Skip to main content
bioRxiv
  • Home
  • About
  • Submit
  • ALERTS / RSS
Advanced Search
New Results

Application of Long Read Sequencing to Determine Expressed Antigen Diversity in Trypanosoma Brucei Infections

Siddharth Jayaraman, Claire Harris, Edith Paxton, Anne-Marie Donachie, Heli Vaikkinen, Richard McCulloch, James P. J. Hall, John Kenny, Luca Lenzi, Christiane Hertz-Fowler, Christina Cobbold, Richard Reeve, View ORCID ProfileTom Michoel, View ORCID ProfileLiam J. Morrison
doi: https://doi.org/10.1101/432245
Siddharth Jayaraman
1Roslin Institute, University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, United Kingdom
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Claire Harris
2Boyd Orr Centre for Population and Ecosystem Health, Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical and Life Sciences, University of Glasgow, 120 University Place, Glasgow G12 8TA, United Kingdom
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Edith Paxton
1Roslin Institute, University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, United Kingdom
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Anne-Marie Donachie
3Wellcome Centre for Molecular Parasitology, Institute of Infection, Immunity and Inflammation, College of Medical and Life Sciences, University of Glasgow, 120 University Place, Glasgow G12 8TA, United Kingdom
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Heli Vaikkinen
3Wellcome Centre for Molecular Parasitology, Institute of Infection, Immunity and Inflammation, College of Medical and Life Sciences, University of Glasgow, 120 University Place, Glasgow G12 8TA, United Kingdom
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Richard McCulloch
3Wellcome Centre for Molecular Parasitology, Institute of Infection, Immunity and Inflammation, College of Medical and Life Sciences, University of Glasgow, 120 University Place, Glasgow G12 8TA, United Kingdom
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
James P. J. Hall
4Department of Biology, Wentworth Way, University of York, York YO10 5DD, United Kingdom
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
John Kenny
5Centre for Genomic Research, Institute of Integrative Biology, University of Liverpool, Crown Street, Liverpool L69 7ZB, United Kingdom
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Luca Lenzi
5Centre for Genomic Research, Institute of Integrative Biology, University of Liverpool, Crown Street, Liverpool L69 7ZB, United Kingdom
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Christiane Hertz-Fowler
5Centre for Genomic Research, Institute of Integrative Biology, University of Liverpool, Crown Street, Liverpool L69 7ZB, United Kingdom
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Christina Cobbold
2Boyd Orr Centre for Population and Ecosystem Health, Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical and Life Sciences, University of Glasgow, 120 University Place, Glasgow G12 8TA, United Kingdom
6School of Mathematics and Statistics, University of Glasgow, University Place, Glasgow, G12 8QS, United Kingdom
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Richard Reeve
2Boyd Orr Centre for Population and Ecosystem Health, Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical and Life Sciences, University of Glasgow, 120 University Place, Glasgow G12 8TA, United Kingdom
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Tom Michoel
1Roslin Institute, University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, United Kingdom
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Tom Michoel
Liam J. Morrison
1Roslin Institute, University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, United Kingdom
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Liam J. Morrison
  • For correspondence: Liam.Morrison@roslin.ed.ac.uk
  • Abstract
  • Full Text
  • Info/History
  • Metrics
  • Preview PDF
Loading

