Evaluation On The Relationship Among Higher Taxa Of Bacteria Domain By Comparison Of Coregenes

The16S rRNA-based hierarchical system is considered to be the backbone of prokaryotetaxonomy. In the current taxonomic scheme, the phylogenetic positions of higher taxa weremainly based on analyses of the nucleotide sequences of16S rRNA. However, thephylogenetic relationships among a number of higher taxonomic ranks were difficult todetermine based on16S rRNA analysis. Recently, phylogenomic information was claimed toprovide a more comprehensive understanding of prokaryotic systematics in the genomics era.It was significant to construct the natural tree of life using a set of newer, fitter molecularmarkers.In our work, we found56phylogenetic markers at the level of the Bacteria domain and108markers at the level of the phylum by searching among206coreproteins reported, half ofwhich were ribosomal proteins. Similar to ribosomal RNAs, ribosomal proteins were essentialribosome components, whose evolution was correlated to that of rRNAs and can reflect theevolution of the whole genome. All fitter ribosomal proteins were concatenated and used forphylogenetic analysis, while the other coreproteins were analyzed together. Then, thephylogenetic affliations among higher taxa of the Bacteria was discussed by comparing theresults deduced by coreproteins and16S rRNA.Phylogenies based on concatenated core proteins were generally congruent with16SrRNA phylogenies, but higher bootstrap values supported the branching orders in the formertrees. It should be noted that part of the topology of the16S rRNA-based tree was highlyunsteady, and relationships deduced were ambiguous. The coreproteins-based phylogenyapproach may thus provide a sound basis for assessing the affliation among different highertaxa, especially in the phyla Actinobacteria, Proteobacteria and Firmicutes.Compared with the traditional phylogenetic analysis, the research based on characteristicsequences provided a powerful means for identification of different taxanomic ranks withinBacteria in clear molecular terms, and for evolutionary studies. In our work, we found anumber of new insertion/deletion sequences (indel) in coreproteins, which were uniquelyshared by different groups, such as the class Alphaproteobacteria and the phyla Bacteroidetesand Chloroflexi. And these new characteristic indels provided novel means for thecircumscription of corresponding taxa. In addition, a large indel in23S rRNA, which was considered as the signature sequences of the phylum Actinobacteria before, was uniquelypresent in the species belonging to the class Actinobacteria and not found in the other classesof that phylum. Thus, it was necessary to modify the previous conclusion.