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Genome and transcriptome of the porcine whipworm Trichuris suis

Jex, Aaron R. and Nejsum, Peter and Schwarz, Erich M. and Hu, Li and Young, Neil D. and Hall, Ross S. and Korhonen, Pasi K. and Liao, Shengguang and Thamsborg, Stig and Xia, Jinquan and Xu, Pengwei and Wang, Shaowei and Scheerlinck, Jean-Pierre Y. and Hofmann, Andreas and Sternberg, Paul W. and Wang, Jun and Gasser, Robin B. (2014) Genome and transcriptome of the porcine whipworm Trichuris suis. Nature Genetics, 46 (7). pp. 701-706. ISSN 1061-4036. PMCID PMC4105696. https://resolver.caltech.edu/CaltechAUTHORS:20140623-125424513

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Abstract

Trichuris (whipworm) infects 1 billion people worldwide and causes a disease (trichuriasis) that results in major socioeconomic losses in both humans and pigs. Trichuriasis relates to an inflammation of the large intestine manifested in bloody diarrhea, and chronic disease can cause malnourishment and stunting in children. Paradoxically, Trichuris of pigs has shown substantial promise as a treatment for human autoimmune disorders, including inflammatory bowel disease (IBD) and multiple sclerosis. Here we report whole-genome sequencing at ~140-fold coverage of adult male and female T. suis and ~80-Mb draft assemblies. We explore stage-, sex- and tissue-specific transcription of mRNAs and small noncoding RNAs.


Item Type:Article
Related URLs:
URLURL TypeDescription
http://dx.doi.org/10.1038/ng.3012DOIArticle
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4105696/PubMed CentralArticle
http://rdcu.be/cmpwPublisherFree ReadCube access
ORCID:
AuthorORCID
Schwarz, Erich M.0000-0003-3151-4381
Sternberg, Paul W.0000-0002-7699-0173
Additional Information:© 2014 Macmillan Publishers Limited. This work is licensed under a Creative Commons Attribution-NonCommercial-ShareAlike 3.0 Unported 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-nc-sa/3.0/. Received 15 December 2013; Accepted 22 May 2014; Published online 15 June 2014. We are indebted to the staff of the BGI-Shenzhen who assisted this study but whose names are not included in the authorship. We also acknowledge the continued contributions of staff at WormBase. This project was funded by the Australian Research Council (ARC), the National Health and Medical Research Council (NHMRC) of Australia and BGI-Shenzhen. This research was supported by a Victorian Life Sciences Computation Initiative (VLSCI) grant number VR0007 on its Peak Computing Facility at the University of Melbourne, an initiative of the Victorian Government (A.R.J. and R.B.G.). Other support to R.B.G. from the Alexander von Humboldt Foundation, Australian Academy of Science, the Australian-American Fulbright Commission, Melbourne Water Corporation and the IBM Research Collaboratory for Life Sciences – Melbourne is gratefully acknowledged. P.N. was supported by Danish Agency for Science, Technology and Innovation. N.D.Y. holds an NHMRC Early Career Research Fellowship. E.M.S. was supported by startup funds from Cornell University. P.W.S. is an investigator with the Howard Hughes Medical Institute (HHMI) and acknowledges support from the US National Institutes of Health (NIH). Author Contributions: P.N. and S.T. provided T. suis, and N.D.Y. purified nucleic acids for sequencing. L.H. and S.W. coordinated sequencing. A.R.J., S.L., P.K.K., R.S.H., J.X. and P.X. undertook the assembly, annotation and analyses of genomic and transcriptomic data. A.R.J., R.S.H., A.H., P.K.K. and E.M.S. planned and performed additional, detailed bioinformatic analyses. A.R.J., P.W.S., J.-P.Y.S. and R.B.G. drafted and edited the manuscript, tables, figures and supplementary information. A.R.J., N.D.Y., J.W. and R.B.G. conceived and planned the project. A.R.J., N.D.Y. and R.B.G. supervised and coordinated the research.
Funders:
Funding AgencyGrant Number
Australian Research Council (ARC)UNSPECIFIED
National Health and Medical Research Council (NHMRC) (Australia)UNSPECIFIED
BGI-ShenzhenUNSPECIFIED
Victorian Life Sciences Computation Initiative (VLSCI)VR0007
Alexander von Humboldt FoundationUNSPECIFIED
Australian Academy of ScienceUNSPECIFIED
Australian-American Fulbright CommissionUNSPECIFIED
Melbourne Water CorporationUNSPECIFIED
IBM Research Collaboratory for Life Sciences-MelbourneUNSPECIFIED
Danish Agency for Science, Technology and InnovationUNSPECIFIED
NHMRC Early Career Research FellowshipUNSPECIFIED
Cornell UniversityUNSPECIFIED
Howard Hughes Medical Institute (HHMI)UNSPECIFIED
NIHUNSPECIFIED
Issue or Number:7
PubMed Central ID:PMC4105696
Record Number:CaltechAUTHORS:20140623-125424513
Persistent URL:https://resolver.caltech.edu/CaltechAUTHORS:20140623-125424513
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:46436
Collection:CaltechAUTHORS
Deposited By: Tony Diaz
Deposited On:23 Jun 2014 21:06
Last Modified:29 Oct 2019 21:42

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