Haloarchaeal comparative genomics and the local context model of genomic evolution

Genomics is a rapidly expanding field of research that seeks to study the structure, function and evolution of an organism's genome. Genomic investigations were conducted on three species of haloarchaea, a monophyletic group of prokaryotes belonging to the kingdom Euryarchaeota of the domain Archaea that are adapted to high-salt environments. A physical and genetic map of the genome of Halobacterium salinarum GRB is described. This map and the previously published map of the genome of Haloferax volcanii DS2 were compared with the object of detecting any conservation in the order or spacing of homologous loci between the two genomes. A computer program--COMPAGEN--was developed to aid in the analysis of the data generated by this comparison. No map order conservation could be detected at the 15 kbp average resolution of this comparison between genomes estimated to have diverged 600 million years ago. A second comparison was performed between the chromosomes of Haloferax volcanii DS2 and Haloferax mediterranei ATCC 33500 (R-4). Extensive conservation was found between these two genomes which diverged approximately 80 million years ago showing only three rearrangements: two inversions and a transposition. Conclusions drawn from an analysis of the comparisons include: (1) that higher resolution is required to deal with distantly related genomes, likely making use of sequence data, and (2) that it is important to compare genomes that have diverged at different times if one wishes to investigate the dynamics of genomic evolution within a phylogenetic group. The local context model was developed in an effort to explain the pattern of conservation and divergence seen in these and other prokaryotic genome comparisons. This model states that since the expression of genes is affected by flanking genetic elements, genes will resist changing their position relative to one another so long as this change is likely to alter gene expression in a way deleterious to the cell. The local context model thus provides a force promoting the conservation of genomic map order. The implications of this model for the evolution of the haloarchaea is discussed and future directions of prokaryotic genomics in general is explored.