A Case Study into Microbial Genome Assembly Gap Sequences and Finishing Strategies

Utturkar, Sagar M.; Klingeman, Dawn M.; Hurt, Jr., Richard A.; Brown, Steven D.

doi:10.3389/fmicb.2017.01272

A Case Study into Microbial Genome Assembly Gap Sequences and Finishing Strategies

Journal Article · Tue Jul 18 00:00:00 EDT 2017 · Frontiers in Microbiology

DOI:https://doi.org/10.3389/fmicb.2017.01272· OSTI ID:1376350

Utturkar, Sagar M. ^[1]; Klingeman, Dawn M. ^[2]; Hurt, Jr., Richard A. ^[3]; Brown, Steven D. ^[4]

Univ. of Tennessee, Knoxville, TN (United States); Purdue Univ., West Lafayette, IN (United States)
Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); BioEnergy Science Center, Oak Ridge, TN (United States)
Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)
Univ. of Tennessee, Knoxville, TN (United States); Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); BioEnergy Science Center, Oak Ridge, TN (United States)

This study characterized regions of DNA which remained unassembled by either PacBio and Illumina sequencing technologies for seven bacterial genomes. Two genomes were manually finished using bioinformatics and PCR/Sanger sequencing approaches and regions not assembled by automated software were analyzed. Gaps present within Illumina assemblies mostly correspond to repetitive DNA regions such as multiple rRNA operon sequences. PacBio gap sequences were evaluated for several properties such as GC content, read coverage, gap length, ability to form strong secondary structures, and corresponding annotations. Our hypothesis that strong secondary DNA structures blocked DNA polymerases and contributed to gap sequences was not accepted. PacBio assemblies had few limitations overall and gaps were explained as cumulative effect of lower than average sequence coverage and repetitive sequences at contig termini. An important aspect of the present study is the compilation of biological features that interfered with assembly and included active transposons, multiple plasmid sequences, phage DNA integration, and large sequence duplication. Furthermore, our targeted genome finishing approach and systematic evaluation of the unassembled DNA will be useful for others looking to close, finish, and polish microbial genome sequences.

View Accepted Manuscript (DOE)

Research Organization:: Oak Ridge National Laboratory (ORNL), Oak Ridge, TN (United States)

Sponsoring Organization:: USDOE

Grant/Contract Number:: AC05-00OR22725

OSTI ID:: 1376350

Journal Information:: Frontiers in Microbiology, Journal Name: Frontiers in Microbiology Vol. 8; ISSN 1664-302X

Publisher:: Frontiers Research FoundationCopyright Statement

Country of Publication:: United States

Language:: English

References (99)

