halorhodospira halochloris is an anoxygenic photosynthetic halophile that was isolated from the hypersaline wadi natrun lakes in egypt , residing in the mats near the sediments 8 .
the genus halorhodospira was formed by separating species h. halophila , h. halochloris and h. abdelmalekii from genus ectothiorhodospira based on their 16s rrna sequences 4,6 .
its cells are vibroid , motile by bipolar flagella and have internal photosynthetic membranes as lamellar stacks 13 .
h. halochloris exhibits growth over an unusually wide range of medium nacl concentrations and is capable of growth down to 5% nacl , which is unusual for extremely halophilic bacteria .
halophilic bacteria employ two differing strategies to protect their cytoplasmic volume against osmotic movement of water to the hypersaline environment 12 .
, organic compounds are accumulated in the cytoplasm - these osmoprotectants are known as compatible solutes .
the second biochemically , more radical adaptation involves the selective influx of k ions into the cytoplasm .
h. halochloris accumulates glycine betaine ( n , n , n - trimethylglycine ) , a compatible solute as its osmoprotectant 5 .
in addition to its osmoprotectant activity , glycine betaine also provides protection against mutagenic compounds and radiation - induced damage 9 .
glycine betaine can either be taken up directly from the environment , or be synthesized de novo 11 .
we recently used isoelectric focusing of total cell proteins to demonstrate that h. halochloris does not exhibit an acidic proteome , matching its inability to accumulate k 
 2 . in striking contrast
we found that a closely related organism h. halophila accumulates molar concentrations of kcl when grown in high salt medium and has an acidic proteome .
comparative genomics of h. halochloris and h. halophila promises to provide insights into this issue , which has implications both for genome - wide evolutionary processes and the mechanisms of halophilic adaptations .
these considerations led us to determine the genome of h.halochloris , which we report on here .
recently we reported the complete genome of h. halophila 
 1 . in this study , we report the draft genome sequence of h. halochloris , which was obtained through standard roche 454 pyrosequencing using the roche 454-junior instrument .
the raw data obtained were trimmed at either end based on the quality score analysis performed using fastqc tool .
poor or bad quality bases , probably originating from sequencing mis - calls , were trimmed off before subjecting it to the assembly software .
we performed genome assembly using three different assemblers , namely newbler 16 , mira 17 and phrap 18 , with the default set of parameters .
after comparisons of these assembly attempts based on contig sizes , genome representation and its functional elements , the output of mira 3.4.1 was selected to proceed with further analysis .
the final output had some low quality contigs in terms of length and average coverage .
all contigs of length less than 1kbp and average coverage < 10 were removed as being uninformative , from annotation point of view , and subjected to an individual annotation check using blast 14 .
most of these individual contigs yielded relatively high e - value or no scores with halophiles .
processed contigs were mapped against a distant reference genome ( thioalkalivibrio sulphidophilus ) , as no true known reference genome is currently available , based on 16s analysis , using contiguator 15 .
the assembled scaffold comprises 137 contigs , 3,460,134 bases at 20 fold coverage and has a gc content of 63% . for comparison
the genome of h. halophila is 2.7 mb in size and has gc content of 67% 1 .
the jgi img / er annotation pipeline ( http://img.jgi.doe.gov/er ) was employed for gene annotation with img submission i d and img project i d , 15725 and 50543 respectively . the numbers of trna and rrna genes were predicted as 46 and 8 , respectively . a total of 3,301 putative protein coding genes ( cdss ) or open reading frames ( orfs ) were predicted with a total gene count of 3,376 .
the genome has been submitted in public databases , ncbi , genbank ( gi number : 589289709 , genbank accession number : cp007268 ) .
the draft genome information reported here provides opportunity for further research into the mechanism involved in halophilic adaptations and allow organisms to thrive in hyper saline environments , how these evolve and how they differ for bacteria and archaea 10 .
 halorhodospira halochloris is an extremely halophilic bacterium isolated from hypersaline wadi nantrun lakes in egypt . here 
 we report the draft genome sequence of this gammaproteobacteria ( gi number : 589289709 , genbank accession number : cp007268 ) . 
 the 3.5-mb genome encodes for photosynthesis and biosynthesis of organic osmoprotectants . 
 comparison with the genome of h.halophila promises to yield insights into the evolution of halophilic adaptations . 