Bioinformatics researchers have compared extensively multiple genomes to correlate and classify the genomes into various families and to study evolution. It has been established by many researchers that overall evolution is a combination of point based mutation giving rise to speciation and restructuring of genomes based upon gene duplications, gene insertion, gene deletion, gene-fusion/fission, horizontal gene transfer, and domain level restructuring [11,17,45].
The evolutionary study efforts can be classified into three approaches: (1) point based mutation approaches used to build traditional evolutionary tree using multiple sequence alignment of 16SrRNA [72], (2) study of genome restructuring based upon inversion and transposition at the gene level [17,45], and (3) the study based upon whole genome comparisons using gene identity of orthologous genes across multiple microbial genomes [13].
The 16SrRNA approach is rooted in the concept of point mutation of conserved genes due to their slow mutation rate, uses 16SrRNA database and multiple sequence alignment [22], and uses neighbor join algorithm [36] to build an evolutionary tree. Before microbial genomes were sequenced, this technique was considered quantitatively sound, and using 16SrRNA database three distinct domains – bacteria, archaea, and eukaryotes – were identified. Archea domain is hyperthermophilic, and its 16SrRNA is somewhat different from 16SrRNA of bacteria.
Since 1998, after the availability of multiple microbial genomes, the researchers have tried to build the evolutionary tree by comparing other highly conserved genes. The results have shown that the evolutionary tree varies a lot depending upon the choice of the conserved genes, and shows no clear distinction between archaea and bacteria. This observation combined with the knowledge of genome restructuring caused by domain level and gene level restructuring such as horizontal gene transfer has shaken up the traditional evolutionary trees based upon point mutations in 16SrRNA [54].
The second approach uses the genome rearrangement caused by gene shuffling as a measure for the genomic distance between the two organisms [17,45]. Gene shuffling is caused by inversion and transposition. This scheme is based upon the distance measure as the breakaway from the standard gene-order in two genomes. Under this scheme the breakaway distance for each orthologous gene is added to give a cumulative score for the genome. This score is used as a distance between two genomes. Building large scale evolutionary tree using this approach was cost prohibitive due to pair-wise comparison until recently when a new development in parallel algorithms made such an evolutionary tree possible [45]. Is this scheme horizontal transfer of genes do not play a role: insertion and deletion are not counted in the assumption, and duplications are mapped to a single gene. It has been shown that duplication, insertion, deletion of gene-domains and genes are a major component of evolution [11]. Specially duplicated genes are involved in multiple sensor and transportation pathways such as ABC transporters, and cannot be ignored.
The third approach [13] is based on comparing overall gene-content of functionally equivalent genes to identify the cumulative similarity of two genomes. The data is normalized to take care of different size of genomes. The major assumption in this scheme is that conserved genes are very few and do not give a consensus, and slow mutation rate only contributes to good multiple sequence alignment. Whole genome comparisons can balance out the error introduced by comparing a single conserved gene. The results show that the overall amino-acid composition in the microorganisms does not differ significantly between archaea and bacteria to give a separate domain status to archaea [13]. In addition, the composition of other hyperthermophilic bacteria cannot be distinguished from archaea.
Currently no proteomic level approach has been suggested to classify the genomes. In future, one such approach could be based upon comparative analysis and alignment of pathways of multiple genomes [38]. Under this scheme, after the pathways are aligned, a combination of the cumulative number insertion and deletion of genes in the pathways, gene duplication in the same pathway, and gene shuffling could be used to describe the distance between two genomes since all three factors are directly involved in the pathway variations. However, exact mechanism of combining these three components of pathway evolution has to be studied.
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