Identification of putative microRNAs in the complete genome of Mycobacterium avium and their possible interaction with human transcripts Nath, Durbba; Chakraborty, Supriyo Journal of Applied Genetics, Vol. 63, Issue 1 https://doi.org/10.1007/s13353-021-00666-9	journal	October 2021
Mind the gap; seven reasons to close fragmented genome assemblies Thomma, Bart P. H. J.; Seidl, Michael F.; Shi-Kunne, Xiaoqian Fungal Genetics and Biology, Vol. 90 https://doi.org/10.1016/j.fgb.2015.08.010	journal	May 2016
Nanopore-based Fourth-generation DNA Sequencing Technology Feng, Yanxiao; Zhang, Yuechuan; Ying, Cuifeng Genomics, Proteomics & Bioinformatics, Vol. 13, Issue 1 https://doi.org/10.1016/j.gpb.2015.01.009	journal	February 2015
PacBio Sequencing and Its Applications Rhoads, Anthony; Au, Kin Fai Genomics, Proteomics & Bioinformatics, Vol. 13, Issue 5 https://doi.org/10.1016/j.gpb.2015.08.002	journal	October 2015
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
A biologist's guide to de novo genome assembly using next-generation sequence data: A test with fungal genomes Haridas, Sajeet; Breuill, Colette; Bohlmann, Joerg Journal of Microbiological Methods, Vol. 86, Issue 3 https://doi.org/10.1016/j.mimet.2011.06.019	journal	September 2011
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
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
A hybrid approach for the automated finishing of bacterial genomes Bashir, Ali; Klammer, Aaron A.; Robins, William P. Nature Biotechnology, Vol. 30, Issue 7 https://doi.org/10.1038/nbt.2288	journal	July 2012
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
A post-assembly genome-improvement toolkit (PAGIT) to obtain annotated genomes from contigs Swain, Martin T.; Tsai, Isheng J.; Assefa, Samual A. Nature Protocols, Vol. 7, Issue 7 https://doi.org/10.1038/nprot.2012.068	journal	June 2012
Acapsular Staphylococcus aureus with a non-functional agr regains capsule expression after passage through the bloodstream in a bacteremia mouse model Suligoy, Carlos M.; Díaz, Rocío E.; Gehrke, Ana-Katharina Scientific Reports, Vol. 10, Issue 1 https://doi.org/10.1038/s41598-020-70671-1	journal	August 2020
Sequence data for Clostridium autoethanogenum using three generations of sequencing technologies Utturkar, Sagar M.; Klingeman, Dawn M.; Bruno-Barcena, José M. Scientific Data, Vol. 2, Issue 1 https://doi.org/10.1038/sdata.2015.14	journal	April 2015
Characterization, correction and de novo assembly of an Oxford Nanopore genomic dataset from Agrobacterium tumefaciens Deschamps, Stéphane; Mudge, Joann; Cameron, Connor Scientific Reports, Vol. 6, Issue 1 https://doi.org/10.1038/srep28625	journal	June 2016
Iterative Correction of Reference Nucleotides (iCORN) using second generation sequencing technology Otto, Thomas D.; Sanders, Mandy; Berriman, Matthew Bioinformatics, Vol. 26, Issue 14 https://doi.org/10.1093/bioinformatics/btq269	journal	June 2010
QUAST: quality assessment tool for genome assemblies Gurevich, Alexey; Saveliev, Vladislav; Vyahhi, Nikolay Bioinformatics, Vol. 29, Issue 8 https://doi.org/10.1093/bioinformatics/btt086	journal	February 2013
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
REBASE—a database for DNA restriction and modification: enzymes, genes and genomes Roberts, Richard J.; Vincze, Tamas; Posfai, Janos Nucleic Acids Research, Vol. 43, Issue D1, p. D298-D299 https://doi.org/10.1093/nar/gku1046	journal	November 2014
