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

Table 1 General characteristics of O. bayeri and other microsporidian genomes

General characteristics	O. bayeri	Enc. cuniculi	Ent. Bieneusi
Number of chromosomes	NA	11	6
Genome size (Mb)	≤24.2*	2.9	6
Assembled Mb	13.3	2.5	3.86
Genome coverage (%)	55^†	86	64
G+C content (%)	26	47	25
Gene density	1 per 4,593 bases^‡	1 per 1,025 bases	1 per 1,148 bases
Mean intergenic region (bp)	429^§	129	127
Presence of overlapping genes	No	Yes	Yes
Number of SSU-LSU rRNA genes	2^¶	22	Unkown^¥
Number of 5S rRNA genes	2^¶	3	Unkown^¥
Number of tRNAs	37	46	46
Number of tRNA synthetases	21	21	21
Number of tRNA introns (size in bp)	≥1 (50)	2 (16, 42)	2 (13, 30)
Number of splicesomal introns (size in bp)	≥6 (24-33)	13 (23-52)	19 (36-306)
Number of predicted ORFs	2,174^#	1,997	3,804**
Number of ORFs assigned to functional categories	894 (41%)	884 (44%)	669 (39%)
Mean size of CDS (bp)	1,056^††	1,017^††	1,002^††

*The genome size has been estimated using total number of bases sequenced divided by the average coverage. ^†Based on the 24.2-Mb estimated genome size. ^‡Based on the 200 largest contigs. ^§Based on contigs (n = 23) in which two or more ORFs of at least 100 amino acids have been identified. ^¶Only two contigs harboring an SSU-5.8S-LSU gene array have been identified in the O. bayeri genome survey. ^¥Based on [33]. ^#Includes ORFs with assigned functions, homologs of Enc. cuniculi hypothetical proteins, and hypothetical proteins of at least 200 amino acids identified in the O. bayeri genome. **The Ent. bieneusi genome has been subjected to several segmental duplications and the number of ORFs identified in that study includes a very large number of duplicates [33]. This number should, therefore, not be taken into account to determine the haploid coding capacity of this species. ^††Based on 95 and 63 complete Enc. cuniculi and Ent. bieneusi orthologs, respectively. CDS, coding sequence.

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