Metatranscriptome Library Preparation Influences Analyses of Viral Community Activity During a Brown Tide Bloom.
Metatranscriptome Library Preparation Influences Analyses of Viral Community Activity During a Brown Tide Bloom.
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宏转录组文库制备影响褐潮爆发期间病毒群落活动的分析。
DOI：
10.3389/fmicb.2021.664189
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发表时间：
2021
影响因子：
5.2
通讯作者：
Wilhelm SW
中科院分区：
文献类型：
--
作者：
Gann ER;Kang Y;Dyhrman ST;Gobler CJ;Wilhelm SW
使用元转录组学研究病毒群落动态的兴趣越来越大。我们使用的RNA样品收集有害的棕色潮汐引起的真核Aureococcus anophagefferens在纽约（美国）河口，并在此过程中观察如何预处理库的选择聚腺苷酸化或减少核糖体RNA（rRNA）的影响病毒群落分析。正如预期的那样，更多的读取映射到A。与rRNA减少的文库相比，在多聚腺苷酸化选择的文库中的噬菌体基因组中，每个样品中映射的读数彼此相关，而不管文库的预处理如何。然而，对于定位到嗜酸金黄色球菌病毒（AaV）的读段没有看到这种趋势，其中显著更多的读段（大约两个数量级）定位到rRNA减少的文库中的AaV基因组。在rRNA还原文库中，AaV和A的读段映射之间存在强烈且显著的相关性。嗜食动物总的来说，与其rRNA减少的对相比，多聚腺苷酸化选择的文库产生更少的病毒重叠群，更少的映射到病毒重叠群的读段，以及跨病毒领域和家族的不同比例。这项研究提供的证据表明，由rRNA减少，而不是选择多聚腺苷酸化产生的文库更适合于定量表征的病毒群落在水生生态系统中的元转录组学。
There is growing interest in the use of metatranscriptomics to study virus community dynamics. We used RNA samples collected from harmful brown tides caused by the eukaryotic alga Aureococcus anophagefferens within New York (United States) estuaries and in the process observed how preprocessing of libraries by either selection for polyadenylation or reduction in ribosomal RNA (rRNA) influenced virus community analyses. As expected, more reads mapped to the A. anophagefferens genome in polyadenylation-selected libraries compared to the rRNA-reduced libraries, with reads mapped in each sample correlating to one another regardless of preprocessing of libraries. Yet, this trend was not seen for reads mapping to the Aureococcus anophagefferens Virus (AaV), where significantly more reads (approximately two orders of magnitude) were mapped to the AaV genome in the rRNA-reduced libraries. In the rRNA-reduced libraries, there was a strong and significant correlation between reads mappings to AaV and A. anophagefferens. Overall, polyadenylation-selected libraries produced fewer viral contigs, fewer reads mapped to viral contigs, and different proportions across viral realms and families, compared to their rRNA-reduced pairs. This study provides evidence that libraries generated by rRNA reduction and not selected for polyadenylation are more appropriate for quantitative characterization of viral communities in aquatic ecosystems by metatranscriptomics.
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DOI：
10.1093/bioinformatics/bts565
发表时间：
2012-12-01
期刊：
Bioinformatics (Oxford, England)
影响因子：
--
作者：
Fu L;Niu B;Zhu Z;Wu S;Li W
通讯作者：
Li W
影响因子：
4.4
作者：
Bellec, Laure;Grimsley, Nigel;Desdevises, Yves
通讯作者：
Desdevises, Yves
影响因子：
1.4
作者：
Lawrence, JE;Suttle, CA
通讯作者：
Suttle, CA
影响因子：
11
作者：
Correa, Adrienne M. S.;Welsh, Rory M.;Thurber, Rebecca L. Vega
通讯作者：
Thurber, Rebecca L. Vega
DOI：
10.1007/bf02803565
发表时间：
2004-02-01
期刊：
ESTUARIES
影响因子：
--
作者：
Gastrich, MD;Leigh-Bell, JA;Bryan, M
通讯作者：
Bryan, M