title: 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.
authors: Genomic Medicine, J Craig Venter Institute, Rockville, MD 20850, USA. rcoyne@jcvi.org
authors: Robert S
authors: RS
authors: Coyne
authors: Linda
authors: L
authors: Hannick
authors: Dhanasekaran
authors: D
authors: Shanmugam
authors: Jessica B
authors: JB
authors: Hostetler
authors: Daniel
authors: D
authors: Brami
authors: Vinita S
authors: VS
authors: Joardar
authors: Justin
authors: J
authors: Johnson
authors: Diana
authors: D
authors: Radune
authors: Irtisha
authors: I
authors: Singh
authors: Jonathan H
authors: JH
authors: Badger
authors: Ujjwal
authors: U
authors: Kumar
authors: Milton
authors: M
authors: Saier
authors: Yufeng
authors: Y
authors: Wang
authors: Hong
authors: H
authors: Cai
authors: Jianying
authors: J
authors: Gu
authors: Michael W
authors: MW
authors: Mather
authors: Akhil B
authors: AB
authors: Vaidya
authors: David E
authors: DE
authors: Wilkes
authors: Vidyalakshmi
authors: V
authors: Rajagopalan
authors: David J
authors: DJ
authors: Asai
authors: Chad G
authors: CG
authors: Pearson
authors: Robert C
authors: RC
authors: Findly
authors: Harry W
authors: HW
authors: Dickerson
authors: Martin
authors: M
authors: Wu
authors: Cindy
authors: C
authors: Martens
authors: Yves
authors: Y
authors: Van de Peer
authors: David S
authors: DS
authors: Roos
authors: Donna M
authors: DM
authors: Cassidy-Hanley
authors: Theodore G
authors: TG
authors: Clark
mesh_terms: D000818:Animals; D000953:Antigens, Protozoan / Q000235:genetics; D001482:Base Composition; D002874:Chromosome Mapping; D016770:Ciliophora Infections / Q000517:prevention & control*; D004272:DNA, Mitochondrial / Q000235:genetics; D016054:DNA, Protozoan / Q000235:genetics; D030541:Databases, Genetic; D017125:Genes, Protozoan; D059646:Genome Size; D023281:Genomics / Q000379:methods*; D006790:Host-Parasite Interactions; D016803:Hymenostomatida / Q000145:classification / Q000235:genetics* / Q000254:growth & development / Q000472:pathogenicity; D007059:Ictaluridae / Q000469:parasitology; D008018:Life Cycle Stages; D048648:Macronucleus / Q000235:genetics; D026901:Membrane Transport Proteins / Q000235:genetics; D053858:Metabolic Networks and Pathways; D008928:Mitochondria / Q000201:enzymology / Q000235:genetics; D025261:Mitochondrial Proton-Translocating ATPases / Q000235:genetics; D058977:Molecular Sequence Annotation; D010802:Phylogeny; D011494:Protein Kinases / Q000145:classification / Q000235:genetics; D015800:Protozoan Proteins / Q000235:genetics; D016053:RNA, Protozoan / Q000235:genetics; D015027:Zebrafish / Q000235:genetics / Q000469:parasitology*
chemical_list: D000953:Antigens, Protozoan; D004272:DNA, Mitochondrial; D016054:DNA, Protozoan; D026901:Membrane Transport Proteins; D015800:Protozoan Proteins; D016053:RNA, Protozoan; D011494:Protein Kinases; D025261:Mitochondrial Proton-Translocating ATPases