BMC Genomics Research article Genome sequence surveys of Brachiola algerae and Edhazardia aedis reveal microsporidia with low gene densities Bryony AP Williams†1, Renny CH Lee†1, James J Becnel2, Louis M Weiss3, Naomi M Fast1 and Patrick J Keeling*1 Address: 1Canadian Institute for Advanced Research, Department of Botany, University of British Columbia, 3529-6270 University Boulevard, Vancouver, BC, V6T 1Z4, Canada, 2Center for Medical, Agricultural and Veterinary Entomology, USDA/ARS, Gainesville, FL 32608, USA and 3Department of Pathology, Division of Tropical Medicine and Parasitology, Albert Einstein College of Medicine, Bronx, New York 10461, USA Email: Bryony AP Williams - B.A.P.Williams@exeter.ac.uk; Renny CH Lee - renny@interchange.ubc.ca; James J Becnel - James.Becnel@ars.usda.gov; Louis M Weiss - lmweiss@aecom.yu.edu; Naomi M Fast - nfast@interchange.ubc.ca; Patrick J Keeling* - pkeeling@interchange.ubc.ca * Corresponding author †Equal contributors BioMed Central Open Access Published: 29 April 2008 BMC Genomics 2008, 9:200 doi:10.1186/1471-2164-9-200 This article is available from: http://www.biomedcentral.com/1471-2164/9/200 Received: 12 September 2007 Accepted: 29 April 2008 © 2008 Williams et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Abstract Background: Microsporidia are well known models of extreme nuclear genome reduction and compaction. The smallest microsporidian genomes have received the most attention, but genomes of different species range in size from 2.3 Mb to 19.5 Mb and the nature of the larger genomes remains unknown. Results: Here we have undertaken genome sequence surveys of two diverse microsporidia, Brachiola algerae and Edhazardia aedis. In both species we find very large intergenic regions, many transposable elements, and a low gene-density, all in contrast to the small, model microsporidian genomes. We also find no recognizable genes that are not also found in other surveyed or sequenced microsporidian genomes. Conclusion: Our results demonstrate that microsporidian genome architecture varies greatly between microsporidia. Much of the genome size difference could be accounted for by non-coding material, such as intergenic spaces and retrotransposons, and this suggests that the forces dictating genome size may vary across the phylum. Background Microsporidia are obligate intracellular eukaryotic para- sites that have been found to infect members of all major animal lineages [1]. The many apparently "primitive" fea- tures of microsporidian cells led evolutionary biologists to suggest that they were an early-branching lineage of the eukaryotes [2,3], but molecular phylogeny has since shown that they are instead a derived relative of fungi [4,5]. In light of this, their seemingly primitive features have been re-evaluated as products of reduction and adap- tation to life inside another cell [4-8]. One such feature that has attracted considerable attention is their highly reduced genomes. The genome size has been determined for numerous microsporidian species, and they range from 19.5 Mbp in Glugea atherinae to just 2.3 Mbp in Encephalitozoon intestinalis, the smallest eukaryotic genome known [9]. The two best-studied examples are the vertebrate parasite Encephalitozoon Page 1 of 9 (page number not for citation purposes)