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Phased Diploid Genome Assembly with Single Molecule Real-Time Sequencing

Chen-Shan Chin, Paul Peluso, Fritz J. Sedlazeck, Maria Nattestad, Gregory T. Concepcion, Alicia Clum, Christopher Dunn, Ronan O'Malley, Rosa Figueroa-Balderas, Abraham Morales-Cruz, Grant R. Cramer, Massimo Delledonne, Chongyuan Luo, Joseph R. Ecker, Dario Cantu, David R. Rank, Michael C. Schatz
doi: https://doi.org/10.1101/056887
Chen-Shan Chin
1Pacific Biosciences, Menlo Park, CA 94025, USA
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Paul Peluso
1Pacific Biosciences, Menlo Park, CA 94025, USA
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Fritz J. Sedlazeck
2Departments of Computer Science and Biology, Johns Hopkins University, Baltimore, MD 21211, US
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Maria Nattestad
3Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
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Gregory T. Concepcion
1Pacific Biosciences, Menlo Park, CA 94025, USA
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Alicia Clum
4DOE Joint Genome Institute, Walnut Creek, California 94598, USA
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Christopher Dunn
1Pacific Biosciences, Menlo Park, CA 94025, USA
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Ronan O'Malley
5Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA.
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Rosa Figueroa-Balderas
6Department of Viticulture and Enology, University of California Davis, CA 95616, USA
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Abraham Morales-Cruz
6Department of Viticulture and Enology, University of California Davis, CA 95616, USA
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Grant R. Cramer
7Department of Biochemistry and Molecular Biology, University of Nevada, Reno, NV 89557, USA
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Massimo Delledonne
8Dipartimento di Biotecnologie, Universita’ degli Studi di Verona, 37134 Verona, Italy
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Chongyuan Luo
5Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA.
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Joseph R. Ecker
5Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA.
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Dario Cantu
6Department of Viticulture and Enology, University of California Davis, CA 95616, USA
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David R. Rank
1Pacific Biosciences, Menlo Park, CA 94025, USA
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Michael C. Schatz
2Departments of Computer Science and Biology, Johns Hopkins University, Baltimore, MD 21211, US
3Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
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Abstract

While genome assembly projects have been successful in a number of haploid or inbred species, one of the current main challenges is assembling non-inbred or rearranged heterozygous genomes. To address this critical need, we introduce the open-source FALCON and FALCON-Unzip algorithms (https://github.com/PacificBiosciences/FALCON/) to assemble Single Molecule Real-Time (SMRT®) Sequencing data into highly accurate, contiguous, and correctly phased diploid genomes. We demonstrate the quality of this approach by assembling new reference sequences for three heterozygous samples, including an F1 hybrid of the model species Arabidopsis thaliana, the widely cultivated V. vinifera cv. Cabernet Sauvignon, and the coral fungus Clavicorona pyxidata that have challenged short-read assembly approaches. The FALCON-based assemblies were substantially more contiguous and complete than alternate short or long-read approaches. The phased diploid assembly enabled the study of haplotype structures and heterozygosities between the homologous chromosomes, including identifying widespread heterozygous structural variations within the coding sequences.

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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 June 03, 2016.
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Phased Diploid Genome Assembly with Single Molecule Real-Time Sequencing
Chen-Shan Chin, Paul Peluso, Fritz J. Sedlazeck, Maria Nattestad, Gregory T. Concepcion, Alicia Clum, Christopher Dunn, Ronan O'Malley, Rosa Figueroa-Balderas, Abraham Morales-Cruz, Grant R. Cramer, Massimo Delledonne, Chongyuan Luo, Joseph R. Ecker, Dario Cantu, David R. Rank, Michael C. Schatz
bioRxiv 056887; doi: https://doi.org/10.1101/056887
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Phased Diploid Genome Assembly with Single Molecule Real-Time Sequencing
Chen-Shan Chin, Paul Peluso, Fritz J. Sedlazeck, Maria Nattestad, Gregory T. Concepcion, Alicia Clum, Christopher Dunn, Ronan O'Malley, Rosa Figueroa-Balderas, Abraham Morales-Cruz, Grant R. Cramer, Massimo Delledonne, Chongyuan Luo, Joseph R. Ecker, Dario Cantu, David R. Rank, Michael C. Schatz
bioRxiv 056887; doi: https://doi.org/10.1101/056887

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