Comparative genomics of the pathogenic ciliate Ichthyophthirius multifiliis, its free-living relatives and a host species provide insights into adoption of a parasitic lifestyle and prospects for disease control

Abstract

Background: Ichthyophthirius multifiliis, commonly known as Ich, is a highly pathogenic ciliate responsible for 'white spot', a disease causing significant economic losses to the global aquaculture industry. Options for disease control are extremely limited, and Ich's obligate parasitic lifestyle makes experimental studies challenging. Unlike most well-studied protozoan parasites, Ich belongs to a phylum composed primarily of free-living members. Indeed, it is closely related to the model organism Tetrahymena thermophila. Genomic studies represent a promising strategy to reduce the impact of this disease and to understand the evolutionary transition to parasitism.

Results: We report the sequencing, assembly and annotation of the Ich macronuclear genome. Compared with its free-living relative T. thermophila, the Ich genome is reduced approximately two-fold in length and gene density and three-fold in gene content. We analyzed in detail several gene classes with diverse functions in behavior, cellular function and host immunogenicity, including protein kinases, membrane transporters, proteases, surface antigens and cytoskeletal components and regulators. We also mapped by orthology Ich's metabolic pathways in comparison with other ciliates and a potential host organism, the zebrafish Danio rerio.

Conclusions: Knowledge of the complete protein-coding and metabolic potential of Ich opens avenues for rational testing of therapeutic drugs that target functions essential to this parasite but not to its fish hosts. Also, a catalog of surface protein-encoding genes will facilitate development of more effective vaccines. The potential to use T. thermophila as a surrogate model offers promise toward controlling 'white spot' disease and understanding the adaptation to a parasitic lifestyle.

Figure 1

Life cycle of Ich. Infective theronts bore through the surface mucus and take up residence within the epithelium of susceptible fish. Theronts differentiate into feeding trophonts that grow and exit the host (as tomonts) within 4 to 7 days. Tomonts swim for a brief period and then adhere to an inert support where they secrete a gelatinous capsule. Tomonts divide within the capsule to form hundreds of tomites that differentiate into infective theronts within 18 to 24 hours at room temperature. Theronts that fail to infect fish die within 1 to 2 days.

Figure 2

GC content of reads and scaffolds. (a) Percentage of GC content is plotted against percentage of combined quality Sanger and 454 reads of whole cell Ich DNA, showing a prominent shoulder of reads more GC-rich than expected for Ich. (b) Following assembly, mean GC content was plotted against the aggregate scaffold length within each percent GC bin, showing clean separation between scaffolds that make up the bacterial genomes and those that make up the much larger Ich genome.

Figure 3

Ortholog grouping. (a) Phyletic grouping of Ich genes with previously grouped orthologs from other species. Numbers in parentheses indicate the total number of ortholog groups to which the respective genes belong. (b) Shared orthology between the three ciliate genomes. The numbers depict the total number of ortholog groups in each category. The numbers within the brackets indicate ortholog groups specific for Tetrahymena only and accordingly there are 341 ciliate specific ortholog groups shared with all 3 ciliates compared here. See Additional file 6 for more details regarding shared orthology between the three ciliates.

Figure 4

Immobilization antigens. (a) Unrooted neighbor-joining phylogenetic tree [123] of the 17 Ich immobilization antigen genes. The three described in the text as being related to previously identified genes are in blue. (b) Scaffolds containing arrays or tandem duplications of putative immobilization antigen genes (blue arrows) and pseudogenes (red outlined arrows). Locus accessions identify the individual genes. GenBank accession numbers for scaffolds 1 to 4 are as follows: 1, GL983567; 2, GL983846; 3, GL984331; 4, GL984394.