Sequence heterogeneities among 16S ribosomal RNA sequences, and their effect on phylogenetic analyses at the species level
Sequence heterogeneities among 16S ribosomal RNA sequences, and their effect on phylogenetic analyses at the species level
复制标题
DOI：
10.1093/oxfordjournals.molbev.a025606
复制
发表时间：
1996-03-01
影响因子：
10.7
通讯作者：
Christen, R
中科院分区：
文献类型：
--
作者：
Cilia, V;Lafay, B;Christen, R
我们分析了不同但密切相关的属（肠杆菌）的细菌和单个属内的不同物种或菌株（大肠杆菌或沙门氏菌）的小亚基 rRNA 比较可以得出什么系统发育信号，最后分析了单个生物体（大肠杆菌）内的核糖体操纵子有多相似。这些序列已通过邻接、最大似然和简约进行了分析。通过 bootstrap 评估每种拓扑的稳健性。获得了大肠杆菌菌株 PK3 的 7 个 rrn 操纵子的序列。这些数据证明了三个高度可变领域的差异。它们的性质和定位表明，由于大肠杆菌和鼠伤寒沙门氏菌的分歧，每个基因内发生的大多数点突变已经通过涉及短结构域的转换在基因家族中传播，并且通过转换实现的同质化可能不会影响每个基因的整个序列。我们表明，当克隆单个操纵子后或直接从聚合酶链式反应（PCR）产物获得序列时，不同操纵子之间存在的差异被忽略。 PCR 产物的直接测序产生平均序列，其中存在于最可变域中的突变被隐藏。克隆单个操纵子会产生与其他操纵子和平均序列不同的序列，其中有几个点突变。因此，为了在物种水平或以下水平鉴定未知细菌，应避免平均序列或单个未鉴定操纵子的序列。考虑到七个操纵子以及在最可变域中积累的突变可能会提高树的分辨率。然而，如果使 rRNA 多基因家族同质化的基因转换是罕见事件，则系统发育树中的某些节点将反映这些重组事件，因此这些树可能是基因树而不是生物树。
We have analyzed what phylogenetic signal can be derived by small subunit rRNA comparison for bacteria of different but closely related genera (enterobacteria) and for different species or strains within a single genus (Escherichia or Salmonella), and finally how similar are the ribosomal operons within a single organism (Escherichia coli). These sequences have been analyzed by neighbor-joining, maximum likelihood, and parsimony. The robustness of each topology was assessed by bootstrap.Sequences were obtained for the seven rrn operons of E. coli strain PK3. These data demonstrated differences located in three highly variable domains. Their nature and localization suggest that since the divergence of E. coli and Salmonella typhimurium, most point mutations that occurred within each gene have been propagated among the gene family by conversions involving short domains, and that homogenization by conversions may not have affected the entire sequence of each gene. We show that the differences that exist between the different operons are ignored when sequences are obtained either after cloning of a single operon or directly from polymerase chain reaction (PCR) products. Direct sequencing of PCR products produces a mean sequence in which mutations present in the most variable domains become hidden. Cloning a single operon results in a sequence that differs from that of the other operons and of the mean sequence by several point mutations. For identification of unknown bacteria at the species level or below, a mean sequence or the sequence of a single nonidentified operon should therefore be avoided. Taking into account the seven operons and therefore mutations that accumulate in the most variable domains would perhaps increase tree resolution. However, if gene conversions that homogenize the rRNA multigene family are rare events, some nodes in phylogenetic trees will reflect these recombination events and these trees may therefore be gene trees rather than organismal trees.