BMC Genomics 2008, 9:200 http://www.biomedcentral.com/1471-2164/9/200 The level of similarity between the Ty3/gypsy elements from N. bombycis, S. lophii, E. aedis and B. algerae and the fact that the host groups for these four species are not closely related, is strongly suggestive that an ancestral family of retrotransposons existed in the common ances- tor of these microsporidia. In molecular phylogenies of microsporidia, the true Nosema-group is consistently found to be a sister-lineage of the Encephalitozoon-group to the exclusion of lineages that include E. aedis, B. algerae and S. lophii [28-30]. If the Ty3/gypsy retroelements iden- tified here are ancestral to the genomes where they have been found, it means that it was also ancestral to E. cuniculi and must have been completely purged from its genome. This raises some curious questions about the N. bombycis genome. Here, the Ty3/gypsy retrotransposons were found to be nested within blocks of compacted genes that were often conserved in order with homologues from other microsporidian genomes [22]. Based on this it was suggested that the elements could have invaded a compact genome, and perhaps later facilitated some genomic rear- rangements [22]. Reconciling the ancient presence of these elements with the nature of the N. bombycis genome is complicated. It is possible that the ancestral genome contained many such elements and had a low gene den- sity. This genome could have subsequently compacted in several lineages, some of which lost the retroelements as part of the compaction process (e.g., E. cuniculi), while others kept them and compacted the genome around them (e.g., N. bombycis). It is also possible that compac- tion happened in an earlier common ancestor of some of these lineages and that certain genomes have 're- expanded'. In either event, the retention of large numbers of selfish elements in an otherwise compact genome is of interest, as one might expect that compaction would be strongly inclined to lead to the loss of non-coding mate- rial such as selfish elements. It serves to illustrate the way compaction affects different aspects of the genome in dif- ferent lineages, another possible example being the differ- ential loss or retention of introns in relict nucleomorph genomes [31,32]. Gene density, order, and size The small number of genes identified and the large con- tinuous stretches of non-coding sequence in both surveys lead to the obvious conclusion that the gene-density of these genomes is much lower than those of E. cuniculi or A. locustae. The average intergenic distances in these genomes cannot readily be determined since few have been completely sequenced. In B. algerae four clones encoded two genes and the distances between them are 108, 206, 276, and 552 bp. In E. aedis a single clone encoded two adjacent genes, and the intergenic spaces between them is 1,324 bp. At the same time, the largest continuous stretches of sequence from which we could identify no genes were 2,412 (or 2,943 in a likely subtelo- meric region next to an SSU gene) and 2,068 bp in B. alge- rae and E. aedis, respectively. The average distance between genes in E. cuniculi and A. locustae samples is 129 and 211 bp [10,12]. From the existing data it seems likely that the average distance between genes in B. algerae and E. aedis is much larger than that of either of the well stud- ied microsporidian genomes, and that the density across at least the B. algerae genome may be more heterogene- ous. Of the pairs of adjacent genes we identified, one B. algerae pair is also adjacent in both A. locustae and E. cuniculi (Fig- ure 1) (the pair separated by 206 bp in B. algerae). It has previously been shown that the order of gene pairs in A. locustae and E. cuniculi is highly conserved, and this has been hypothesized to be related to the compaction of the genome [12]. The conservation of one of four B. algerae gene pairs suggests that areas of this genome may be under similar constraints. If the conservation of genome order is related to compaction, this also suggests that the compacted state may have existed in the ancestor of B. algerae, E. cuniculi and A. locustae, which is consistent with 31 bp 08_1830 08_1840 61 bp 206 bp 08_1830 08_1840 08_1830 08_1840 A. locustae E. cuniculi B. algerae FAmirigceuraorosepfo1corindsiaerved gene synteny between three species of Area of conserved gene synteny between three spe- cies of microsporidia. A fragment of the B. algerae genome aligned to corresponding regions from E. cunculi and A. locus- tae. The gene order, but not orientation, is conserved. Arrowheads indicate gene orientation and dashed white line indicates incomplete gene sequences. Intergenic space lengths are indicated. Page 4 of 9 (page number not for citation purposes)