Reconstructing viral genomes from the environment using fosmid clones: the case of haloviruses.
Reconstructing viral genomes from the environment using fosmid clones: the case of haloviruses.
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DOI：
10.1371/journal.pone.0033802
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发表时间：
2012
期刊：
影响因子：
3.7
通讯作者：
Rodriguez-Valera F
中科院分区：
文献类型：
--
作者：
Garcia-Heredia I;Martin-Cuadrado AB;Mojica FJ;Santos F;Mira A;Antón J;Rodriguez-Valera F
偏毒体是存在于环境中的病毒基因组，已通过病毒DNA直接测序或在小插入库中克隆来研究。这两种方法产生的短读数使组装和注释这种灵活的基因组实体变得非常困难。许多环境病毒属于未知群体，或以未培养和鲜为人知的细胞谱系为猎物，因此可能不存在于数据库中。在这里，我们使用了一种不同的方法，在测序之前将病毒DNA克隆到融合体中，以获得接近病毒基因组大小的自然重叠群。我们研究了一个相对低多样性的极端环境：饱和氯化钠盐水，这简化了数据的分析和解释。获得了42个不同的病毒基因组，其中一些几乎完成，可以初步鉴定为头尾噬菌体(尾状病毒目)。我们发现了一组噬菌体基因组，最有可能感染HaloQuratum walsbyi，这是方形考古体，也是这些高盐度栖息地群落的主要组成部分。猎物的身份可以通过病毒和一个现有毒株基因组共享的CRISPR间隔区序列的存在来确认。检测到的其他病毒群似乎捕食纳米盐生细菌和细菌Salinibacter ruber，覆盖了在这种环境中发现的大多数微生物多样性。因此，这种方法似乎是一种可行的替代方法，可以比基于直接测序的更常见的方法以更详细和更可靠的方式描述后基因组。意外地发现了一个包括重复序列和间隔区的CRISPR簇转移的例子，支持这种特殊的原核细胞保护机制的动态性质和频繁转移。
Metaviriomes, the viral genomes present in an environment, have been studied by direct sequencing of the viral DNA or by cloning in small insert libraries. The short reads generated by both approaches make it very difficult to assemble and annotate such flexible genomic entities. Many environmental viruses belong to unknown groups or prey on uncultured and little known cellular lineages, and hence might not be present in databases. Here we have used a different approach, the cloning of viral DNA into fosmids before sequencing, to obtain natural contigs that are close to the size of a viral genome. We have studied a relatively low diversity extreme environment: saturated NaCl brines, which simplifies the analysis and interpretation of the data. Forty-two different viral genomes were retrieved, and some of these were almost complete, and could be tentatively identified as head-tail phages (Caudovirales). We found a cluster of phage genomes that most likely infect Haloquadratum walsbyi, the square archaeon and major component of the community in these hypersaline habitats. The identity of the prey could be confirmed by the presence of CRISPR spacer sequences shared by the virus and one of the available strain genomes. Other viral clusters detected appeared to prey on the Nanohaloarchaea and on the bacterium Salinibacter ruber, covering most of the diversity of microbes found in this type of environment. This approach appears then as a viable alternative to describe metaviriomes in a much more detailed and reliable way than by the more common approaches based on direct sequencing. An example of transfer of a CRISPR cluster including repeats and spacers was accidentally found supporting the dynamic nature and frequent transfer of this peculiar prokaryotic mechanism of cell protection.
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影响因子：
5.1
作者：
Casamayor, EO;Massana, R;Pedrós-Alió, C
通讯作者：
Pedrós-Alió, C
影响因子：
4.2
作者：
Anderson, Rika E.;Brazelton, William J.;Baross, John A.
通讯作者：
Baross, John A.
影响因子：
14.9
作者：
Aravind, L;Koonin, EV
通讯作者：
Koonin, EV
影响因子：
3.7
作者：
Dyall-Smith ML;Pfeiffer F;Klee K;Palm P;Gross K;Schuster SC;Rampp M;Oesterhelt D
通讯作者：
Oesterhelt D
影响因子：
3.7
作者：
Bath, Carolyn;Cukalac, Tania;Dyall-Smith, Michael L.
通讯作者：
Dyall-Smith, Michael L.