this whole genome shotgun project has been deposited at ddbj / embl / genbank under the accession jpul02000000 ( http://www.ncbi.nlm.nih.gov/nuccore/jpul00000000.2 ) .
the stramenopile blastocystis is a common anaerobic protist living in the digestive tract of several animal groups .
its prevalence in human often exceeds 5% in industrialized countries   and can reach 100% in developing countries .
although the role of blastocystis as a human pathogen remains unclear , it has been associated with acute or chronic digestive disorders and some epidemiological surveys have suggested an association with irritable bowel syndrome ( ibs ) , . in patients with ibs , blastocystis seems to be associated with a decrease of the fecal microbiota protective bacteria , bifidobacterium sp . and faecalibacterium prausnitzii 

. the life cycle of the parasite is poorly documented . among the parasitic forms described in the literature , the vacuolar stage which is maintained in vitro in axenic culture ,
blastocystis exhibits an extensive genetic diversity and seventeen subtypes ( st1st17 ) have been identified based on the gene coding for the small - subunit ribosomal rna   among which the first nine are found in humans .
briefly , it consists of an 18.8  mbp nuclear genome with 6020 predicted genes   and a circular genome of 29  kbp   located within mitochondria - like organelles ( mlo ) . other mlo genomes with conserved gene synteny
we report the sequencing of the blastocystis st4-wr1 genome from an isolate of a laboratory rodent and cultured axenically .
genomic dna was isolated using a qiagen dneasy blood and tissue kit and sequencing was performed with the illumina hiseq 2000 system ( genoscreen , lille , france ) .
a total of 43.855.085 of 100-bp high quality paired - end reads were generated and were de novo assembled using the idba - ud algorithm  .
the output was then scaffolded using sspace   and gaps were filled by gapfiller software . in total ,
1301 scaffolds from 494  bp to 133,271  bp were obtained , with a scaffold n50 of 29,931  bp .
the draft genome sequence of blastocystis st4 has a deduced total length of 12.91  mbp and a g  +  c content of 39.7% .
assembly also provided a circular dna molecule of 27,717  bp in size with a g  +  c content of 21.9% corresponding to the whole mlo genome sequence .
the maker pipeline was set with the results of ab initio gene prediction algorithms augustus   and snap , the 6020 protein - coding genes of blastocystis st7 , ests of both blastocystis st7   and st1   and 414 manually - designed genes of the st4-wr1 isolate .
basic information about the assembled genome and predicted genes are shown in table  1 .
gene functions were annotated by blast2go   and blast analyses with ncbi ( http://www.ncbi.nlm.nih.gov/ ) .
the preliminary annotation data revealed that blastocystis st4-wr1 nuclear genome harbors 5713 protein - coding genes .
the presence of proteases was determined using blast against merops database , and secreted proteases were identified using signalp 3.0   and wolf psort .
this comparative analysis revealed that the st4 genome contains less duplicated genes than st7 and that more than 30% of st4 genes have no ortholog in the st7 genome at an e value cutoff of 10 .
this also led to the identification of new candidate genes , in particular some potential virulence factors , including 20 secreted proteases that may be involved in the physiopathology of this parasite . among these proteases ,
7 seem to be specific to st4 as no ortholog has been found in the st7 genome .
sequencing and annotation of additional st ( st1 , st2 , st3 and st8 ) genomes are under progress and should be helpful for a better understanding of the genetic diversity , pathogenesis , metabolic potential and genome evolution of this highly prevalent human parasite .
 the intestinal protistan parasite blastocystis is characterized by an extensive genetic variability with 17 subtypes ( st1st17 ) described to date . 
 only the whole genome of a human st7 isolate was previously sequenced . here 
 we report the draft genome sequence of blastocystis st4-wr1 isolated from a laboratory rodent at singapore . 