PacBio Single Molecule Real Time (SMRT) sequencing of the Babesia canis genome (BcH-CHIPZ strain). Genome sequence assembly and annotation of Babesia canis

Infections of dogs with virulent strains of Babesia canis are characterized by rapid onset and high mortality, comparable to complicated human malaria. To provide the molecular underpinning for targeted appraoches to diagnosis, vaccination and clinical management of canine babesiosis we untertook complete sequencing, assembly, annotation and characterization of the B. canis genome of a virulent Hungarian field isolate (strain BcH-CHIPZ). We implemented a next-generation high throughput approach (PacBio® SMRT) for sequencing BcH-CHIPZ genomic DNA prepared after enrichment of infected RBCs (iRBCs). Assembly of the parasite-specific sequence reads after elimination of all reads from host DNA and gap-filling yielded 43 high-quality scaffolds at 55-fold average coverage representing a total of 7 Mb with a median weighted contig size (N50) of 185 kb. The quality of this assembly, based on the presence of core eukaryotic genes, indicates the B. canis genome sequence to be 92.6% complete.