Clostridium paradoxum DSM 7308T contains multiple 16S rRNA genes with heterogeneous intervening sequences Rainey, F. A.; Ward-Rainey, N. L.; Janssen, P. H. Microbiology, Vol. 142, Issue 8 https://doi.org/10.1099/13500872-142-8-2087	journal	August 1996
ABySS: A parallel assembler for short read sequence data Simpson, J. T.; Wong, K.; Jackman, S. D. Genome Research, Vol. 19, Issue 6 https://doi.org/10.1101/gr.089532.108	journal	February 2009
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
HINGE: long-read assembly achieves optimal repeat resolution Kamath, Govinda M.; Shomorony, Ilan; Xia, Fei Genome Research, Vol. 27, Issue 5 https://doi.org/10.1101/gr.216465.116	journal	March 2017
Genome Project Standards in a New Era of Sequencing Chain, P. S. G.; Grafham, D. V.; Fulton, R. S. Science, Vol. 326, Issue 5950 https://doi.org/10.1126/science.1180614	journal	October 2009
Near-Complete Genome Sequence of Clostridium paradoxum Strain JW-YL-7 Lancaster, W. Andrew; Utturkar, Sagar M.; Poole, Farris L. Genome Announcements, Vol. 4, Issue 3 https://doi.org/10.1128/genomea.00229-16	journal	May 2016
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
Genome Sequence of Halomonas sp. Strain KO116, an Ionic Liquid-Tolerant Marine Bacterium Isolated from a Lignin-Enriched Seawater Microcosm O’Dell, Kaela B.; Woo, Hannah L.; Utturkar, Sagar Genome Announcements, Vol. 3, Issue 3 https://doi.org/10.1128/genomea.00402-15	journal	May 2015
Draft Genome Sequence of Erwinia tracheiphila , an Economically Important Bacterial Pathogen of Cucurbits Shapiro, Lori R.; Scully, Erin D.; Roberts, Dana Genome Announcements, Vol. 3, Issue 3 https://doi.org/10.1128/genomea.00482-15	journal	June 2015
De Novo Assembly of the Streptomyces sp. Strain Mg1 Genome Using PacBio Single-Molecule Sequencing Hoefler, B. C.; Konganti, K.; Straight, P. D. Genome Announcements, Vol. 1, Issue 4 https://doi.org/10.1128/genomea.00535-13	journal	June 2013
Draft Genome Sequences of Bacillus anthracis Strains Stored for Several Decades in Japan Okutani, Akiko; Osaki, Makoto; Takamatsu, Daisuke Genome Announcements, Vol. 3, Issue 3 https://doi.org/10.1128/genomea.00633-15	journal	June 2015
Draft Genome Sequence of the Lignin-Degrading Burkholderia sp. Strain LIG30, Isolated from Wet Tropical Forest Soil Woo, H. L.; Utturkar, S.; Klingeman, D. Genome Announcements, Vol. 2, Issue 3 https://doi.org/10.1128/genomea.00637-14	journal	May 2014
Draft Genome Sequence of a Natural Root Isolate, Bacillus subtilis UD1022, a Potential Plant Growth-Promoting Biocontrol Agent Bishnoi, Usha; Polson, Shawn W.; Sherrier, D. Janine Genome Announcements, Vol. 3, Issue 4 https://doi.org/10.1128/genomea.00696-15	journal	July 2015
Improved Draft Genome Sequence of Clostridium pasteurianum Strain ATCC 6013 (DSM 525) Using a Hybrid Next-Generation Sequencing Approach Pyne, M. E.; Utturkar, S.; Brown, S. D. Genome Announcements, Vol. 2, Issue 4 https://doi.org/10.1128/genomea.00790-14	journal	July 2014
First Complete Genome Sequence of Clostridium sporogenes DSM 795 ^T , a Nontoxigenic Surrogate for Clostridium botulinum , Determined Using PacBio Single-Molecule Real-Time Technology Nakano, Kazuma; Terabayashi, Yasunobu; Shiroma, Akino Genome Announcements, Vol. 3, Issue 4 https://doi.org/10.1128/genomea.00832-15	journal	July 2015
Improved Complete Genome Sequence of the Extremely Radioresistant Bacterium Deinococcus radiodurans R1 Obtained Using PacBio Single-Molecule Sequencing Hua, Xiaoting; Hua, Yuejin Genome Announcements, Vol. 4, Issue 5 https://doi.org/10.1128/genomea.00886-16	journal	September 2016
