Analysis of a viral metagenomic library from 200 m depth in Monterey Bay, California constructed by direct shotgun cloning.
Analysis of a viral metagenomic library from 200 m depth in Monterey Bay, California constructed by direct shotgun cloning.
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DOI：
10.1186/1743-422x-8-287
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发表时间：
2011-06-09
期刊：
影响因子：
4.8
通讯作者：
Preston CM
中科院分区：
文献类型：
--
作者：
Steward GF;Preston CM
病毒对海洋浮游生物的生态和进化都有深远的影响，但病毒组合的遗传多样性，特别是在更深的海洋沃茨中的遗传多样性，仍然没有得到很好的描述。在这里，我们报告的建设和分析的病毒宏基因组准备从下面的透光带在温带，富营养化海湾沿海加州。我们从加利福尼亚州蒙特雷湾200米深处收集的约1立方米海水中纯化病毒。从病毒组分中提取DNA，剪切，并在没有预先扩增的情况下克隆到质粒载体中，并在E. coli中构建MBv 200 m文库。通过桑格法对随机克隆进行测序。组装序列，然后使用BLAST分析与GenBank中的序列和其他病毒宏基因组文库进行比较。在组装后剩余的881个序列中，只有26%与GenBank nr数据库中的序列具有显著（E ≤ 0.001）BLAST命中，其中大多数与细菌（15%）和病毒（8%）匹配。当BLAST分析包括环境序列时，MBv 200 m文库中74%的序列具有显著匹配。这些命中中的大多数（70%）是微生物宏基因组序列，只有0.7%是病毒宏基因组序列。在与已知病毒有显著匹配的121个序列中，94%匹配噬菌体（Podo-、Sipho-和Myoviridae），6%匹配藻DNA病毒科（5个序列）或拟病毒（2个序列）中的真核生物病毒。对已知功能的病毒基因的最大百分比是那些涉及DNA修饰（25%）或结构基因（17%）。基于相互BLAST分析，MBv 200 m文库似乎与来自其他两个海湾的病毒宏基因组最相似，与来自北冰洋的病毒宏基因组最不相似。从各种海洋病毒中直接克隆DNA是可行的，并导致病毒类型和功能基因在深度上的分布在细节上有所不同，但与在海洋表面沃茨中发现的大致相似。有针对性的病毒分析是有用的，以确定那些成分的大型海洋宏基因组循环中的亚细胞大小的部分。
Viruses have a profound influence on both the ecology and evolution of marine plankton, but the genetic diversity of viral assemblages, particularly those in deeper ocean waters, remains poorly described. Here we report on the construction and analysis of a viral metagenome prepared from below the euphotic zone in a temperate, eutrophic bay of coastal California. We purified viruses from approximately one cubic meter of seawater collected from 200m depth in Monterey Bay, CA. DNA was extracted from the virus fraction, sheared, and cloned with no prior amplification into a plasmid vector and propagated in E. coli to produce the MBv200m library. Random clones were sequenced by the Sanger method. Sequences were assembled then compared to sequences in GenBank and to other viral metagenomic libraries using BLAST analyses. Only 26% of the 881 sequences remaining after assembly had significant (E ≤ 0.001) BLAST hits to sequences in the GenBank nr database, with most being matches to bacteria (15%) and viruses (8%). When BLAST analysis included environmental sequences, 74% of sequences in the MBv200m library had a significant match. Most of these hits (70%) were to microbial metagenome sequences and only 0.7% were to sequences from viral metagenomes. Of the 121 sequences with a significant hit to a known virus, 94% matched bacteriophages (Families Podo-, Sipho-, and Myoviridae) and 6% matched viruses of eukaryotes in the Family Phycodnaviridae (5 sequences) or the Mimivirus (2 sequences). The largest percentages of hits to viral genes of known function were to those involved in DNA modification (25%) or structural genes (17%). Based on reciprocal BLAST analyses, the MBv200m library appeared to be most similar to viral metagenomes from two other bays and least similar to a viral metagenome from the Arctic Ocean. Direct cloning of DNA from diverse marine viruses was feasible and resulted in a distribution of virus types and functional genes at depth that differed in detail, but were broadly similar to those found in surface marine waters. Targeted viral analyses are useful for identifying those components of the greater marine metagenome that circulate in the subcellular size fraction.