Searching the Most Conserved Sequence in Bacterial Whole Genomes

Since the first complete sequence determination of a bacterial whole genome, more than 30 bacterial genomes have been completely sequenced and these genomes have been extensively analyzed. What is the most conserved sequence preserved over the interspecies in the bacteria whole genomes? Many hurdles exist in order to answer the above apparently simple question. However, at present, more than 30 species eubacterial and archaeal whole genome sequences are determined, and we are able to answer that simple question. When we perform the phylogenetic analysis, the most widely used molecule is a small-subunit ribosomal RNA (rRNA), because the structure stability of rRNA is very high, and they are of fundamental importance and so occur in all organisms [1]. However, it is not clear analytically that which sequence or gene is the most conserved sequence in the bacterial whole genomes among various species until many whole genome sequences are obtained and compare all genome sequences in mutually. When we search the most conserved sequence in whole bacterial genomes among various species, it is insufficient to perform the homology analysis only ORF’s regions because such regions dose not includes non-coding intergenic regions. Therefore, we tried to search the most conserved nucleic acid sequence in 31 bacterial whole genomes include both coding and non-coding regions by using CONSERV program [2].