title: The Fasciola hepatica genome: gene duplication and polymorphism reveals adaptation to the host environment and the capacity for rapid evolution.
abstract: BACKGROUND
  The liver fluke Fasciola hepatica is a major pathogen of livestock worldwide, causing huge economic losses to agriculture, as well as 2.4 million human infections annually.
  
  
  RESULTS
  Here we provide a draft genome for F. hepatica, which we find to be among the largest known pathogen genomes at 1.3 Gb. This size cannot be explained by genome duplication or expansion of a single repeat element, and remains a paradox given the burden it may impose on egg production necessary to transmit infection. Despite the potential for inbreeding by facultative self-fertilisation, substantial levels of polymorphism were found, which highlights the evolutionary potential for rapid adaptation to changes in host availability, climate change or to drug or vaccine interventions. Non-synonymous polymorphisms were elevated in genes shared with parasitic taxa, which may be particularly relevant for the ability of the parasite to adapt to a broad range of definitive mammalian and intermediate molluscan hosts. Large-scale transcriptional changes, particularly within expanded protease and tubulin families, were found as the parasite migrated from the gut, across the peritoneum and through the liver to mature in the bile ducts. We identify novel members of anti-oxidant and detoxification pathways and defined their differential expression through infection, which may explain the stage-specific efficacy of different anthelmintic drugs.
  
  
  CONCLUSIONS
  The genome analysis described here provides new insights into the evolution of this important pathogen, its adaptation to the host environment and external selection pressures. This analysis also provides a platform for research into novel drugs and vaccines.
authors.affiliation: Institute of Infection and Global Health, University of Liverpool, Liverpool, UK. K.Cwiklinski@qub.ac.uk.|School of Biological Sciences, Medical Biology Centre, Queen's University of Belfast, Belfast, Northern Ireland, UK. K.Cwiklinski@qub.ac.uk.
authors.forename: Krystyna
authors.initials: K
authors.lastname: Cwiklinski
authors.affiliation: School of Biological Sciences, Medical Biology Centre, Queen's University of Belfast, Belfast, Northern Ireland, UK. j.dalton@qub.ac.uk.|Institute of Parasitology, McGill University, Montreal, Quebec, Canada. j.dalton@qub.ac.uk.
authors.forename: John Pius
authors.initials: JP
authors.lastname: Dalton
authors.affiliation: Institute of Parasitology, McGill University, Montreal, Quebec, Canada. Philippe.Dufresne@inspq.qc.ca.|Institut National de Santé Publique du Québec, Montreal, Quebec, Canada. Philippe.Dufresne@inspq.qc.ca.
authors.forename: Philippe J
authors.initials: PJ
authors.lastname: Dufresne
authors.affiliation: Liverpool School of Tropical Medicine, Liverpool, UK. James.LaCourse@lstmed.ac.uk.
authors.forename: James
authors.initials: J
authors.lastname: La Course
authors.affiliation: Institute of Infection and Global Health, University of Liverpool, Liverpool, UK. williadj@liverpool.ac.uk.
authors.forename: Diana Jl
authors.initials: DJ
authors.lastname: Williams
authors.affiliation: Institute of Infection and Global Health, University of Liverpool, Liverpool, UK. jhodgkin@liverpool.ac.uk.
authors.forename: Jane
authors.initials: J
authors.lastname: Hodgkinson
authors.affiliation: Institute of Integrative Biology, University of Liverpool, Liverpool, UK. s.paterson@liv.ac.uk.
authors.forename: Steve
authors.initials: S
authors.lastname: Paterson
mesh_terms: D000222:Adaptation, Physiological / Q000235:genetics*; D000818:Animals; D005210:Fasciola hepatica / Q000235:genetics* / Q000472:pathogenicity; D005211:Fascioliasis / Q000235:genetics* / Q000469:parasitology / Q000473:pathology; D020440:Gene Duplication / Q000235:genetics*; D020869:Gene Expression Profiling; D049751:Genome, Helminth; D054884:Host-Pathogen Interactions / Q000235:genetics; D006801:Humans; D011110:Polymorphism, Genetic