BMC Genomics 2008, 9:200 http://www.biomedcentral.com/1471-2164/9/200 dense, gene-rich genome of E. cuniculi (Table 1) reveals a sharp contrast in the overall nature of the genomes. From the B. algerae survey, 34 genes with identifiable homo- logues in other organisms were identified, and a further 33 potential ORFs greater than 100 codons but with no recognizable similarity to any other gene were found, resulting in a protein-coding content of 11% identifiable coding sequence and 20% including putative ORFs. In E. aedis, only 25 identifiable protein-coding genes and 21 ORFs were found, pushing the range of coding sequence still lower, to 8% identifiable coding sequence or 14% if putative ORFs are included (Table 1). In contrast, 52% of the E. cuniculi genome consists of protein-coding sequences with recognizable similarity to other genes, and the proportion of coding sequence is 87% when ORFs are included [10]. The gene density of A. locustae is similar to that of E. cuniculi [12], as are small regions of other micro- sporidian genomes that have been sampled [20]. Overall, the gene-densities of B. algerae and E. aedis are about an order of magnitude lower than other microsporidia that have been examined to date. The overall GC content for both B. algerae (24%) and E. aedis (25%) is also significantly lower than that of E. cuniculi (47%). Not surprisingly, the GC content in the coding regions is slightly higher: 28% for B. algerae and 31% for E. aedis. A smaller sequence survey from Spraguea lophii with a genome size of 6.2 Mb has revealed a bias of Table 2: List of hits to suspected transposable elements: Top Blast hit annotation Brachiola algerae Pol polyprotein Nosema bombycis Pol polyprotein Nosema bombycis Pol polyprotein Nosema bombycis Pol polyprotein Nosema bombycis Pol polyprotein Nosema bombycis Pol polyprotein Nosema bombycis Pol polyprotein Nosema bombycis Pol polyprotein Nosema bombycis Pol polyprotein Nosema bombycis Transposase, putative Acaryochloris marina Predicted protein, Nematostella vectensis Conserved hypothetical protein Akkermansia muciniphila Neisseria meningitidis IS1016 transposase Caenorhabditis briggsae hypothetical protein CBG18017 Caenorhabditis briggsae hypothetical protein CBG18017 Caenorhabditis briggsae Hypothetical protein CBG00277 Caenorhabditis briggsae Hypothetical protein CBG21915 Edhazardia aedis Pol polyprotein Nosema bombycis 6 different Pol polyproteins Nosema bombycis Pol polyprotein Nosema bombycis 28% [20,26]. There is therefore no obvious correlation between genome size and drift towards low GC content in microsporidia, and similarly no pronounced lineage-spe- cific bias. Presence of transposable elements In contrast to the E. cuniculi genome, which does not encode any selfish genetic elements, fragments of reverse transcriptase or complete retrotransposons have been reported in the genomes of N. bombycis, V. corneae and S. lophii [20-22], and repeated sequences suggested to be mobile were reported in N. bombycis and N. costelytrae [27]. The V. corneae reverse transcriptase is closely related to a human LINE sequence, and both the N. bombycis and S. lophii retrotransposons have sequence similarity to each other and to Ty3/gypsy retrotransposons. In both B. algerae and E. aedis surveys we found extensive evidence of numerous transposable elements (Table 2). The E. aedis fragments all share high similarity to Ty3/ gypsy retrotransposons from the N. bombycis and S. lophii. Nine of the seventeen fragments of putatively selfish ele- ments identified in B. algerae are also members of the same family, and once more also share a high degree of similarity to the N. bombycis and S. lophii elements. The remaining fragments from B. algerae were similar to hypo- thetical proteins resembling transposases. Accession no. 91176517 91176521 91176521 91176521 91176521 91176523 91176523 91176525 91176525 158337326 156394155 166832600 161869234 157775203 157775203 157771110 157749299 91176525 91176519 91176525 Page 3 of 9 (page number not for citation purposes)