Comparing the Hyper-Variable V4 and V9 Regions of the Small Subunit rDNA for Assessment of Ciliate Environmental Diversity
Comparing the Hyper-Variable V4 and V9 Regions of the Small Subunit rDNA for Assessment of Ciliate Environmental Diversity
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DOI：
10.1111/j.1550-7408.2011.00602.x
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发表时间：
2012-03-01
影响因子：
2.2
通讯作者：
Stoeck, Thorsten
中科院分区：
文献类型：
--
作者：
Dunthorn, Micah;Klier, Julia;Stoeck, Thorsten
小亚基 (SSU) rDNA 的高变 V4 和 V9 区域已成为使用下一代测序技术评估微生物真核生物环境多样性的目标。在这里，我们通过比较所有成对估计值以及纤毛虫物种内部和物种之间的情况，探讨这些短片段之间的遗传距离与从近全长 SSU-rDNA 序列获得的距离的比较。结果表明，与 V4 的成对距离与接近全长的 SSU-rDNA 更接近，并且与之前基于更长的 SSU-rDNA 片段的研究（然后与 V9 的成对距离）更具可比性。因此，使用 V4 的研究将估计与使用全长 SSU-rDNA 估计的相似的系统发育型丰富度和群落结构值。
The hyper-variable V4 and V9 regions of the small subunit (SSU) rDNA have been targeted for assessing environmental diversity of microbial eukaryotes using next generation sequencing technologies. Here, we explore how the genetic distances among these short fragments compare with the distances obtained from near full-length SSU-rDNA sequences by comparing all pairwise estimates, as well as within and among species of ciliates. Results show that pairwise distances from V4 more closely match the near full-length SSU-rDNA and are more comparable with previous studies based on much longer SSU-rDNA fragments, then pairwise distances from V9. Thus, studies that use the V4 will estimate similar values of phylotype richness and community structure as would have been estimated using the full-length SSU-rDNA.