Cilia V, Lafay B, Christen R
CNRS & Université Paris, France.
Mol Biol Evol. 1996 Mar;13(3):451-61. doi: 10.1093/oxfordjournals.molbev.a025606.
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.
我们分析了通过小亚基rRNA比较，能从不同但亲缘关系密切的属（肠杆菌）的细菌以及单个属（大肠杆菌或沙门氏菌）内的不同物种或菌株中获得哪些系统发育信号，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法、最大似然法和简约法进行分析。通过自展法评估每种拓扑结构的稳健性。获得了大肠杆菌PK3菌株的7个rrn操纵子的序列。这些数据表明差异位于三个高度可变的结构域。它们的性质和定位表明，自大肠杆菌和鼠伤寒沙门氏菌分化以来，每个基因内发生的大多数点突变已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并未影响每个基因的整个序列。我们表明，当从单个操纵子克隆后或直接从聚合酶链反应（PCR）产物中获得序列时，不同操纵子之间存在的差异会被忽略。对PCR产物进行直接测序会产生一个平均序列，其中最可变结构域中存在的突变会被隐藏。克隆单个操纵子会产生一个与其他操纵子和平均序列不同的序列，该序列存在几个点突变。因此，为了在物种水平及以下鉴定未知细菌，应避免使用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因此在最可变结构域中积累的突变，可能会提高系统发育树的分辨率。然而，如果使rRNA多基因家族同质化的基因转换是罕见事件，系统发育树中的一些节点将反映这些重组事件，因此这些树可能是基因树而非生物体树。
