No retraction, correction or concern found when last checked on Oct 18, 2026.

Reducing assembly complexity of microbial genomes with single-molecule sequencing

Sergey Koren, Gregory P Harhay, Timothy PL Smith and 6 more

Genome Biology · 2013 · CC BY

doi:10.1186/gb-2013-14-9-r101

Abstract

Background. The short reads output by first- and second-generation DNA sequencing instruments cannot completely reconstruct microbial chromosomes. Therefore, most genomes have been left unfinished due to the significant resources required to manually close gaps in draft assemblies. Third-generation, single-molecule sequencing addresses this problem by greatly increasing sequencing read length, which simplifies the assembly problem.

Results. To measure the benefit of single-molecule sequencing on microbial genome assembly, we sequenced and assembled the genomes of six bacteria and analyzed the repeat complexity of 2,267 complete bacteria and archaea. Our results indicate that the majority of known bacterial and archaeal genomes can be assembled without gaps, at finished-grade quality, using a single PacBio RS sequencing library. These single-library assemblies are also more accurate than typical short-read assemblies and hybrid assemblies of short and long reads.

Conclusions. Automated assembly of long, single-molecule sequencing data reduces the cost of microbial finishing to $1,000 for most genomes, and future advances in this technology are expected to drive the cost lower. This is expected to increase the number of completed genomes, improve the quality of microbial genome databases, and enable high-fidelity, population-scale studies of pan-genomes and chromosomal organization.

Full text

Its licence does not allow us to show the full text. Read it at PubMed Central:

