Application of Long Sequence Reads To Improve Genomes for Clostridium thermocellum AD2, Clostridium thermocellum LQRI, and Pelosinus fermentans R7

Sagar M Utturkar; Edward A Bayer; Ilya Borovok; Raphael Lamed; Richard A Hurt; Miriam L Land; Dawn M Klingeman; Dwayne Elias; Jizhong Zhou; Marcel Huntemann; Alicia Clum; Manoj Pillay; Krishnaveni Palaniappan; Neha Varghese; Natalia Mikhailova; Dimitrios Stamatis; T B K Reddy; Chew Yee Ngan; Chris Daum; Nicole Shapiro; Victor Markowitz; Natalia Ivanova; Nikos Kyrpides; Tanja Woyke; Steven D Brown

doi:10.1128/genomeA.01043-16

Application of Long Sequence Reads To Improve Genomes for Clostridium thermocellum AD2, Clostridium thermocellum LQRI, and Pelosinus fermentans R7

Genome Announc. 2016 Sep 29;4(5):e01043-16. doi: 10.1128/genomeA.01043-16.

Authors

Sagar M Utturkar¹, Edward A Bayer², Ilya Borovok³, Raphael Lamed³, Richard A Hurt⁴, Miriam L Land⁴, Dawn M Klingeman⁵, Dwayne Elias⁴, Jizhong Zhou⁶, Marcel Huntemann⁷, Alicia Clum⁷, Manoj Pillay⁷, Krishnaveni Palaniappan⁷, Neha Varghese⁷, Natalia Mikhailova⁷, Dimitrios Stamatis⁷, T B K Reddy⁷, Chew Yee Ngan⁷, Chris Daum⁷, Nicole Shapiro⁷, Victor Markowitz⁷, Natalia Ivanova⁷, Nikos Kyrpides⁷, Tanja Woyke⁷, Steven D Brown⁸

Affiliations

¹ Graduate School of Genome Science and Technology, University of Tennessee, Knoxville, Tennessee, USA.
² Department of Biological Chemistry, The Weizmann Institute of Science, Rehovot, Israel.
³ Department of Molecular Microbiology and Biotechnology, Tel-Aviv University, Ramat Aviv, Israel.
⁴ Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA.
⁵ Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA BioEnergy Science Center, Oak Ridge, Tennessee, USA.
⁶ Institute for Environmental Genomics, University of Oklahoma, Norman, Oklahoma, USA.
⁷ DOE Joint Genome Institute, Walnut Creek, California, USA.
⁸ Graduate School of Genome Science and Technology, University of Tennessee, Knoxville, Tennessee, USA Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA BioEnergy Science Center, Oak Ridge, Tennessee, USA [email protected].

Abstract

We and others have shown the utility of long sequence reads to improve genome assembly quality. In this study, we generated PacBio DNA sequence data to improve the assemblies of draft genomes for Clostridium thermocellum AD2, Clostridium thermocellum LQRI, and Pelosinus fermentans R7.

Grants and funding

The work conducted by the U.S. Department of Energy Joint Genome Institute, a DOE Office of Science User Facility, is supported by the Office of Science of the U.S. Department of Energy under contract no. DE-AC02-05CH11231. This research was supported by the Bioenergy Science Center (BESC), which is a U.S. Department of Energy Bioenergy Research Center supported by the Office of Biological and Environmental Research in the DOE Office of Science. ORNL is managed by UT-Battelle, LLC, Oak Ridge, TN, for the DOE under contract DE-AC05-00OR22725.