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

Hi-C yields chromosome-length scaffolds for a legume genome, Trifolium subterraneum

Olga Dudchenko, Melanie Pham, Christopher Lui, Sanjit S. Batra, Marie Hoeger, Sarah K. Nyquist, Neva C. Durand, Muhammad S. Shamim, Ido Machol, William Erskine, Erez Lieberman Aiden, View ORCID ProfileParwinder Kaur
doi: https://doi.org/10.1101/473553
Olga Dudchenko
1The Center for Genome Architecture, Baylor College of Medicine, Houston, TX 77030, USA.
2Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA.
3Departments of Computer Science and Computational and Applied Mathematics, Rice University, Houston, TX 77030, USA.
4Center for Theoretical and Biological Physics, Rice University, Houston, TX 77030, USA.
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Melanie Pham
1The Center for Genome Architecture, Baylor College of Medicine, Houston, TX 77030, USA.
2Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA.
3Departments of Computer Science and Computational and Applied Mathematics, Rice University, Houston, TX 77030, USA.
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Christopher Lui
1The Center for Genome Architecture, Baylor College of Medicine, Houston, TX 77030, USA.
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Sanjit S. Batra
1The Center for Genome Architecture, Baylor College of Medicine, Houston, TX 77030, USA.
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Marie Hoeger
1The Center for Genome Architecture, Baylor College of Medicine, Houston, TX 77030, USA.
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Sarah K. Nyquist
1The Center for Genome Architecture, Baylor College of Medicine, Houston, TX 77030, USA.
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Neva C. Durand
1The Center for Genome Architecture, Baylor College of Medicine, Houston, TX 77030, USA.
2Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA.
3Departments of Computer Science and Computational and Applied Mathematics, Rice University, Houston, TX 77030, USA.
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Muhammad S. Shamim
1The Center for Genome Architecture, Baylor College of Medicine, Houston, TX 77030, USA.
2Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA.
3Departments of Computer Science and Computational and Applied Mathematics, Rice University, Houston, TX 77030, USA.
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Ido Machol
1The Center for Genome Architecture, Baylor College of Medicine, Houston, TX 77030, USA.
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
William Erskine
5Centre for Plant Genetics and Breeding, UWA School of Agriculture and Environment, The University of Western Australia, 35 Stirling Highway, Crawley, WA 6009, Australia
6Institute of Agriculture, The University of Western Australia, 35 Stirling Highway, Crawley, WA 6009, Australia
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Erez Lieberman Aiden
1The Center for Genome Architecture, Baylor College of Medicine, Houston, TX 77030, USA.
2Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA.
3Departments of Computer Science and Computational and Applied Mathematics, Rice University, Houston, TX 77030, USA.
4Center for Theoretical and Biological Physics, Rice University, Houston, TX 77030, USA.
7Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA.
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Parwinder Kaur
5Centre for Plant Genetics and Breeding, UWA School of Agriculture and Environment, The University of Western Australia, 35 Stirling Highway, Crawley, WA 6009, Australia
6Institute of Agriculture, The University of Western Australia, 35 Stirling Highway, Crawley, WA 6009, Australia
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Parwinder Kaur
  • Abstract
  • Full Text
  • Info/History
  • Metrics
  • Preview PDF
Loading

Abstract

We present a chromosome-length assembly of the genome of subterranean clover, Trifolium subterraneum, a key Australian pasture legume. Specifically, in situ Hi-C data (48X) was used to correct misjoins and anchor, order, and orient scaffolds in a previously published genome assembly (TSUd_r1.1; scaffold N50: 287kb). This resulted in an improved genome assembly (TrSub3; scaffold N50: 56Mb) containing eight chromosome-length scaffolds that span 95% of the sequenced bases in the input assembly.

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 November 20, 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.
Hi-C yields chromosome-length scaffolds for a legume genome, Trifolium subterraneum
(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
Hi-C yields chromosome-length scaffolds for a legume genome, Trifolium subterraneum
Olga Dudchenko, Melanie Pham, Christopher Lui, Sanjit S. Batra, Marie Hoeger, Sarah K. Nyquist, Neva C. Durand, Muhammad S. Shamim, Ido Machol, William Erskine, Erez Lieberman Aiden, Parwinder Kaur
bioRxiv 473553; doi: https://doi.org/10.1101/473553
Digg logo Reddit logo Twitter logo Facebook logo Google logo LinkedIn logo Mendeley logo
Citation Tools
Hi-C yields chromosome-length scaffolds for a legume genome, Trifolium subterraneum
Olga Dudchenko, Melanie Pham, Christopher Lui, Sanjit S. Batra, Marie Hoeger, Sarah K. Nyquist, Neva C. Durand, Muhammad S. Shamim, Ido Machol, William Erskine, Erez Lieberman Aiden, Parwinder Kaur
bioRxiv 473553; doi: https://doi.org/10.1101/473553

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 (3573)
  • Biochemistry (7517)
  • Bioengineering (5479)
  • Bioinformatics (20675)
  • Biophysics (10257)
  • Cancer Biology (7931)
  • Cell Biology (11578)
  • Clinical Trials (138)
  • Developmental Biology (6563)
  • Ecology (10135)
  • Epidemiology (2065)
  • Evolutionary Biology (13537)
  • Genetics (9497)
  • Genomics (12788)
  • Immunology (7870)
  • Microbiology (19451)
  • Molecular Biology (7613)
  • Neuroscience (41871)
  • Paleontology (306)
  • Pathology (1252)
  • Pharmacology and Toxicology (2179)
  • Physiology (3249)
  • Plant Biology (7005)
  • Scientific Communication and Education (1291)
  • Synthetic Biology (1942)
  • Systems Biology (5405)
  • Zoology (1107)