Near-Complete Genome Sequence of the Cellulolytic Bacterium Bacteroides ( Pseudobacteroides ) cellulosolvens ATCC 35603 Dassa, Bareket; Utturkar, Sagar; Hurt, Richard A. Genome Announcements, Vol. 3, Issue 5 https://doi.org/10.1128/genomea.01022-15	journal	September 2015
Complete Genome Sequence of Pelosinus fermentans JBW45, a Member of a Remarkably Competitive Group of Negativicutes in the Firmicutes Phylum De León, Kara B.; Utturkar, Sagar M.; Camilleri, Laura B. Genome Announcements, Vol. 3, Issue 5 https://doi.org/10.1128/genomea.01090-15	journal	September 2015
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
Draft Genome Sequences of Escherichia coli Strains Isolated from Septic Patients Dunitz, M. I.; Coil, D. A.; Jospin, G. Genome Announcements, Vol. 2, Issue 6 https://doi.org/10.1128/genomea.01278-14	journal	November 2014
The Value of Complete Microbial Genome Sequencing (You Get What You Pay For) Fraser, C. M.; Eisen, J. A.; Nelson, K. E. Journal of Bacteriology, Vol. 184, Issue 23 https://doi.org/10.1128/jb.184.23.6403-6405.2002	journal	December 2002
Prodigal: prokaryotic gene recognition and translation initiation site identification Hyatt, Doug; Chen, Gwo-Liang; LoCascio, Philip F. BMC Bioinformatics, Vol. 11, Issue 1 https://doi.org/10.1186/1471-2105-11-119	journal	March 2010
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
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
PerPlot & PerScan: tools for analysis of DNA curvature-related periodicity in genomic nucleotide sequences Mrázek, Jan; Chaudhari, Tejas; Basu, Aryabrata Microbial Informatics and Experimentation, Vol. 1, Issue 1 https://doi.org/10.1186/2042-5783-1-13	journal	November 2011
A single chromosome assembly of Bacteroides fragilis strain BE1 from Illumina and MinION nanopore sequencing data Risse, Judith; Thomson, Marian; Patrick, Sheila GigaScience, Vol. 4, Issue 1 https://doi.org/10.1186/s13742-015-0101-6	journal	December 2015
Mind the Gap: Upgrading Genomes with Pacific Biosciences RS Long-Read Sequencing Technology English, Adam C.; Richards, Stephen; Han, Yi PLoS ONE, Vol. 7, Issue 11 https://doi.org/10.1371/journal.pone.0047768	journal	November 2012
Investigating the Interplay between Nucleoid-Associated Proteins, DNA Curvature, and CRISPR Elements Using Comparative Genomics Tong, Hao; Mrázek, Jan PLoS ONE, Vol. 9, Issue 3 https://doi.org/10.1371/journal.pone.0090940	journal	March 2014
Evaluation and Validation of Assembling Corrected PacBio Long Reads for Microbial Genome Completion via Hybrid Approaches Lin, Hsin-Hung; Liao, Yu-Chieh PLOS ONE, Vol. 10, Issue 12 https://doi.org/10.1371/journal.pone.0144305	journal	December 2015
A5-miseq: an updated pipeline to assemble microbial genomes from Illumina MiSeq data Coil, David; Jospin, Guillaume; Darling, Aaron E. arXiv https://doi.org/10.48550/arxiv.1401.5130	preprint	January 2014
Phylogenetic Methods for Genome-Wide Association Studies in Bacteria Didelot, Xavier Bacterial Pangenomics https://doi.org/10.1007/978-1-0716-1099-2_13	book	January 2021
Morphological and genetic characterization of the first Isospora species (I. lugensae n. sp.) from a Kerguelen petrel (Lugensa brevirostris) Yang, Rongchang; Brice, Belinda; Liu, Qier Parasitology Research, Vol. 120, Issue 3 https://doi.org/10.1007/s00436-021-07046-6	journal	January 2021
