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Title: Long-read, whole-genome shotgun sequence data for five model organisms

Abstract

Single molecule, real-time (SMRT) sequencing from Pacific Biosciences is increasingly used in many areas of biological research including de novo genome assembly, structural-variant identification, haplotype phasing, mRNA isoform discovery, and base-modification analyses. High-quality, public datasets of SMRT sequences can spur development of analytic tools that can accommodate unique characteristics of SMRT data (long read lengths, lack of GC or amplification bias, and a random error profile leading to high consensus accuracy). In this paper, we describe eight high-coverage SMRT sequence datasets from five organisms (Escherichia coli, Saccharomyces cerevisiae, Neurospora crassa, Arabidopsis thaliana, and Drosophila melanogaster) that have been publicly released to the general scientific community (NCBI Sequence Read Archive ID SRP040522). Data were generated using two sequencing chemistries (P4C2 and P5C3) on the PacBio RS II instrument. The datasets reported here can be used without restriction by the research community to generate whole-genome assemblies, test new algorithms, investigate genome structure and evolution, and identify base modifications in some of the most widely-studied model systems in biological research.

Authors:
 [1];  [1];  [1];  [2];  [3];  [3];  [1];  [1];  [1];  [4];  [2];  [3];  [5];  [6];  [1]
+ Show Author Affiliations
  1. Pacific Biosciences of California Inc., Menlo Park, CA (United States)
  2. Flinders Univ., Adelaide, SA (Australia). School of Biological Sciences
  3. Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Dept. of Genome Dynamics
  4. Univ. of California, San Francisco, CA (United States). Dept. of Microbiology and Immunology
  5. National Biodefense Analysis and Countermeasures Center, Frederick, MD (United States)
  6. Univ. of Manchester (United Kingdom). Faculty of Life Sciences
Publication Date:
Research Org.:
Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Biological and Environmental Research (BER). Biological Systems Science Division
OSTI Identifier:
1624538
Grant/Contract Number:  
AC02-05CH11231
Resource Type:
Accepted Manuscript
Journal Name:
Scientific Data
Additional Journal Information:
Journal Volume: 1; Journal Issue: 1; Journal ID: ISSN 2052-4463
Publisher:
Nature Publishing Group
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; Science & Technology - Other Topics

Citation Formats

Kim, Kristi E., Peluso, Paul, Babayan, Primo, Yeadon, P. Jane, Yu, Charles, Fisher, William W., Chin, Chen-Shan, Rapicavoli, Nicole A., Rank, David R., Li, Joachim, Catcheside, David E. A., Celniker, Susan E., Phillippy, Adam M., Bergman, Casey M., and Landolin, Jane M. Long-read, whole-genome shotgun sequence data for five model organisms. United States: N. p., 2014. Web. doi:10.1038/sdata.2014.45.
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Kim, Kristi E., Peluso, Paul, Babayan, Primo, Yeadon, P. Jane, Yu, Charles, Fisher, William W., Chin, Chen-Shan, Rapicavoli, Nicole A., Rank, David R., Li, Joachim, Catcheside, David E. A., Celniker, Susan E., Phillippy, Adam M., Bergman, Casey M., & Landolin, Jane M. Long-read, whole-genome shotgun sequence data for five model organisms. United States. https://doi.org/10.1038/sdata.2014.45
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Kim, Kristi E., Peluso, Paul, Babayan, Primo, Yeadon, P. Jane, Yu, Charles, Fisher, William W., Chin, Chen-Shan, Rapicavoli, Nicole A., Rank, David R., Li, Joachim, Catcheside, David E. A., Celniker, Susan E., Phillippy, Adam M., Bergman, Casey M., and Landolin, Jane M. Tue . "Long-read, whole-genome shotgun sequence data for five model organisms". United States. https://doi.org/10.1038/sdata.2014.45. https://www.osti.gov/servlets/purl/1624538.
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@article{osti_1624538,
title = {Long-read, whole-genome shotgun sequence data for five model organisms},
author = {Kim, Kristi E. and Peluso, Paul and Babayan, Primo and Yeadon, P. Jane and Yu, Charles and Fisher, William W. and Chin, Chen-Shan and Rapicavoli, Nicole A. and Rank, David R. and Li, Joachim and Catcheside, David E. A. and Celniker, Susan E. and Phillippy, Adam M. and Bergman, Casey M. and Landolin, Jane M.},
abstractNote = {Single molecule, real-time (SMRT) sequencing from Pacific Biosciences is increasingly used in many areas of biological research including de novo genome assembly, structural-variant identification, haplotype phasing, mRNA isoform discovery, and base-modification analyses. High-quality, public datasets of SMRT sequences can spur development of analytic tools that can accommodate unique characteristics of SMRT data (long read lengths, lack of GC or amplification bias, and a random error profile leading to high consensus accuracy). In this paper, we describe eight high-coverage SMRT sequence datasets from five organisms (Escherichia coli, Saccharomyces cerevisiae, Neurospora crassa, Arabidopsis thaliana, and Drosophila melanogaster) that have been publicly released to the general scientific community (NCBI Sequence Read Archive ID SRP040522). Data were generated using two sequencing chemistries (P4C2 and P5C3) on the PacBio RS II instrument. The datasets reported here can be used without restriction by the research community to generate whole-genome assemblies, test new algorithms, investigate genome structure and evolution, and identify base modifications in some of the most widely-studied model systems in biological research.},
doi = {10.1038/sdata.2014.45},
journal = {Scientific Data},
number = 1,
volume = 1,
place = {United States},
year = {Tue Nov 25 00:00:00 EST 2014},
month = {Tue Nov 25 00:00:00 EST 2014}
}
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    High-Quality Draft Genome Sequence and Annotation of the Basidiomycete Yeast Sporisorium graminicola CBS10092, a Producer of Mannosylerythritol Lipids
    journal, October 2019

