Research
Draft genome sequence of the Daphnia pathogen Octosporea bayeri: insights into the gene content of a large microsporidian genome and a model for host-parasite interactions
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* Corresponding author: Patrick J Keeling pkeeling@interchange.ubc.ca
- † Equal contributors
1 Canadian Institute for Advanced Research, The Biodiversity Research Centre, University of British Columbia, University Boulevard, Vancouver, BC, V6T 1Z4, Canada
2 Universität Basel, Zoologisches Institut, Evolutionsbiologie, Vesalgasse, CH-4051 Basel, Switzerland
3 Department of Genetics, UFRGS, Porto Alegre, RS 91501-970, Brazil
Genome Biology 2009, 10:R106 doi:10.1186/gb-2009-10-10-r106
Published: 6 October 2009Abstract
Background
The highly compacted 2.9-Mb genome of Encephalitozoon cuniculi placed the microsporidia in the spotlight, encoding a mere 2,000 proteins and a highly reduced suite of biochemical pathways. This extreme level of reduction is not universal across the microsporidia, with genomes known to vary up to sixfold in size, suggesting that some genomes may harbor a gene content that is not as reduced as that of Enc. cuniculi. In this study, we present an in-depth survey of the large genome of Octosporea bayeri, a pathogen of Daphnia magna, with an estimated genome size of 24 Mb, in order to shed light on the organization and content of a large microsporidian genome.
Results
Using Illumina sequencing, 898 Mb of O. bayeri genome sequence was generated, resulting in 13.3 Mb of unique sequence. We annotated a total of 2,174 genes, of which 893 encodes proteins with assigned function. The gene density of the O. bayeri genome is very low on average, but also highly uneven, so gene-dense regions also occur. The data presented here suggest that the O. bayeri proteome is well represented in this analysis and is more complex that that of Enc. cuniculi. Functional annotation of O. bayeri proteins suggests that this species might be less biochemically dependent on its host for its metabolism than its more reduced relatives.
Conclusions
The combination of the data presented here, together with the imminent annotated genome of Daphnia magna, will provide a wealth of genetic and genomic tools to study host-parasite interactions in an interesting model for pathogenesis.