Real-Time DNA Sequencing from Single Polymerase Molecules Korlach, Jonas; Bjornson, Keith P.; Chaudhuri, Bidhan P. Methods in Enzymology, Vol. 472, p. 431-455 https://doi.org/10.1016/S0076-6879(10)72001-2	book	January 2010
Next generation sequencing technology: Advances and applications Buermans, H. P. J.; den Dunnen, J. T. Biochimica et Biophysica Acta (BBA) - Molecular Basis of Disease, Vol. 1842, Issue 10 https://doi.org/10.1016/j.bbadis.2014.06.015	journal	October 2014
Erratum: Repetitive DNA and next-generation sequencing: computational challenges and solutions Treangen, Todd J.; Salzberg, Steven L. Nature Reviews Genetics, Vol. 13, Issue 2 https://doi.org/10.1038/nrg3164	journal	January 2012
Sequence assembly demystified Nagarajan, Niranjan; Pop, Mihai Nature Reviews Genetics, Vol. 14, Issue 3 https://doi.org/10.1038/nrg3367	journal	January 2013
Mutations in virus-derived small RNAs Nigam, Deepti; LaTourrette, Katherine; Garcia-Ruiz, Hernan Scientific Reports, Vol. 10, Issue 1 https://doi.org/10.1038/s41598-020-66374-2	journal	June 2020
SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing Bankevich, Anton; Nurk, Sergey; Antipov, Dmitry Journal of Computational Biology, Vol. 19, Issue 5 https://doi.org/10.1089/cmb.2012.0021	journal	May 2012
Gepard: a rapid and sensitive tool for creating dotplots on genome scale Krumsiek, J.; Arnold, R.; Rattei, T. Bioinformatics, Vol. 23, Issue 8 https://doi.org/10.1093/bioinformatics/btm039	journal	February 2007
Geneious Basic: An integrated and extendable desktop software platform for the organization and analysis of sequence data Kearse, M.; Moir, R.; Wilson, A. Bioinformatics, Vol. 28, Issue 12 https://doi.org/10.1093/bioinformatics/bts199	journal	April 2012
GAGE-B: an evaluation of genome assemblers for bacterial organisms Magoc, Tanja; Pabinger, Stephan; Canzar, Stefan Bioinformatics, Vol. 29, Issue 14 https://doi.org/10.1093/bioinformatics/btt273	journal	May 2013
A5-miseq: an updated pipeline to assemble microbial genomes from Illumina MiSeq data Coil, David; Jospin, Guillaume; Darling, Aaron E. Bioinformatics, Vol. 31, Issue 4 https://doi.org/10.1093/bioinformatics/btu661	journal	October 2014
plasmidSPAdes: assembling plasmids from whole genome sequencing data Antipov, Dmitry; Hartwick, Nolan; Shen, Max Bioinformatics https://doi.org/10.1093/bioinformatics/btw493	journal	July 2016
Mfold web server for nucleic acid folding and hybridization prediction Zuker, M. Nucleic Acids Research, Vol. 31, Issue 13 https://doi.org/10.1093/nar/gkg595	journal	July 2003
REBASE—a database for DNA restriction and modification: enzymes, genes and genomes Roberts, Richard J.; Vincze, Tamas; Posfai, Janos Nucleic Acids Research, Vol. 38, Issue suppl_1 https://doi.org/10.1093/nar/gkp874	journal	October 2009
Robust high-throughput prokaryote de novo assembly and improvement pipeline for Illumina data Page, Andrew J.; De Silva, Nishadi; Hunt, Martin Microbial Genomics, Vol. 2, Issue 8 https://doi.org/10.1099/mgen.0.000083	journal	August 2016
Canu: scalable and accurate long-read assembly via adaptive k -mer weighting and repeat separation Koren, Sergey; Walenz, Brian P.; Berlin, Konstantin Genome Research, Vol. 27, Issue 5 https://doi.org/10.1101/gr.215087.116	journal	March 2017
The Value of Complete Microbial Genome Sequencing (You Get What You Pay For) Fraser, C. M.; Eisen, J. A.; Nelson, K. E. Journal of Bacteriology, Vol. 184, Issue 23 https://doi.org/10.1128/JB.184.23.6403-6405.2002	journal	December 2002
