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

doi:10.1101/473553

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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.

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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.

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Christopher Lui

1The Center for Genome Architecture, Baylor College of Medicine, Houston, TX 77030, USA.

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Sanjit S. Batra

1The Center for Genome Architecture, Baylor College of Medicine, Houston, TX 77030, USA.

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Marie Hoeger

1The Center for Genome Architecture, Baylor College of Medicine, Houston, TX 77030, USA.

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Sarah K. Nyquist

1The Center for Genome Architecture, Baylor College of Medicine, Houston, TX 77030, USA.

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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.

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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.

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Ido Machol

1The Center for Genome Architecture, Baylor College of Medicine, Houston, TX 77030, USA.

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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

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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.

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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

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ORCID record for Parwinder Kaur

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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.

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.

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Posted November 20, 2018.

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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

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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

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