Sequence Data for Clostridium autoethanogenum using Three Generations of Sequencing Technologies

Utturkar, Sagar M.; Klingeman, Dawn Marie; Bruno-Barcena, José M.; Chinn, Mari S.; Grunden, Amy; Köpke, Michael; Brown, Steven D.

doi:10.1038/sdata.2015.14

Title: Sequence Data for Clostridium autoethanogenum using Three Generations of Sequencing Technologies

Journal Article · Tue Apr 14 00:00:00 EDT 2015 · Scientific Data

DOI:https://doi.org/10.1038/sdata.2015.14· OSTI ID:1185931

Utturkar, Sagar M. ^[1]; Klingeman, Dawn Marie ^[1]; Bruno-Barcena, José M. ^[2]; Chinn, Mari S. ^[1]; Grunden, Amy ^[2]; Köpke, Michael ^[3]; Brown, Steven D. ^[1]

Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)
North Carolina State Univ., Raleigh, NC (United States)
LanzaTech, Skokie, IL (United States)

During the past decade, DNA sequencing output has been mostly dominated by the second generation sequencing platforms which are characterized by low cost, high throughput and shorter read lengths for example, Illumina. The emergence and development of so called third generation sequencing platforms such as PacBio has permitted exceptionally long reads (over 20 kb) to be generated. Due to read length increases, algorithm improvements and hybrid assembly approaches, the concept of one chromosome, one contig and automated finishing of microbial genomes is now a realistic and achievable task for many microbial laboratories. In this paper, we describe high quality sequence datasets which span three generations of sequencing technologies, containing six types of data from four NGS platforms and originating from a single microorganism, Clostridium autoethanogenum. The dataset reported here will be useful for the scientific community to evaluate upcoming NGS platforms, enabling comparison of existing and novel bioinformatics approaches and will encourage interest in the development of innovative experimental and computational methods for NGS data.

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Research Organization:: Oak Ridge National Laboratory (ORNL), Oak Ridge, TN (United States). BioEnergy Science Center (BESC)

Sponsoring Organization:: USDOE

Grant/Contract Number:: AC05-00OR22725

OSTI ID:: 1185931

Journal Information:: Scientific Data, Vol. 2; ISSN 2052-4463

Publisher:: Nature Publishing GroupCopyright Statement

Country of Publication:: United States

Language:: English

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Cited by: 33 works

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References (41)

