Genome sequence surveys of Brachiola algerae and Edhazardia aedis reveal microsporidia with low gene densities

Bryony Ap Williams,Naomi M Fast,Louis M Weiss,Renny Ch Lee,Patrick J Keeling,James J Becnel

doi:10.1186/1471-2164-9-200

Abstract

BackgroundMicrosporidia 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.ResultsHere 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.ConclusionOur 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.

Highlights

Microsporidia are well known models of extreme nuclear genome reduction and compaction
We examined the only five full-length genes identified in the B. algerae survey with homologues in yeast and found that all five were shorter than S. cerevisiae homologues, and more surprisingly most were shorter than the E. cuniculi homologues (Figure 2)
The E. cuniculi genome is a model for compacted nuclear genomes, but potentially not a good model for microsporidian genomes generally

Summary

Introduction

Microsporidia are well known models of extreme nuclear genome reduction and compaction. Their seemingly primitive features have been re-evaluated as products of reduction and adaptation to life inside another cell [4,5,6,7,8]. 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 The two best-studied examples are the vertebrate parasite Encephalitozoon (page number not for citation purposes)

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Conclusion