Complete Closed Genome Sequences of Three Bibersteinia trehalosi Nasopharyngeal Isolates from Cattle with Shipping Fever Harhay, G. P.; McVey, D. S.; Koren, S. Genome Announcements, Vol. 2, Issue 1 https://doi.org/10.1128/genomeA.00084-14	journal	January 2014
Near-Complete Genome Sequence of Clostridium paradoxum Strain JW-YL-7 Lancaster, W. Andrew; Utturkar, Sagar M.; Poole, Farris L. Genome Announcements, Vol. 4, Issue 3 https://doi.org/10.1128/genomeA.00229-16	journal	May 2016
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
Genome Sequence of Halomonas sp. Strain KO116, an Ionic Liquid-Tolerant Marine Bacterium Isolated from a Lignin-Enriched Seawater Microcosm O’Dell, Kaela B.; Woo, Hannah L.; Utturkar, Sagar Genome Announcements, Vol. 3, Issue 3 https://doi.org/10.1128/genomeA.00402-15	journal	May 2015
Draft Genome Sequence of Erwinia tracheiphila , an Economically Important Bacterial Pathogen of Cucurbits Shapiro, Lori R.; Scully, Erin D.; Roberts, Dana Genome Announcements, Vol. 3, Issue 3 https://doi.org/10.1128/genomeA.00482-15	journal	June 2015
De Novo Assembly of the Streptomyces sp. Strain Mg1 Genome Using PacBio Single-Molecule Sequencing Hoefler, B. C.; Konganti, K.; Straight, P. D. Genome Announcements, Vol. 1, Issue 4 https://doi.org/10.1128/genomeA.00535-13	journal	June 2013
Draft Genome Sequences of Bacillus anthracis Strains Stored for Several Decades in Japan Okutani, Akiko; Osaki, Makoto; Takamatsu, Daisuke Genome Announcements, Vol. 3, Issue 3 https://doi.org/10.1128/genomeA.00633-15	journal	June 2015
Draft Genome Sequence of the Lignin-Degrading Burkholderia sp. Strain LIG30, Isolated from Wet Tropical Forest Soil Woo, H. L.; Utturkar, S.; Klingeman, D. Genome Announcements, Vol. 2, Issue 3 https://doi.org/10.1128/genomeA.00637-14	journal	May 2014
Draft Genome Sequence of a Natural Root Isolate, Bacillus subtilis UD1022, a Potential Plant Growth-Promoting Biocontrol Agent Bishnoi, Usha; Polson, Shawn W.; Sherrier, D. Janine Genome Announcements, Vol. 3, Issue 4 https://doi.org/10.1128/genomeA.00696-15	journal	July 2015
Complete Genome Sequence of Bacillus thuringiensis Serovar Tolworthi Strain Pasteur Institute Standard Kanda, Kohzo; Nakashima, Kaede; Nagano, Yukio Genome Announcements, Vol. 3, Issue 4 https://doi.org/10.1128/genomeA.00710-15	journal	July 2015
Improved Draft Genome Sequence of Clostridium pasteurianum Strain ATCC 6013 (DSM 525) Using a Hybrid Next-Generation Sequencing Approach Pyne, M. E.; Utturkar, S.; Brown, S. D. Genome Announcements, Vol. 2, Issue 4 https://doi.org/10.1128/genomeA.00790-14	journal	July 2014
First Complete Genome Sequence of Clostridium sporogenes DSM 795 ^T , a Nontoxigenic Surrogate for Clostridium botulinum , Determined Using PacBio Single-Molecule Real-Time Technology Nakano, Kazuma; Terabayashi, Yasunobu; Shiroma, Akino Genome Announcements, Vol. 3, Issue 4 https://doi.org/10.1128/genomeA.00832-15	journal	July 2015
Complete Genome Sequence of Pelosinus sp. Strain UFO1 Assembled Using Single-Molecule Real-Time DNA Sequencing Technology Brown, S. D.; Utturkar, S. M.; Magnuson, T. S. Genome Announcements, Vol. 2, Issue 5 https://doi.org/10.1128/genomeA.00881-14	journal	September 2014
Improved Complete Genome Sequence of the Extremely Radioresistant Bacterium Deinococcus radiodurans R1 Obtained Using PacBio Single-Molecule Sequencing Hua, Xiaoting; Hua, Yuejin Genome Announcements, Vol. 4, Issue 5 https://doi.org/10.1128/genomeA.00886-16	journal	September 2016
