BMC Genomics 2008, 9:200 http://www.biomedcentral.com/1471-2164/9/200 Table 3: List of genes identified by BLAST search E. cuniculi locus Hit E. cuniculi locus Brachiola algerae Hit Cell Division Kinase Coatomer coat delta DNA directed RNA pol DNA ligase DNA mismatch repair Dnm1 E. cuniculi hypothetical protein E. cuniculi hypothetical protein E. cuniculi hypothetical protein E. cuniculi hypothetical protein E. cuniculi hypothetical protein E. cuniculi hypothetical protein E. cuniculi hypothetical protein E. cuniculi hypothetical protein E. cuniculi hypothetical protein E. cuniculi hypothetical protein E. cuniculi hypothetical protein GPI Anchor Biosynthesis Hsp70 Isopentyl pyrophosphate δ isomerase LSU gene Pelota protein Phenylalanine tRNA synthase RAD31 DNA damage tolerance RAS-like GTP binding protein Septin SER/THR protein kinase Signal Recognition Particle SSU gene Syntaxin TFIID 111 KDa TFIID 72/90 KDa TFIID 150 kDa TFIID I U5 Associated snRNP Ubiquitin Conjugating Enzyme E2 08_0230 08_0340 01_0600 02_1220 11_1260 01_1210 01_0390 04_0270 05_1460 06_0970 07_0810 08_1830 08_1840 09_0300 09_1240 10_1360 11_0260 09_1210 02_0100 02_0230 03_1380 07_1660 08_0460 10_0350 09_0820 08_1620 04_0980 05_0820 01_0760 11_1750 09_0090 04_1440 11_0870 08_0860 Edhazardia aedis 14-3-3 Protein 1 26S proteasome beta-type subunit 40S ribosomal protein S28 60S ribosomal protein L8 Aldose Reductase DNA Mismatch Repair Protein Endochitinase E. cuniculi hypothetical protein E. cuniculi hypothetical protein E. cuniculi hypothetical protein E. cuniculi hypothetical protein Myosin heavy chain NIFS-like protein Phospholipid-transporting ATPase Putative methyltransferase RING-finger-containing ubiquitin ligase Similarity to oxidoreductase SSU gene Topoisomerase 1 TPR domain hypothetical protein Transcriptional activator Translation initiation factor IF-2P Trehalose-6-phosphate synthase U6 snRNA-associated small RNP UTP glucose-1-phosphate uridyltransferase Vacuolar protein sorting-associated protein 03_1010 05_0290 09_1275 01_0310 01_0970 05_0300 09_1320 03_0870 05_1000 05_1080 09_1690 09_1970 11_1770 09_1440 05_0950 07_0330 11_1070 06_1520 09_1180 10_1430 09_0070 01_0870 05_1310 03_0280 03_0900 but the proportion of ORFs we found (47% and 43% for B. algerae and E. aedis, respectively) is similar to that found in E. cuniculi (39%). This issue is also complicated by the fact that we identified several E. cuniculi "ORFs" in our sample, and therefore the proportions of putative ORFs is changing. Third, the genome size estimates may be wrong. Lastly, it is possible that there are many more than 2,000 genes in these organisms, but that the excess is mostly due to recent duplications. We did not sample any duplicates in either genome, though we did find areas of repeats amongst the non-coding areas in both B. algerae and E. aedis. If gene duplications are common, the genome could contain more genes without an increased complexity in the proteome. Evolution of genome compaction in microsporidia Though the phylogenetic relationships of major micro- sporidian lineages are not well resolved, phylogenies of rRNA [28] and concatenated tubulin genes (unpublished data) suggest a relationship between B. algerae and A. locustae to the exclusion of E. aedis or E. cuniculi (Figure 3). This raises interesting questions about whether micro- sporidian genomes have compacted more than once dur- ing the diversification of the phylum, or if some have re- expanded from a compacted state. An obvious factor in the dynamics of genome size is trans- posable elements. One could imagine a genome expand- ing due to the invasion of such elements, and indeed Page 6 of 9 (page number not for citation purposes)