PBHoney: identifying genomic variants via long-read discordance and interrupted mapping English, Adam C.; Salerno, William J.; Reid, Jeffrey G. BMC Bioinformatics, Vol. 15, Issue 1 https://doi.org/10.1186/1471-2105-15-180	journal	June 2014
Disk Compression of k-mer Sets Rahman, Amatur; Chikhi, Rayan; Medvedev, Paul Schloss Dagstuhl - Leibniz-Zentrum für Informatik https://doi.org/10.4230/lipics.wabi.2020.16	text	January 2020
Hybrid error correction and de novo assembly of single-molecule sequencing reads Koren, Sergey; Schatz, Michael C.; Walenz, Brian P. Nature Biotechnology, Vol. 30, Issue 7 https://doi.org/10.1038/nbt.2280	journal	July 2012
LoRDEC: accurate and efficient long read error correction Salmela, Leena; Rivals, Eric Bioinformatics, Vol. 30, Issue 24 https://doi.org/10.1093/bioinformatics/btu538	journal	August 2014
A tale of three next generation sequencing platforms: comparison of Ion torrent, pacific biosciences and illumina MiSeq sequencers Quail, Michael; Smith, Miriam E.; Coupland, Paul BMC Genomics, Vol. 13, Article No. 341 https://doi.org/10.1186/1471-2164-13-341	journal	January 2012
Data from: Sequence data for Clostridium autoethanogenum using three generations of sequencing technologies Utturkar, Sagar M.; Klingeman, Dawn M.; Bruno-Barcena, José M. Dryad Digital Repository-Supplementary information for journal article at DOI: 10.1038/sdata.2015.14, 3 files https://doi.org/10.5061/dryad.6fm1p	dataset	April 2015
Continuous base identification for single-molecule nanopore DNA sequencing Clarke, James; Wu, Hai-Chen; Jayasinghe, Lakmal Nature Nanotechnology, Vol. 4, Issue 4, p. 265-270 https://doi.org/10.1038/nnano.2009.12	journal	February 2009
Genome Sequence of the Autotrophic Acetogen Clostridium autoethanogenum JA1-1 Strain DSM 10061, a Producer of Ethanol from Carbon Monoxide Bruno-Barcena, J. M.; Chinn, M. S.; Grunden, A. M. Genome Announcements, Vol. 1, Issue 4 https://doi.org/10.1128/genomeA.00628-13	journal	June 2013
Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data Chin, Chen-Shan; Alexander, David H.; Marks, Patrick Nature Methods, Vol. 10, Issue 6 https://doi.org/10.1038/nmeth.2474	journal	May 2013
Development of an electrotransformation protocol for genetic manipulation of Clostridium pasteurianum Pyne, Michael E.; Moo-Young, Murray; Chung, Duane A. Biotechnology for Biofuels, Vol. 6, Issue 1 https://doi.org/10.1186/1754-6834-6-50	journal	January 2013
ExSPAnder: a universal repeat resolver for DNA fragment assembly Prjibelski, A. D.; Vasilinetc, I.; Bankevich, A. Bioinformatics, Vol. 30, Issue 12 https://doi.org/10.1093/bioinformatics/btu266	journal	June 2014
Sanger_Sequence_Data Utturkar, Sagar M.; Köpke, Michael; Brown, Steven D. Dryad Digital Repository https://doi.org/10.5061/dryad.6fm1p/1	dataset	January 2015
DSM10061_PacBio_Data Utturkar, Sagar M.; Köpke, Michael; Brown, Steven D. Dryad Digital Repository https://doi.org/10.5061/dryad.6fm1p/4	dataset	January 2015
Motif_GFF_File Utturkar, Sagar M.; Köpke, Michael; Brown, Steven D. Dryad Digital Repository https://doi.org/10.5061/dryad.6fm1p/2	dataset	January 2015
Single-molecule sequencing of an individual human genome Pushkarev, Dmitry; Neff, Norma F.; Quake, Stephen R. Nature Biotechnology, Vol. 27, Issue 9 https://doi.org/10.1038/nbt.1561	journal	August 2009
Long-read, whole-genome shotgun sequence data for five model organisms Kim, Kristi E.; Peluso, Paul; Babayan, Primo Scientific Data, Vol. 1, Issue 1 https://doi.org/10.1038/sdata.2014.45	journal	November 2014
Four-color DNA sequencing by synthesis using cleavable fluorescent nucleotide reversible terminators Ju, J.; Kim, D. H.; Bi, L. Proceedings of the National Academy of Sciences, Vol. 103, Issue 52 https://doi.org/10.1073/pnas.0609513103	journal	December 2006
Reducing assembly complexity of microbial genomes with single-molecule sequencing Koren, Sergey; Harhay, Gregory P.; Smith, Timothy PL Genome Biology, Vol. 14, Issue 9 https://doi.org/10.1186/gb-2013-14-9-r101	journal	January 2013
Clostridium ljungdahlii represents a microbial production platform based on syngas Kopke, M.; Held, C.; Hujer, S. Proceedings of the National Academy of Sciences, Vol. 107, Issue 29, p. 13087-13092 https://doi.org/10.1073/pnas.1004716107	journal	July 2010
Ten years of next-generation sequencing technology van Dijk, Erwin L.; Auger, Hélène; Jaszczyszyn, Yan Trends in Genetics, Vol. 30, Issue 9 https://doi.org/10.1016/j.tig.2014.07.001	journal	September 2014
Mapping single molecule sequencing reads using basic local alignment with successive refinement (BLASR): application and theory Chaisson, Mark J.; Tesler, Glenn BMC Bioinformatics, Vol. 13, Issue 1 https://doi.org/10.1186/1471-2105-13-238	journal	September 2012
In vivo methylation in Escherichia coli by the Bacillus subtilis phage phi 3T I methyltransferase to protect plasmids from restriction upon transformation of Clostridium acetobutylicum ATCC 824. Mermelstein, L. D.; Papoutsakis, E. T. Applied and Environmental Microbiology, Vol. 59, Issue 4 https://doi.org/10.1128/AEM.59.4.1077-1081.1993	journal	January 1993
