Eukaryotic diversity and phylogeny using small- and large-subunit ribosomal RNA genes from environmental samples
Eukaryotic diversity and phylogeny using small- and large-subunit ribosomal RNA genes from environmental samples
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DOI：
10.1111/j.1462-2920.2009.02023.x
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发表时间：
2009-12-01
影响因子：
5.1
通讯作者：
Moreira, David
中科院分区：
文献类型：
--
作者：
Marande, William;Lopez-Garcia, Purificacion;Moreira, David
最近在真核微生物多样性研究中引入的分子技术，特别是基于小亚基核糖体DNA （SSU rDNA）的扩增和测序的技术，揭示了意想不到的各种新种型的存在。具有这些序列的生物的分类归属通常是从系统发育分析中推断出来的。不幸的是，单靠SSU rDNA序列往往没有足够的系统发育信息来解决快速进化或非常分化的序列的系统发育问题，从而导致它们的错误分类。为了解决这一问题，我们试图通过扩增环境样本中完整的真核rDNA集群（即SSU rDNA、内部转录间隔序列、5.8S rDNA和大亚基（LSU） rDNA）来增加系统发育信号，并对克隆的SSU和LSU rDNA部分进行测序。利用海洋浮游生物样本，我们发现基于SSU或SSU + LSU rDNA的调查获得了可比的多样性模式。此外，基于SSU + LSU rDNA序列串联的系统发育树具有较好的分辨率，对主要真核类群（如Opisthokonta、Rhizaria和Excavata）有较好的支持。最后，高度分化的SSU rDNA序列，其系统发育位置无法用单独的SSU rDNA数据确定，可以用SSU + LSU rDNA方法正确定位。这些结果表明，这种方法可以是有用的，特别是对真核微生物群落丰富的系统发育归属困难的系统发育类型的分析。
P>The recent introduction of molecular techniques in eukaryotic microbial diversity studies, in particular those based in the amplification and sequencing of small-subunit ribosomal DNA (SSU rDNA), has revealed the existence of an unexpected variety of new phylotypes. The taxonomic ascription of the organisms bearing those sequences is generally deduced from phylogenetic analysis. Unfortunately, the SSU rDNA sequence alone has often not enough phylogenetic information to resolve the phylogeny of fast-evolving or very divergent sequences, leading to their misclassification. To address this problem, we tried to increase the phylogenetic signal by amplifying the complete eukaryotic rDNA cluster [i.e. the SSU rDNA, the internal transcribed spacers, the 5.8S rDNA and the large-subunit (LSU) rDNA] from environmental samples, and sequencing the SSU and LSU rDNA part of the clones. Using marine planktonic samples, we showed that surveys based on either SSU or SSU + LSU rDNA retrieved comparable diversity patterns. In addition, phylogenetic trees based on the concatenated SSU + LSU rDNA sequences showed better resolution, yielding good support for major eukaryotic groups such as the Opisthokonta, Rhizaria and Excavata. Finally, highly divergent SSU rDNA sequences, whose phylogenetic position was impossible to determine with the SSU rDNA data alone, could be placed correctly with the SSU + LSU rDNA approach. These results suggest that this method can be useful, in particular for the analysis of eukaryotic microbial communities rich in phylotypes of difficult phylogenetic ascription.