On the suitability of short reads of 16S rRNA for phylogeny-based analyses in environmental surveys
On the suitability of short reads of 16S rRNA for phylogeny-based analyses in environmental surveys
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DOI：
10.1111/j.1462-2920.2011.02577.x
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发表时间：
2011-11-01
影响因子：
5.1
通讯作者：
Goldenfeld, Nigel
中科院分区：
文献类型：
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作者：
Jeraldo, Patricio;Chia, Nicholas;Goldenfeld, Nigel
焦磷酸测序平台已广泛用于从环境调查中取样的生物体的16S rRNA深度测序。尽管这些平台产生了大量的读段，但读段仅覆盖基因的短区域，并且这些短读段的使用最近被质疑用于基于遗传学和多样性的分析。我们通过量化信息的损失及其对遗传学的影响来探索短读码的使用限制。使用已发表的克隆文库和数据库中可用的近全长读段，以及从这些读段创建的模拟短读段，我们表明，对于基因的选定区域，短读段包含令人惊讶的大量生物信息，使其适合于解析近似同源性。特别是，我们发现，V6区是显着较差的比V1V3区在其代表性的系统发育关系。我们的结论是，使用短读段，结合使用的基因区域的仔细选择，和一个彻底的比对程序，可以产生系统发育的信息，从近全长16S rRNA读取获得的。
Pyrosequencing platforms have been widely used in 16S rRNA deep sequencing of organisms sampled from environmental surveys. Despite the massive number of reads generated by these platforms, the reads only cover short regions of the gene, and the use of these short reads has recently been called into question for phylogeny-based and diversity analyses. We explore the limits of the use of short reads by quantifying the loss of information, and its effect on phylogeny. Using available nearly-full-length reads from published clone libraries and databases, and simulated short reads created from these reads, we show that for selected regions of the gene, short reads contain a surprisingly high amount of biological information, making them suitable to resolve an approximate phylogeny. In particular, we find that the V6 region is significantly poorer than the V1V3 region in its representation of phylogenetic relationships. We conclude that the use of short reads, combined with a careful choice of the gene region used, and a thorough alignment procedure, can yield phylogenetic information comparable with that obtained from nearly-full-length 16S rRNA reads.