Comparative genomics: Using the complete genome sequence of Halobacterium salinarum NRC-1 to assess gene order conservation within the Halobacteriaceae

Comparative mapping and comparative genomics can be used to study genome stability. The genome organization of different strains, species or genera are compared by using physical maps or complete genome sequences. A previous comparative study determined that there was no gene order conservation between Haloferax volcanii and Halobacterium salinarum at a 15-kbp resolution. My research was designed to assess gene order conservation between certain halophiles at a much finer resolution. This was accomplished by using the only available haloarchaeal genome sequence as a reference. Random gene fragments obtained from other related halophiles were compared to the complete genome sequence and the level of gene order conservation was estimated. The hypothesis of this study was that gene order will not be conserved among haloarchaeal genera. Significant linkage (conserved gene fragments) was detected between Halobacterium salinarum NRC-1 and the five analyzed species. The hypothesis was refuted as some gene fragments have maintained similar gene organization in different genera. Furthermore, many genes from the selected halophiles have no homologs in the NRC-1 genome. The use of gene order as a tool to measure phylogeny is discussed.