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.
Additional Information
© 2016 Nature Publishing Group. This work is licensed under a Creative Commons Attribution 4.0 International License. The images or other third party material in this article are included in the article's Creative Commons license, unless indicated otherwise in the credit line; if the material is not included under the Creative Commons license, users will need to obtain permission from the license holder to reproduce the material. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/ Received 05 May 2015. Accepted 18 December 2015. Published 01 February 2016. Funding from the Australian Research Council, the National Health and Medical Research Council (NHMRC) of Australia, Yourgene Bioscience and Melbourne Water Corporation is gratefully acknowledged (R.B.G. et al.). This project was funded in part through DG SANCO of the European Commission and Istituto Superiore di Sanità , Rome (E.P.). This project was also supported by a Victorian Life Sciences Computation Initiative (grant number VR0007) on its Peak Computing Facility at the University of Melbourne, an initiative of the Victorian Government (R.B.G.). N.D.Y. holds an NHMRC Early Career Research Fellowship. P.W.S. thanks the Howard Hughes Medical Institute (HHMI) and the National Institutes of Health (NIH). We thank the staff of Yourgene Bioscience for their contributions. We would specifically like to acknowledge all scientists who developed the programmes used in this study. Given restrictions on the number of articles that could be cited, we were unable to include all original articles in the Methods section. Instead, we have included links to respective websites. P.K.K. is the recipient of a scholarship (STRAPA) from the University of Melbourne. These authors contributed equally to this work: Pasi K. Korhonen, Edoardo Pozio & Giuseppe La Rosa. Contributions: P.K.K., N.D.Y. and R.B.G. wrote the paper with inputs from all other co-authors including B.C.H.C., A.R.J., P.T. and P.R.B. G.L.R., E.P. and colleagues produced parasite material. G.L.R. prepared all nucleic acids and undertook laboratory-based evaluations. P.K.K. undertook the genome assembly and all bioinformatic analyses, with support from N.D.Y. and R.B.G. A.V.K. provided initial support with phylogeny. A.H. provided support with structural modelling. E.P.H. explored aspects of historical biogeography and faunal assembly. With support from G.L.R. and E.P., R.B.G. led the project. The authors declare no competing financial interests.Attached Files
Published - ncomms10513.pdf
Supplemental Material - ncomms10513-s1.pdf
Supplemental Material - ncomms10513-s2.xlsx
Supplemental Material - ncomms10513-s3.xlsx
Supplemental Material - ncomms10513-s4.xlsx
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Additional details
- PMCID
- PMC4740406
- Eprint ID
- 64297
- Resolver ID
- CaltechAUTHORS:20160208-092710363
- Australian Research Council
- National Health and Medical Research Council (NHMRC)
- Directorate-General for Health and Consumers
- Victorian Life Sciences Computation Initiative (VLSCI)
- VR0007
- Howard Hughes Medical Institute (HHMI)
- NIH
- University of Melbourne
- Istituto Superiore di Sanita
- Yourgene Bioscience
- Melbourne Water Corporation
- Created
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2016-02-08Created from EPrint's datestamp field
- Updated
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2023-10-17Created from EPrint's last_modified field