title: Phylogenomic and biogeographic reconstruction of the Trichinella complex.
abstract: Trichinellosis is a globally important food-borne parasitic disease of humans caused by roundworms of the Trichinella complex. Extensive biological diversity is reflected in substantial ecological and genetic variability within and among Trichinella taxa, and major controversy surrounds the systematics of this complex. Here we report the sequencing and assembly of 16 draft genomes representing all 12 recognized Trichinella species and genotypes, define protein-coding gene sets and assess genetic differences among these taxa. Using thousands of shared single-copy orthologous gene sequences, we fully reconstruct, for the first time, a phylogeny and biogeography for the Trichinella complex, and show that encapsulated and non-encapsulated Trichinella taxa diverged from their most recent common ancestor ∼21 million years ago (mya), with taxon diversifications commencing ∼10-7 mya.
authors.affiliation: Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Melbourne, Victoria 3010, Australia.
authors.forename: Pasi K
authors.initials: PK
authors.lastname: Korhonen
authors.affiliation: Istituto Superiore di Sanità, Viale Regina Elena 299, 00161 Rome, Italy.
authors.forename: Edoardo
authors.initials: E
authors.lastname: Pozio
authors.affiliation: Istituto Superiore di Sanità, Viale Regina Elena 299, 00161 Rome, Italy.
authors.forename: Giuseppe
authors.initials: G
authors.lastname: La Rosa
authors.affiliation: Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Melbourne, Victoria 3010, Australia.|Yourgene Bioscience, Shu-Lin District, New Taipei City 23863, Taiwan.
authors.forename: Bill C H
authors.initials: BC
authors.lastname: Chang
authors.affiliation: Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Melbourne, Victoria 3010, Australia.
authors.forename: Anson V
authors.initials: AV
authors.lastname: Koehler
authors.affiliation: United States National Parasite Collection, US Department of Agriculture, Agricultural Research Service, Beltsville, Maryland 20705, USA.
authors.forename: Eric P
authors.initials: EP
authors.lastname: Hoberg
authors.affiliation: Department of Biochemistry and Molecular Biology, Monash University, Melbourne, Victoria 3800, Australia.
authors.forename: Peter R
authors.initials: PR
authors.lastname: Boag
authors.affiliation: Genome Institute of Singapore, 60 Biopolis Street, Singapore 138672, Republic of Singapore.|Cancer and Stem Cell Biology, Duke-NUS Graduate Medical School, Singapore 138672, Republic of Singapore.
authors.forename: Patrick
authors.initials: P
authors.lastname: Tan
authors.affiliation: Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Melbourne, Victoria 3010, Australia.
authors.forename: Aaron R
authors.initials: AR
authors.lastname: Jex
authors.affiliation: Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Melbourne, Victoria 3010, Australia.|Structural Chemistry Program, Eskitis Institute, Griffith University, Brisbane, Queensland 4111, Australia.
authors.forename: Andreas
authors.identifier: http://orcid.org/0000-0003-4408-5467
authors.initials: A
authors.lastname: Hofmann
authors.affiliation: Division of Biology, Howard Hughes Medical Institute, California Institute of Technology, Pasadena, California 91125, USA.
authors.forename: Paul W
authors.identifier: http://orcid.org/0000-0002-7699-0173
authors.initials: PW
authors.lastname: Sternberg
authors.affiliation: Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Melbourne, Victoria 3010, Australia.
authors.forename: Neil D
authors.initials: ND
authors.lastname: Young
authors.affiliation: Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Melbourne, Victoria 3010, Australia.
authors.forename: Robin B
authors.initials: RB
authors.lastname: Gasser
mesh_terms: D000818:Animals; D005786:Gene Expression Regulation / Q000502:physiology; D049751:Genome, Helminth; D023281:Genomics; D005838:Genotype; D010802:Phylogeny; D014234:Trichinella / Q000235:genetics*
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