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

High contiguity Arabidopsis thaliana genome assembly with a single nanopore flow cell

View ORCID ProfileTodd P. Michael, View ORCID ProfileFlorian Jupe, View ORCID ProfileFelix Bemm, Stanley T. Motley, Justin P. Sandoval, View ORCID ProfileOlivier Loudet, View ORCID ProfileDetlef Weigel, View ORCID ProfileJoseph R. Ecker
doi: https://doi.org/10.1101/149997
Todd P. Michael
J. Craig Venter Institute;
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Todd P. Michael
  • For correspondence: toddpmichael@gmail.com
Florian Jupe
The Salk Institute for Biological Studies;
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Florian Jupe
Felix Bemm
Max Planck Institute for Developmental Biology;
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Felix Bemm
Stanley T. Motley
J. Craig Venter Institute;
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Justin P. Sandoval
The Salk Institute for Biological Studies;
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Olivier Loudet
Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS;
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Olivier Loudet
Detlef Weigel
Max Planck Institute for Developmental Biology;
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Detlef Weigel
Joseph R. Ecker
Howard Hughes Medical Institute,The Salk Institute for Biological Studies
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Joseph R. Ecker
  • Abstract
  • Info/History
  • Metrics
  • Supplementary material
  • Preview PDF
Loading

Abstract

While many evolutionary questions can be answered by short read re-sequencing, presence/absence polymorphisms of genes and/or transposons have been largely ignored in large-scale intraspecific evolutionary studies. To enable the rigorous analysis of such variants, multiple high quality and contiguous genome assemblies are essential. Similarly, while genome assemblies based on short reads have made genomics accessible for non-reference species, these assemblies have limitations due to low contiguity. Long-read sequencers and long-read technologies have ushered in a new era of genome sequencing where the lengths of reads exceed those of most repeats. However, because these technologies are not only costly, but also time and compute intensive, it has been unclear how scalable they are. Here we demonstrate a fast and cost effective reference assembly for an Arabidopsis thaliana accession using the USB-sized Oxford Nanopore MinION sequencer and typical consumer computing hardware (4 Cores, 16Gb RAM). We assemble the accession KBS-Mac-74 into 62 contigs with an N50 length of 12.3 Mb covering 100% (119 Mb) of the non-repetitive genome. We demonstrate that the polished KBS-Mac-74 assembly is highly contiguous with BioNano optical genome maps, and of high per-base quality against a likewise polished Pacific Biosciences long-read assembly. The approach we implemented took a total of four days at a cost of less than 1,000 USD for sequencing consumables including instrument depreciation.

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-NC-ND 4.0 International license.
Back to top
PreviousNext
Posted June 14, 2017.
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.
High contiguity Arabidopsis thaliana genome assembly with a single nanopore flow cell
(Your Name) has forwarded a page to you from bioRxiv
(Your Name) thought you would like to see this page from the bioRxiv website.
Share
High contiguity Arabidopsis thaliana genome assembly with a single nanopore flow cell
Todd P. Michael, Florian Jupe, Felix Bemm, Stanley T. Motley, Justin P. Sandoval, Olivier Loudet, Detlef Weigel, Joseph R. Ecker
bioRxiv 149997; doi: https://doi.org/10.1101/149997
Digg logo Reddit logo Twitter logo CiteULike logo Facebook logo Google logo Mendeley logo
Citation Tools
High contiguity Arabidopsis thaliana genome assembly with a single nanopore flow cell
Todd P. Michael, Florian Jupe, Felix Bemm, Stanley T. Motley, Justin P. Sandoval, Olivier Loudet, Detlef Weigel, Joseph R. Ecker
bioRxiv 149997; doi: https://doi.org/10.1101/149997

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 (999)
  • Biochemistry (1493)
  • Bioengineering (946)
  • Bioinformatics (6831)
  • Biophysics (2429)
  • Cancer Biology (1792)
  • Cell Biology (2530)
  • Clinical Trials (106)
  • Developmental Biology (1700)
  • Ecology (2576)
  • Epidemiology (1496)
  • Evolutionary Biology (5029)
  • Genetics (3623)
  • Genomics (4638)
  • Immunology (1175)
  • Microbiology (4252)
  • Molecular Biology (1629)
  • Neuroscience (10801)
  • Paleontology (83)
  • Pathology (240)
  • Pharmacology and Toxicology (409)
  • Physiology (555)
  • Plant Biology (1459)
  • Scientific Communication and Education (412)
  • Synthetic Biology (542)
  • Systems Biology (1878)
  • Zoology (260)