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

An improved assembly and annotation of the allohexaploid wheat genome identifies complete families of agronomic genes and provides genomic evidence for chromosomal translocations

Bernardo J. Clavijo, Luca Venturini, Christian Schudoma, Gonzalo Garcia Accinelli, Gemy Kaithakottil, Jonathan Wright, Philippa Borrill, George Kettleborough, Darren Heavens, Helen Chapman, James Lipscombe, Tom Barker, Fu-Hao Lu, Neil McKenzie, Dina Raats, Ricardo H. Ramirez-Gonzalez, Aurore Coince, Ned Peel, Lawrence Percival-Alwyn, Owen Duncan, Josua Trösch, Guotai Yu, Dan Bolser, Guy Namaati, Arnaud Kerhornou, Manuel Spannagl, Heidrun Gundlach, Georg Haberer, Robert P. Davey, Christine Fosker, Federica Di Palma, Andrew Phillips, A. Harvey Millar, Paul J. Kersey, Cristobal Uauy, Ksenia V. Krasileva, David Swarbreck, Michael W. Bevan, Matthew D. Clark
doi: https://doi.org/10.1101/080796
Bernardo J. Clavijo
1Earlham Institute, Norwich, UK
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Luca Venturini
1Earlham Institute, Norwich, UK
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Christian Schudoma
1Earlham Institute, Norwich, UK
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Gonzalo Garcia Accinelli
1Earlham Institute, Norwich, UK
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Gemy Kaithakottil
1Earlham Institute, Norwich, UK
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Jonathan Wright
1Earlham Institute, Norwich, UK
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Philippa Borrill
2John Innes Centre, Norwich, UK
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
George Kettleborough
1Earlham Institute, Norwich, UK
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Darren Heavens
1Earlham Institute, Norwich, UK
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Helen Chapman
1Earlham Institute, Norwich, UK
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
James Lipscombe
1Earlham Institute, Norwich, UK
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Tom Barker
1Earlham Institute, Norwich, UK
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Fu-Hao Lu
2John Innes Centre, Norwich, UK
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Neil McKenzie
2John Innes Centre, Norwich, UK
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Dina Raats
1Earlham Institute, Norwich, UK
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Ricardo H. Ramirez-Gonzalez
1Earlham Institute, Norwich, UK
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Aurore Coince
1Earlham Institute, Norwich, UK
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Ned Peel
1Earlham Institute, Norwich, UK
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Lawrence Percival-Alwyn
1Earlham Institute, Norwich, UK
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Owen Duncan
3ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, Crawley WA 6009, Australia
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Josua Trösch
3ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, Crawley WA 6009, Australia
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Guotai Yu
2John Innes Centre, Norwich, UK
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Dan Bolser
4EMBL European Bioinformatics Institute, Hinxton, UK
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Guy Namaati
4EMBL European Bioinformatics Institute, Hinxton, UK
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Arnaud Kerhornou
4EMBL European Bioinformatics Institute, Hinxton, UK
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Manuel Spannagl
5PGSB Helmholtz Center, Munich, Germany
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Heidrun Gundlach
5PGSB Helmholtz Center, Munich, Germany
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Georg Haberer
5PGSB Helmholtz Center, Munich, Germany
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Robert P. Davey
1Earlham Institute, Norwich, UK
6University of East Anglia, Norwich, UK
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Christine Fosker
1Earlham Institute, Norwich, UK
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Federica Di Palma
1Earlham Institute, Norwich, UK
6University of East Anglia, Norwich, UK
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Andrew Phillips
7Rothamsted Research, Harpenden, UK
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
A. Harvey Millar
3ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, Crawley WA 6009, Australia
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Paul J. Kersey
4EMBL European Bioinformatics Institute, Hinxton, UK
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Cristobal Uauy
2John Innes Centre, Norwich, UK
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Ksenia V. Krasileva
1Earlham Institute, Norwich, UK
6University of East Anglia, Norwich, UK
8The Sainsbury Laboratory, Norwich UK
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
David Swarbreck
1Earlham Institute, Norwich, UK
6University of East Anglia, Norwich, UK
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Michael W. Bevan
2John Innes Centre, Norwich, UK
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Matthew D. Clark
1Earlham Institute, Norwich, UK
6University of East Anglia, Norwich, UK
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • Abstract
  • Full Text
  • Info/History
  • Metrics
  • Supplementary material
  • Preview PDF
Loading