    • Solano-González, Stefany; Darby, Alistair C.; Cossar, Doug
    • Microbiology Resource Announcements, Vol. 8, Issue 42
    • DOI: 10.1128/mra.00479-19

    Sequence data for Clostridium autoethanogenum using three generations of sequencing technologies
    journal, April 2015

    • Utturkar, Sagar M.; Klingeman, Dawn M.; Bruno-Barcena, José M.
    • Scientific Data, Vol. 2, Issue 1
    • DOI: 10.1038/sdata.2015.14

    A complete bacterial genome assembled de novo using only nanopore sequencing data
    journal, June 2015

    • Loman, Nicholas J.; Quick, Joshua; Simpson, Jared T.
    • Nature Methods, Vol. 12, Issue 8
    • DOI: 10.1038/nmeth.3444

    High resolution annotation of zebrafish transcriptome using long-read sequencing
    journal, July 2018

    • Nudelman, German; Frasca, Antonio; Kent, Brandon
    • Genome Research, Vol. 28, Issue 9
    • DOI: 10.1101/gr.223586.117

    Assembly of long error-prone reads using de Bruijn graphs
    journal, December 2016

    • Lin, Yu; Yuan, Jeffrey; Kolmogorov, Mikhail
    • Proceedings of the National Academy of Sciences, Vol. 113, Issue 52
    • DOI: 10.1073/pnas.1604560113

    Heterochromatin-Enriched Assemblies Reveal the Sequence and Organization of the Drosophila melanogaster Y Chromosome
    journal, November 2018

    Mistranslation can enhance fitness through purging of deleterious mutations
    journal, May 2017

    • Bratulic, Sinisa; Toll-Riera, Macarena; Wagner, Andreas
    • Nature Communications, Vol. 8, Issue 1
    • DOI: 10.1038/ncomms15410

    Sequence data for Clostridium autoethanogenum using three generations of sequencing technologies
    journal, April 2015

    • Utturkar, Sagar M.; Klingeman, Dawn M.; Bruno-Barcena, José M.
    • Scientific Data, Vol. 2, Issue 1
    • DOI: 10.1038/sdata.2015.14

    Contiguous and accurate de novo assembly of metazoan genomes with modest long read coverage
    journal, July 2016

    • Chakraborty, Mahul; Baldwin-Brown, James G.; Long, Anthony D.
    • Nucleic Acids Research
    • DOI: 10.1093/nar/gkw654

    A chromosome-scale assembly of the major African malaria vector Anopheles funestus
    posted_content, December 2018

    • Ghurye, Jay; Koren, Sergey; Small, Scott T.
    • bioRxiv
    • DOI: 10.1101/492777

    Multiplex sequencing of bacterial artificial chromosomes for assembling complex plant genomes
    journal, January 2016

    • Beier, Sebastian; Himmelbach, Axel; Schmutzer, Thomas
    • Plant Biotechnology Journal, Vol. 14, Issue 7
    • DOI: 10.1111/pbi.12511

    Strategies for optimizing BioNano and Dovetail explored through a second reference quality assembly for the legume model, Medicago truncatula
    journal, August 2017

    Gerbil: a fast and memory-efficient k-mer counter with GPU-support
    journal, March 2017

    • Erbert, Marius; Rechner, Steffen; Müller-Hannemann, Matthias
    • Algorithms for Molecular Biology, Vol. 12, Issue 1
    • DOI: 10.1186/s13015-017-0097-9

    Islands of retroelements are major components of Drosophila centromeres
    journal, May 2019

    Widespread Polycistronic Transcripts in Fungi Revealed by Single-Molecule mRNA Sequencing
    journal, July 2015

    Long-Read Single Molecule Sequencing to Resolve Tandem Gene Copies: The Mst77Y Region on the Drosophila melanogaster Y Chromosome
    journal, June 2015

    • Krsticevic, Flavia J.; Schrago, Carlos G.; Carvalho, A. Bernardo
    • G3 Genes|Genomes|Genetics, Vol. 5, Issue 6
    • DOI: 10.1534/g3.115.017277

    Single-Molecule Sequencing of the Drosophila serrata Genome
    journal, January 2017

    • Allen, Scott L.; Delaney, Emily K.; Kopp, Artyom
    • G3: Genes|Genomes|Genetics, Vol. 7, Issue 3
    • DOI: 10.1534/g3.116.037598

    Highly Contiguous Genome Assemblies of 15 Drosophila Species Generated Using Nanopore Sequencing
    journal, August 2018

    • Miller, Danny E.; Staber, Cynthia; Zeitlinger, Julia
    • G3: Genes|Genomes|Genetics, Vol. 8, Issue 10
    • DOI: 10.1534/g3.118.200160

    Identification of thyroid tumor cell vulnerabilities through a siRNA-based functional screening
    journal, September 2015

    Detection of Genomic Structural Variants from Next-Generation Sequencing Data
    journal, June 2015

    • Tattini, Lorenzo; D’Aurizio, Romina; Magi, Alberto
    • Frontiers in Bioengineering and Biotechnology, Vol. 3
    • DOI: 10.3389/fbioe.2015.00092

    Targeting Non-Oncogene Addiction: Focus on Thyroid Cancer
    journal, January 2020

    Next-Generation Sequencing Approaches in Cancer: Where Have They Brought Us and Where Will They Take Us?
    journal, September 2015

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