The advantages of SMRT sequencing Roberts, Richard J.; Carneiro, Mauricio O.; Schatz, Michael C. Genome Biology, Vol. 14, Issue 7 https://doi.org/10.1186/gb-2013-14-7-405	journal	July 2013
Fast gapped-read alignment with Bowtie 2 Langmead, Ben; Salzberg, Steven L. Nature Methods, Vol. 9, Issue 4 https://doi.org/10.1038/nmeth.1923	journal	March 2012
The advantages of SMRT sequencing Roberts, Richard J.; Carneiro, Mauricio O.; Schatz, Michael C. Genome Biology, Vol. 14, Issue 6 https://doi.org/10.1186/gb-2013-14-6-405	journal	June 2013
Comparison of single-molecule sequencing and hybrid approaches for finishing the genome of Clostridium autoethanogenum and analysis of CRISPR systems in industrial relevant Clostridia Brown, Steven D.; Nagaraju, Shilpa; Utturkar, Sagar Biotechnology for Biofuels, Vol. 7, Issue 1 https://doi.org/10.1186/1754-6834-7-40	journal	January 2014
proovread : large-scale high-accuracy PacBio correction through iterative short read consensus Hackl, Thomas; Hedrich, Rainer; Schultz, Jörg Bioinformatics, Vol. 30, Issue 21 https://doi.org/10.1093/bioinformatics/btu392	journal	July 2014
Evaluation and validation of de novo and hybrid assembly techniques to derive high-quality genome sequences Utturkar, Sagar M.; Klingeman, Dawn M.; Land, Miriam L. Bioinformatics, Vol. 30, Issue 19 https://doi.org/10.1093/bioinformatics/btu391	journal	June 2014
Genome sequencing in microfabricated high-density picolitre reactors Margulies, Marcel; Egholm, Michael; Altman, William E. Nature, Vol. 437, Issue 7057, p. 376-380 https://doi.org/10.1038/nature03959	journal	July 2005
Long-read, whole-genome shotgun sequence data for five model organisms Kim, Kristi E.; Peluso, Paul; Babayan, Primo bioRxiv https://doi.org/10.1101/008037	posted_content	October 2014
Pilon: An Integrated Tool for Comprehensive Microbial Variant Detection and Genome Assembly Improvement Walker, Bruce J.; Abeel, Thomas; Shea, Terrance PLoS ONE, Vol. 9, Issue 11 https://doi.org/10.1371/journal.pone.0112963	journal	November 2014
A reference bacterial genome dataset generated on the MinION™ portable single-molecule nanopore sequencer Quick, Joshua; Quinlan, Aaron R.; Loman, Nicholas J. GigaScience, Vol. 3, Issue 1 https://doi.org/10.1186/2047-217X-3-22	journal	October 2014
GAGE: A critical evaluation of genome assemblies and assembly algorithms Salzberg, S. L.; Phillippy, A. M.; Zimin, A. Genome Research, Vol. 22, Issue 3 https://doi.org/10.1101/gr.131383.111	journal	January 2012
Development of an in vivo methylation system for the solventogen Clostridium saccharobutylicum NCP 262 and analysis of two endonuclease mutants Lesiak, Justyna Maria; Liebl, Wolfgang; Ehrenreich, Armin Journal of Biotechnology, Vol. 188 https://doi.org/10.1016/j.jbiotec.2014.07.005	journal	October 2014
Entering the era of bacterial epigenomics with single molecule real time DNA sequencing Davis, Brigid M.; Chao, Michael C.; Waldor, Matthew K. Current Opinion in Microbiology, Vol. 16, Issue 2 https://doi.org/10.1016/j.mib.2013.01.011	journal	April 2013
Ethanol-Tolerant Gene Identification in Clostridium thermocellum Using Pyro-Resequencing for Metabolic Engineering Yang, Shihui; Klingeman, Dawn M.; Brown, Steven D. Microbial Metabolic Engineering https://doi.org/10.1007/978-1-61779-483-4_9	book	November 2011
One chromosome, one contig: complete microbial genomes from long-read sequencing and assembly Koren, Sergey; Phillippy, Adam M. Current Opinion in Microbiology, Vol. 23 https://doi.org/10.1016/j.mib.2014.11.014	journal	February 2015
Complete Genome Sequences of Eight Helicobacter pylori Strains with Different Virulence Factor Genotypes and Methylation Profiles, Isolated from Patients with Diverse Gastrointestinal Diseases on Okinawa Island, Japan, Determined Using PacBio Single-Molecule Real-Time Technology Satou, K.; Shiroma, A.; Teruya, K. Genome Announcements, Vol. 2, Issue 2 https://doi.org/10.1128/genomea.00286-14	journal	March 2014
Complete Genome Sequence of the Sugar Cane Endophyte Pseudomonas aurantiaca PB-St2, a Disease-Suppressive Bacterium with Antifungal Activity toward the Plant Pathogen Colletotrichum falcatum Mehnaz, S.; Bauer, J. S.; Gross, H. Genome Announcements, Vol. 2, Issue 1 https://doi.org/10.1128/genomea.01108-13	journal	January 2014
Complete Genome Sequence of Highly Adherent Pseudomonas aeruginosa Small-Colony Variant SCV20265 Eckweiler, D.; Bunk, B.; Sproer, C. Genome Announcements, Vol. 2, Issue 1 https://doi.org/10.1128/genomea.01232-13	journal	January 2014
Comparison of Next-Generation Sequencing Systems Liu, Lin; Li, Yinhu; Li, Siliang Journal of Biomedicine and Biotechnology, Vol. 2012 https://doi.org/10.1155/2012/251364	journal	January 2012

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