Discordant 16S and 23S rRNA gene phylogenies for the genus Helicobacter:: Implications for phylogenetic inference and systematics
Discordant 16S and 23S rRNA gene phylogenies for the genus Helicobacter:: Implications for phylogenetic inference and systematics
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DOI：
10.1128/jb.187.17.6106-6118.2005
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发表时间：
2005-09-01
影响因子：
3.2
通讯作者：
Fox, JG
中科院分区：
文献类型：
--
作者：
Dewhirst, FE;Shen, ZL;Fox, JG
16S rRNA基因序列分析已成为确定原核生物系统发育的主要方法。系统发育学是目前原核系统学的基础。因此，基于 16S rRNA 基因的系统发育分析的有效性对于原核系统学至关重要。在螺杆菌属中，16S rRNA 基因分析与 DNA-DNA 杂交和表型分析之间存在差异。为了澄清这些差异，我们对代表 41 个分类单元的 55 个螺杆菌菌株的 23S rRNA 基因进行了测序。 （每个序列 > 2,700 个碱基）。使用邻接法、简约法和最大似然法对 23S rRNA 基因序列数据进行系统发育树构建，产生了与其他表型和基因型方法一致的稳定树。 16S rRNA基因序列衍生树与23S rRNA基因树和其他数据不一致。螺杆菌的不一致的 16S rRNA 基因序列数据与 16S rRNA 基因片段的水平转移和丢失系统发育信息的镶嵌分子的创建一致。这些结果表明，当 16S rRNA 基因衍生的系统发育与其他可信的表型和基因型方法不一致时，分类决策必须得到其他系统发育信息大分子的支持，例如 23S rRNA 基因。本研究通过 23S rRNA 基因分析和全基因组比较发现 Wolinella succinogenes 与螺杆菌的无鞘鞭毛簇分支。这项研究还在 12 种螺杆菌菌株的 23S rRNA 基因中发现了插入序列 (IVS)。在螺旋 10、25 和 45 以及螺旋 31' 和 27' 之间发现了 IVS。在 H. mesocricetorum 中发现 IVS 在三个位点同时插入。
Analysis of 16S rRNA gene sequences has become the primary method for determining prokaryotic phylogeny. Phylogeny is currently the basis for prokaryotic systematics. Therefore, the validity of 16S rRNA gene-based phylogenetic analyses is of fundamental importance for prokaryotic systematics. Discrepancies between 16S rRNA gene analyses and DNA-DNA hybridization and phenotypic analyses have been noted in the genus Helicobacter. To clarify these discrepancies, we sequenced the 23S rRNA genes for 55 helicobacter strains representing 41 taxa. (> 2,700 bases per sequence). Phylogenetic-tree construction using neighbor-joining, parsimony, and maximum likelihood methods for 23S rRNA gene sequence data yielded stable trees which were consistent with other phenotypic and genotypic methods. The 16S rRNA gene sequence-derived trees were discordant with the 23S rRNA gene trees and other data. Discrepant 16S rRNA gene sequence data for the helicobacters are consistent with the horizontal transfer of 16S rRNA gene fragments and the creation of mosaic molecules with loss of phylogenetic information. These results suggest that taxonomic decisions must be supported by other phylogenetically informative macromolecules, such as the 23S rRNA gene, when 16S rRNA gene-derived phylogeny is discordant with other credible phenotypic and genotypic methods. This study found Wolinella succinogenes to branch with the unsheathed-flagellum cluster of helicobacters by 23S rRNA gene analyses and whole-genome comparisons. This study also found intervening sequences (IVSs) in the 23S rRNA genes of strains of 12 Helicobacter species. IVSs were found in helices 10, 25, and 45, as well as between helices 31' and 27'. Simultaneous insertion of IVSs at three sites was found in H. mesocricetorum.