Abstract

Antigenic variation is employed by many pathogens to evade the host immune response, and Trypanosoma brucei has evolved a complex system to achieve this phenotype, involving sequential use of variant surface glycoprotein (VSG) genes encoded from a large repertoire of ∼2,000 alleles. T. brucei express multiple, sometimes closely related, VSGs in a population at any one time, and the ability to resolve and analyse this diversity has been limited. We applied long read sequencing (PacBio) to VSG amplicons generated from blood extracted from batches of mice sacrificed at time points (days 3, 6, 10 and 12) post-infection with T. brucei TREU927. The data showed that long read sequencing is reliable for resolving allelic differences between VSGs, and demonstrated that there is significant expressed diversity (449 VSGs detected across 20 mice) and across the timeframe of study there was a clear semi-reproducible pattern of expressed diversity (median of 27 VSGs per sample at day 3 post infection (p.i.), 82 VSGs at day 6 p.i., 187 VSGs at day 10 p.i. and 132 VSGs by day 12 p.i.). There was also consistent detection of one VSG dominating expression across replicates at days 3 and 6, and emergence of a second dominant VSG across replicates by day 12. The innovative application of ecological diversity analysis to VSG reads enabled characterisation of hierarchical VSG expression in the dataset, and resulted in a novel method for analysing such patterns of variation. Additionally, the long read approach allowed detection of mosaic VSG expression from very few reads – this was observed as early as day 3, the earliest that such events have been detected. Therefore, our results indicate that long read analysis is a reliable tool for resolving diverse allele expression profiles, and provides novel insights into the complexity and nature of VSG expression in trypanosomes, revealing significantly higher diversity than previously shown and identifying mosaic gene formation unprecedentedly early during the infection process.

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-ND 4.0 International license.
Back to top
PreviousNext
Posted October 02, 2018.
Download PDF
Email

Thank you for your interest in spreading the word about bioRxiv.

NOTE: Your email address is requested solely to identify you as the sender of this article.

Enter multiple addresses on separate lines or separate them with commas.
Application of Long Read Sequencing to Determine Expressed Antigen Diversity in Trypanosoma Brucei Infections
(Your Name) has forwarded a page to you from bioRxiv
(Your Name) thought you would like to see this page from the bioRxiv website.
CAPTCHA
This question is for testing whether or not you are a human visitor and to prevent automated spam submissions.
Share
Application of Long Read Sequencing to Determine Expressed Antigen Diversity in Trypanosoma Brucei Infections
Siddharth Jayaraman, Claire Harris, Edith Paxton, Anne-Marie Donachie, Heli Vaikkinen, Richard McCulloch, James P. J. Hall, John Kenny, Luca Lenzi, Christiane Hertz-Fowler, Christina Cobbold, Richard Reeve, Tom Michoel, Liam J. Morrison
bioRxiv 432245; doi: https://doi.org/10.1101/432245
Digg logo Reddit logo Twitter logo Facebook logo Google logo LinkedIn logo Mendeley logo
Citation Tools
Application of Long Read Sequencing to Determine Expressed Antigen Diversity in Trypanosoma Brucei Infections
Siddharth Jayaraman, Claire Harris, Edith Paxton, Anne-Marie Donachie, Heli Vaikkinen, Richard McCulloch, James P. J. Hall, John Kenny, Luca Lenzi, Christiane Hertz-Fowler, Christina Cobbold, Richard Reeve, Tom Michoel, Liam J. Morrison
bioRxiv 432245; doi: https://doi.org/10.1101/432245

Citation Manager Formats

  • BibTeX
  • Bookends
  • EasyBib
  • EndNote (tagged)
  • EndNote 8 (xml)
  • Medlars
  • Mendeley
  • Papers
  • RefWorks Tagged
  • Ref Manager
  • RIS
  • Zotero
  • Tweet Widget
  • Facebook Like
  • Google Plus One

Subject Area

  • Genomics
Subject Areas
All Articles
  • Animal Behavior and Cognition (3495)
  • Biochemistry (7341)
  • Bioengineering (5314)
  • Bioinformatics (20245)
  • Biophysics (9998)
  • Cancer Biology (7730)
  • Cell Biology (11289)
  • Clinical Trials (138)
  • Developmental Biology (6429)
  • Ecology (9937)
  • Epidemiology (2065)
  • Evolutionary Biology (13311)
  • Genetics (9357)
  • Genomics (12575)
  • Immunology (7695)
  • Microbiology (18997)
  • Molecular Biology (7432)
  • Neuroscience (40965)
  • Paleontology (300)
  • Pathology (1227)
  • Pharmacology and Toxicology (2133)
  • Physiology (3154)
  • Plant Biology (6855)
  • Scientific Communication and Education (1272)
  • Synthetic Biology (1894)
  • Systems Biology (5308)
  • Zoology (1087)