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.
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.
Christopher Lui
1The Center for Genome Architecture, Baylor College of Medicine, Houston, TX 77030, USA.
Sanjit S. Batra
1The Center for Genome Architecture, Baylor College of Medicine, Houston, TX 77030, USA.
Marie Hoeger
1The Center for Genome Architecture, Baylor College of Medicine, Houston, TX 77030, USA.
Sarah K. Nyquist
1The Center for Genome Architecture, Baylor College of Medicine, Houston, TX 77030, USA.
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.
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.
Ido Machol
1The Center for Genome Architecture, Baylor College of Medicine, Houston, TX 77030, USA.
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
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.
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
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.
Posted November 20, 2018.
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
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
Subject Area
Subject Areas
- Biochemistry (11752)
- Bioengineering (8752)
- Bioinformatics (29200)
- Biophysics (14974)
- Cancer Biology (12096)
- Cell Biology (17411)
- Clinical Trials (138)
- Developmental Biology (9421)
- Ecology (14182)
- Epidemiology (2067)
- Evolutionary Biology (18308)
- Genetics (12245)
- Genomics (16803)
- Immunology (11869)
- Microbiology (28097)
- Molecular Biology (11594)
- Neuroscience (60969)
- Paleontology (451)
- Pathology (1871)
- Pharmacology and Toxicology (3238)
- Physiology (4959)
- Plant Biology (10427)
- Synthetic Biology (2886)
- Systems Biology (7340)
- Zoology (1651)