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

Abstract

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.

Figure 1

Distribution of O. bayeri (blue), Enc. cuniculi (yellow) and Ent. bieneusi (red) proteins among functional categories. The ordinate represents the number of ORFs assigned to the corresponding category. Each of the O. bayeri proteins was assigned to only one of eleven functional categories listed in [25,33]. The corresponding gene list is presented in the online version of this manuscript (Additional data file 3). *Based on a 4× sequence coverage [33].

Figure 2

Examples of sub-functional categories showing sharp differences in distribution between O. bayeri (blue), Enc. cuniculi (yellow) and Ent. bieneusi (red) proteins. (a) Functional sub-categories more highly represented in O. bayeri than in Enc. cuniculi and Ent. bieneusi. (b) Functional sub-categories less represented in O. bayeri than in Enc. cuniculi and Ent. bieneusi. *Based on a 4× sequence coverage [33] (that is, almost 10 times lower than the present genome draft), suggesting a number of these transporters may yet be identified in the Ent. bieneusi genome survey.

Figure 3

Phylogenetic relationships of microsporidia and their ATP transporters. (a) Phylogenetic reconstruction of the microsporidian phylogeny based on available α- and β-tubulin amino acid sequences and gains of ATP and ABC transporters. Known genome sizes and number of transporters are shown. Ent. bieneusi tubulins cluster as a sister group to the clade including Encephalitozoon and Nosema species; this position is represented by a black square. (b) Evolution of the ATP transporter family based on available amino acid sequences from a range of microsporidian parasites. 1, Putative ancestral duplication of ATP transporters within the microsporidia following lateral gene transfer from prokaryotes. 2, A putative secondary gene duplication occurred in the more diverged genera, Nosema, Enterocytozoon and Encephalitozoon. 3, Supported lineage including all three diverged genera. 4, Species-specific duplication of an ATP transporter. *Data from NC, JFP et al., unpublished.

Figure 4

Differences in gene length among microsporidia and their fungal relatives. (a) Comparison of the length (in amino acids) of O. bayeri proteins to orthologs from Enc. cuniculi, Ent. bieneusi, S. cerevisiae, U. maydis, B. dendrobatidis and R. oryzae. In general, O. bayeri proteins are longer than microsporidian orthologues, but shorter than fungal orthologues. Vertical arrows indicate the average reduction or increase in protein size compared to O. bayeri. (b) Specific examples of length variation between orthologs from O. bayeri, Enc. cuniculi, Ent. bieneusi and S. cerevisiae.

Figure 5

Variation in gene density across the O. bayeri genome. (a) Identification and distribution of ORFs (of at least 100 amino acids) among the largest O. bayeri contigs. Only the 100 largest contigs are shown here for convenience. Yellow dots represent contigs in which no ORF could be annotated. Blue and red arrows and dots represent contigs harboring two or one ORF, respectively. (b) Two cases of gene order conservation between O. bayeri and Enc. cuniculi.