembly patterns 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.