Cellular evolution and adaptation have imprinted patterns in microbial genomes through mutation, gene duplication, horizontal gen transfer (HGT) and recombination [1, 2]. The genomes of microorganisms of the three domains of life have experienced such genetic modifications to succeed on their permanence in a particular habitat, where environmental conditions and the size of the microbial populations might influence the organization and number of genes in a particular species throughout the time [1, 3]. Furthermore, the nearly neutral theory of evolution points out that genetic modification of DNA could be neutral or selected, albeit most mutations should be at the border between neutrality and selection, i.e. slightly deleterious base substitutions in DNA are followed by a slightly advantageous substitutions .
The increasing number of genome sequences of different organisms is helping to discern how microbial species diverged. Recent reports on the evolutionary traits followed by different bacteria and archaea have demonstrated that the transfer of genes among these organisms, also referred as horizontal gene transfer, has led to net-like relationships among their genomes [2, 4, 5]. Nevertheless, the phylogenetic association among prokaryotes derived from the sequences of proteins encoded by 102 different genes was consistent to the taxonomic differentiation observed when 16 rRNA sequences of microorganisms are analyzed . The 102 proteins were mainly related to translation and transcription, although proteins involved in the transport and metabolism of amino acids, metal ions and carbohydrates revealed such taxonomic information as well .
The aforementioned studies included the genome sequences of extremely halophilic archaea such as Haloarcula marismortui, Haloquadratum walsbyi and a Halobacterium sp. . These studies on the genome sequences did not include halophilic bacteria. However, a report on the genes of poly(3-hydroxybutyrate) (PHB) polymerases, PHB depolymerases and ectoine synthesis by Halomonas sp. TD01, a halophilic bacterium, suggested that HGT has a role to play on the genome organization of the microorganism . Halophilic microorganisms require salt (NaCl) to grow; a halophile should grow optimally at NaCl concentrations of 5% (w/v) or higher, and tolerate at least 10% (w/v) salt . There are five genome sequences of halophilic bacteria available in public data bases. The sequences of Chromohalobacter salexigens and Halorhodospira halophila were first published followed by the sequence of Halomonas elongata [8, 9], Halomonas sp. TD01  and Halomonas sp. HAL1 . Chromohalobacter and Halomonas species are included in the family Halomonadaceae within the γ-Proteobacteria subgroup. The family Halomonadaceae contains only halophilic and halotolerant aerobic heterotrophs; some of them are able to grow in media with up to 30% (w/v) NaCl . Halophilic bacteria maintain low concentrations of salt intracellularly by accumulating organic compounds of low molecular weight, also known as osmolytes or "compatible solutes" such as ectoine .
Understanding the evolution and levels of polymorphism among genes is attracting much attention in evolutionary biology and biotechnology. Evolution of energy-producing pathways, particularly glycolysis and gluconeogenesis, posses relevance since they determine the type of carbon sources that a species is able to assimilate, and link to metabolic routs that may generate compounds of biotechnological interest . Theories on the evolution of the metabolisms of organisms consider that enzyme polymorphism--alleles for the different enzymes or allozymes--in metabolic pathways was related to genetic mutations [12–14]. A proposal states that the fitness of the pathways associated with an increasing flux is influenced by selected mutations of genes that enhance enzyme activities, albeit enzyme improvements do not continue indefinitely [12, 14]. Mutations will reach a point at which the incremental gains of fitness for a new mutation will be equaled by the noise caused by the random genetic variation [12, 14]. At this stage, the genes or enzymes might evolve under a nearly neutral trend [12, 14]. Moreover, metabolic control in the organisms is also to regulate molecular evolution as well [12, 14]. The proposal assumes no contextual changes such as a change in the functional conditions of an enzyme originated by either epistasis or the environment; or a change in the effective population size of the species .
Halomonas boliviensis is a halophilic bacterium that can develop under a wide range of NaCl concentrations (i.e. 0-25% (w/v)), pH (5-11) and temperatures (0-45°C) . It can also assimilate several carbohydrates as carbon source for growth . Bioprocesses have been designed to attain high productivities of a polyester and osmolytes by H. boliviensis using glucose as the carbon precursor [16, 17]. The polyester accumulated by the bacterium is poly(3-hydroxybutyrate) (PHB), which is used as carbon and energy reservoir . PHB is synthesized by several bacteria from acetyl-CoA when an excess of NADH is present in the bacterial cytoplasm . Such excess can be generated when a high concentration of a carbon source is added to a culture medium and cell growth is limited by the depletion of an essential nutrient, e.g. nitrogen, oxygen, trace elements among others . PHB is attracting much attention in biotechnology because it is a biodegradable plastic-like material, and possesses potential in biomedical applications such as tissue engineering, organ transplants and drug delivery systems . Moreover, the efficiency and economics of the manufacturing process of PHB are determined by the carbon source, fermentation process, and downstream processing of the polymer. The development of cultivation conditions for microorganisms that allow high PHB content and productivity from cheap and renewable carbon sources is therefore important [21, 22].
The present research work reports the genome sequence of H. boliviensis. It also depicts the evolutionary trends that proteins of H. boliviensis have experienced to allow the transport of carbohydrates and their assimilation to achieve acetyl-CoA. The conclusions drawn from these studies were used to create an alternative production system of PHB by H. boliviensis using a combination of carbohydrates. This system should lead to a more economically and environmentally beneficial bioprocess.