Abstract

Advances in genome sequencing and assembly technologies are generating many high quality genome sequences, but assemblies of large, repeat-rich polyploid genomes, such as that of bread wheat, remain fragmented and incomplete. We have generated a new wheat whole-genome shotgun sequence assembly using a combination of optimised data types and an assembly algorithm designed to deal with large and complex genomes. The new assembly represents more than 78% of the genome with a scaffold N50 of 88.8kbp that has a high fidelity to the input data. Our new annotation combines strand-specific Illumina RNAseq and PacBio full-length cDNAs to identify 104,091 high confidence protein-coding genes and 10,156 non-coding RNA genes. We confirmed three known and identified one novel genome rearrangements. Our approach enables the rapid and scalable assembly of wheat genomes, the identification of structural variants, and the definition of complete gene models, all powerful resources for trait analysis and breeding of this key global crop. [Supplemental material is available for this article.]

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 4.0 International license.
Back to top
PreviousNext
Posted October 13, 2016.
Download PDF

Supplementary Material

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.
An improved assembly and annotation of the allohexaploid wheat genome identifies complete families of agronomic genes and provides genomic evidence for chromosomal translocations
(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
An improved assembly and annotation of the allohexaploid wheat genome identifies complete families of agronomic genes and provides genomic evidence for chromosomal translocations
Bernardo J. Clavijo, Luca Venturini, Christian Schudoma, Gonzalo Garcia Accinelli, Gemy Kaithakottil, Jonathan Wright, Philippa Borrill, George Kettleborough, Darren Heavens, Helen Chapman, James Lipscombe, Tom Barker, Fu-Hao Lu, Neil McKenzie, Dina Raats, Ricardo H. Ramirez-Gonzalez, Aurore Coince, Ned Peel, Lawrence Percival-Alwyn, Owen Duncan, Josua Trösch, Guotai Yu, Dan Bolser, Guy Namaati, Arnaud Kerhornou, Manuel Spannagl, Heidrun Gundlach, Georg Haberer, Robert P. Davey, Christine Fosker, Federica Di Palma, Andrew Phillips, A. Harvey Millar, Paul J. Kersey, Cristobal Uauy, Ksenia V. Krasileva, David Swarbreck, Michael W. Bevan, Matthew D. Clark
bioRxiv 080796; doi: https://doi.org/10.1101/080796
Digg logo Reddit logo Twitter logo Facebook logo Google logo LinkedIn logo Mendeley logo
Citation Tools
An improved assembly and annotation of the allohexaploid wheat genome identifies complete families of agronomic genes and provides genomic evidence for chromosomal translocations
Bernardo J. Clavijo, Luca Venturini, Christian Schudoma, Gonzalo Garcia Accinelli, Gemy Kaithakottil, Jonathan Wright, Philippa Borrill, George Kettleborough, Darren Heavens, Helen Chapman, James Lipscombe, Tom Barker, Fu-Hao Lu, Neil McKenzie, Dina Raats, Ricardo H. Ramirez-Gonzalez, Aurore Coince, Ned Peel, Lawrence Percival-Alwyn, Owen Duncan, Josua Trösch, Guotai Yu, Dan Bolser, Guy Namaati, Arnaud Kerhornou, Manuel Spannagl, Heidrun Gundlach, Georg Haberer, Robert P. Davey, Christine Fosker, Federica Di Palma, Andrew Phillips, A. Harvey Millar, Paul J. Kersey, Cristobal Uauy, Ksenia V. Krasileva, David Swarbreck, Michael W. Bevan, Matthew D. Clark
bioRxiv 080796; doi: https://doi.org/10.1101/080796

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 (4116)
  • Biochemistry (8819)
  • Bioengineering (6522)
  • Bioinformatics (23467)
  • Biophysics (11795)
  • Cancer Biology (9213)
  • Cell Biology (13327)
  • Clinical Trials (138)
  • Developmental Biology (7439)
  • Ecology (11416)
  • Epidemiology (2066)
  • Evolutionary Biology (15155)
  • Genetics (10439)
  • Genomics (14045)
  • Immunology (9174)
  • Microbiology (22163)
  • Molecular Biology (8814)
  • Neuroscience (47583)
  • Paleontology (350)
  • Pathology (1429)
  • Pharmacology and Toxicology (2492)
  • Physiology (3731)
  • Plant Biology (8082)
  • Scientific Communication and Education (1437)
  • Synthetic Biology (2221)
  • Systems Biology (6039)
  • Zoology (1253)