Near-Complete Genome Sequence of the Cellulolytic Bacterium Bacteroides ( Pseudobacteroides ) cellulosolvens ATCC 35603 Dassa, Bareket; Utturkar, Sagar; Hurt, Richard A. Genome Announcements, Vol. 3, Issue 5 https://doi.org/10.1128/genomeA.01022-15	journal	September 2015
Application of Long Sequence Reads To Improve Genomes for Clostridium thermocellum AD2, Clostridium thermocellum LQRI, and Pelosinus fermentans R7 Utturkar, Sagar M.; Bayer, Edward A.; Borovok, Ilya Genome Announcements, Vol. 4, Issue 5 https://doi.org/10.1128/genomeA.01043-16	journal	September 2016
Complete Genome Sequence of Pelosinus fermentans JBW45, a Member of a Remarkably Competitive Group of Negativicutes in the Firmicutes Phylum De León, Kara B.; Utturkar, Sagar M.; Camilleri, Laura B. Genome Announcements, Vol. 3, Issue 5 https://doi.org/10.1128/genomeA.01090-15	journal	September 2015
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
Draft Genome Sequences of Escherichia coli Strains Isolated from Septic Patients Dunitz, M. I.; Coil, D. A.; Jospin, G. Genome Announcements, Vol. 2, Issue 6 https://doi.org/10.1128/genomeA.01278-14	journal	November 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
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
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
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
Fine-scale population structure and evidence for local adaptation in Australian giant black tiger shrimp (Penaeus monodon) using SNP analysis Vu, Nga T. T.; Zenger, Kyall R.; Guppy, Jarrod L. BMC Genomics, Vol. 21, Issue 1 https://doi.org/10.1186/s12864-020-07084-x	journal	September 2020
Circlator: automated circularization of genome assemblies using long sequencing reads Hunt, Martin; Silva, Nishadi De; Otto, Thomas D. Genome Biology, Vol. 16, Issue 1 https://doi.org/10.1186/s13059-015-0849-0	journal	December 2015
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
Robust high-throughput prokaryote de novo assembly and improvement pipeline for Illumina data. Page, Andrew J.; De Silva, Nishadi; Hunt, Martin Apollo - University of Cambridge Repository https://doi.org/10.17863/cam.43554	text	January 2016
Draft Genome Sequence of Erwinia tracheiphila, an Economically Important Bacterial Pathogen of Cucurbits R., Shapiro, Lori; D., Scully, Erin; Dana, Roberts, ETH Zurich https://doi.org/10.3929/ethz-b-000103410	text	January 2015
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
Charting the genomic landscape of seed-free plants Péter, Szövényi,; Andika, Gunadi,; Fay-Wei, Li, Nature Publishing Group https://doi.org/10.5167/uzh-203460	text	January 2021
Circlator: automated circularization of genome assemblies using long sequencing reads Hunt, Martin; Silva, Nishadi; Otto, Thomas Figshare https://doi.org/10.6084/m9.figshare.c.3596210	collection	January 2015

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Improved genome of Agrobacterium radiobacter type strain provides new taxonomic insight into Agrobacterium genomospecies 4 Gan, Han Ming; Lee, Melvin V. L.; Savka, Michael A. PeerJ, Vol. 7 https://doi.org/10.7717/peerj.6366	journal	January 2019
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Genomic repeats, misassembly and reannotation: a case study with long-read resequencing of Porphyromonas gingivalis reference strains Acuña-Amador, Luis; Primot, Aline; Cadieu, Edouard BMC Genomics, Vol. 19, Issue 1 https://doi.org/10.1186/s12864-017-4429-4	journal	January 2018
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