References 60

1.
Kyrpides NC Genomes OnLine database (GOLD 1.0): A monitor of complete and ongoing genome projects world-wideBioinformatics1999 14773774
Not in our library10.1093/bioinformatics/15.9.773
2.
Pagani I Liolios K Jansson J Chen IM Smirnova T Nosrat B Markowitz VM Kyrpides NC The genomes OnLine database (GOLD) v. 4: status of genomic and metagenomic projects and their associated metadataNucleic Acids Res2012 14D571579
Not in our library10.1093/nar/gkr1100
3.
Fraser CM Eisen JA Nelson KE Paulsen IT Salzberg SL The value of complete microbial genome sequencing (you get what you pay for)J Bacteriol2002 1464036405
Not in our library10.1128/jb.184.23.6403-6405.2002
4.
Chain PS Grafham DV Fulton RS Fitzgerald MG Hostetler J Muzny D Ali J Birren B Bruce DC Buhay C Cole JR Ding Y Dugan S Field D Garrity GM Gibbs R Graves T Han CS Harrison SH Highlander S Hugenholtz P Khouri HM Kodira CD Kolker E Kyrpides NC Lang D Lapidus A Malfatti SA Markowitz V Metha T Genomics. Genome project standards in a new era of sequencingScience2009 14236237
Not in our library10.1126/science.1180614
5.
Salzberg SL Yorke JA Beware of mis-assembled genomesBioinformatics2005 1443204321
Not in our library10.1093/bioinformatics/bti769
6.
Bashir A Klammer AA Robins WP Chin CS Webster D Paxinos E Hsu D Ashby M Wang S Peluso P Sebra R Sorenson J Bullard J Yen J Valdovino M Mollova E Luong K Lin S LaMay B Joshi A Rowe L Frace M Tarr CL Turnsek M Davis BM Kasarskis A Mekalanos JJ Waldor MK Schadt EE A hybrid approach for the automated finishing of bacterial genomesNat Biotechnol2012 14701707
Not in our library10.1038/nbt.2288
7.
Ribeiro FJ Przybylski D Yin S Sharpe T Gnerre S Abouelleil A Berlin AM Montmayeur A Shea TP Walker BJ Young SK Russ C Nusbaum C MacCallum I Jaffe DB Finished bacterial genomes from shotgun sequence dataGenome Res2012 1422702277
Not in our library10.1101/gr.141515.112
8.
Koren S Schatz MC Walenz BP Martin J Howard JT Ganapathy G Wang Z Rasko DA McCombie WR Jarvis ED Phillippy AM Hybrid error correction and de novo assembly of single-molecule sequencing readsNat Biotechnol2012 14693700
Not in our library10.1038/nbt.2280
9.
Timp W Mirsaidov UM Wang D Comer J Aksimentiev A Timp G Nanopore sequencing: electrical measurements of the code of lifeIEEE Trans Nanotechnol2010 14281294
Not in our library10.1109/tnano.2010.2044418
10.
Branton D Deamer DW Marziali A Bayley H Benner SA Butler T Di Ventra M Garaj S Hibbs A Huang X Jovanovich SB Krstic PS Lindsay S Ling XS Mastrangelo CH Meller A Oliver JS Pershin YV Ramsey JM Riehn R Soni GV Tabard-Cossa V Wanunu M Wiggin M Schloss JA The potential and challenges of nanopore sequencingNat Biotechnol2008 1411461153
Not in our library10.1038/nbt.1495
11.
Clarke J Wu HC Jayasinghe L Patel A Reid S Bayley H Continuous base identification for single-molecule nanopore DNA sequencingNat Nanotechnol2009 14265270
Not in our library10.1038/nnano.2009.12
12.
Eid J Fehr A Gray J Luong K Lyle J Otto G Peluso P Rank D Baybayan P Bettman B Bibillo A Bjornson K Chaudhuri B Christians F Cicero R Clark S Dalal R Dewinter A Dixon J Foquet M Gaertner A Hardenbol P Heiner C Hester K Holden D Kearns G Kong X Kuse R Lacroix Y Lin S Real-time DNA sequencing from single polymerase moleculesScience2009 14133138
Not in our library10.1126/science.1162986
13.
Chin CS Sorenson J Harris JB Robins WP Charles RC Jean-Charles RR Bullard J Webster DR Kasarskis A Peluso P Paxinos EE Yamaichi Y Calderwood SB Mekalanos JJ Schadt EE Waldor MK The origin of the Haitian cholera outbreak strainN Engl J Med2011 143342
Not in our library10.1056/nejmoa1012928
14.
Rasko DA Webster DR Sahl JW Bashir A Boisen N Scheutz F Paxinos EE Sebra R Chin CS Iliopoulos D Klammer A Peluso P Lee L Kislyuk AO Bullard J Kasarskis A Wang S Eid J Rank D Redman JC Steyert SR Frimodt-Møller J Struve C Petersen AM Krogfelt KA Nataro JP Schadt EE Waldor MK Origins of the E. coli strain causing an outbreak of hemolytic-uremic syndrome in GermanyN Engl J Med2011 14709717
Not in our library10.1056/nejmoa1106920
15.
Fang G Munera D Friedman DI Mandlik A Chao MC Banerjee O Feng Z Losic B Mahajan MC Jabado OJ Deikus G Clark TA Luong K Murray IA Davis BM Keren-Paz A Chess A Roberts RJ Korlach J Turner SW Kumar V Waldor MK Schadt EE Genome-wide mapping of methylated adenine residues in pathogenic Escherichia coli using single-molecule real-time sequencingNat Biotechnol2012 1412321239
Not in our library10.1038/nbt.2432
16.
Mind the Gap: Upgrading Genomes with Pacific Biosciences RS Long-Read Sequencing Technology · 2012
No notice
17.
Ono Y Asai K Hamada M PBSIM: PacBio reads simulator–toward accurate genome assemblyBioinformatics2013 14119121
Not in our library10.1093/bioinformatics/bts649
18.
Waldbieser G Kertesz M Pushkarev D Blauwkamp T Liu J Production of long (1.5 kb–15.0 kb), accurate, DNA sequencing reads using an Illumina HiSeq2000 to support de novo assembly of the blue catfish genome2013 San Diego, CA: Plant and Animal Genome XXI Conferencehttps://pag.confex.com/pag/xxi/webprogram/Paper7088.html
Not in our library
19.
Miller JR Koren S Sutton G Assembly algorithms for next-generation sequencing dataGenomics2010 14315327
Not in our library10.1016/j.ygeno.2010.03.001
20.
Pop M Genome assembly reborn: recent computational challengesBrief Bioinformatics2009 14354366
Not in our library10.1093/bib/bbp026
21.
Nagarajan N Pop M Sequence assembly demystifiedNat Rev Genet2013 14157167
Not in our library10.1038/nrg3367
22.
Genome assembly forensics: finding the elusive mis-assembly · 2008
No notice
23.
Hooper SD Berg OG On the nature of gene innovation: duplication patterns in microbial genomesMol Biol Evol2003 14945954
Not in our library10.1093/molbev/msg101
24.
Evolutionary Origins of Genomic Repertoires in Bacteria · 2005
No notice
25.
Barrangou R Fremaux C Deveau H Richards M Boyaval P Moineau S Romero DA Horvath P CRISPR provides acquired resistance against viruses in prokaryotesScience2007 1417091712
Not in our library10.1126/science.1138140
26.
Treangen TJ Abraham A-LL Touchon M Rocha EP Genesis, effects and fates of repeats in prokaryotic genomesFEMS Microbiol Rev2009 14539571
Not in our library10.1111/j.1574-6976.2009.00169.x
27.
Assembly complexity of prokaryotic genomes using short reads · 2010
Not checked
28.
Mapping single molecule sequencing reads using basic local alignment with successive refinement (BLASR): application and theory · 2012
No notice
29.
Lee H Schatz MC Genomic dark matter: the reliability of short read mapping illustrated by the genome mappability scoreBioinformatics2012 1420972105
Not in our library10.1093/bioinformatics/bts330
30.
Pacific Biosciences Delivers Enhanced DNA Sequencing Chemistry and Software to Help Solve Complex Genetic Problemshttp://investor.pacificbiosciences.com/releasedetail.cfm?ReleaseID=718854
Not in our library
31.
Miller JR Delcher AL Koren S Venter E Walenz BP Brownley A Johnson J Li K Mobarry C Sutton G Aggressive assembly of pyrosequencing reads with matesBioinformatics2008 1428182824
Not in our library10.1093/bioinformatics/btn548
32.
Chin CS Alexander DH Marks P Klammer AA Drake J Heiner C Clum A Copeland A Huddleston J Eichler EE Turner SW Korlach J Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing dataNat Methods2013 14563569
Not in our library10.1038/nmeth.2474
33.
Durfee T Nelson R Baldwin S Plunkett G 3rd Burland V Mau B Petrosino JF Qin X Muzny DM Ayele M Gibbs RA Csörgo B Pósfai G Weinstock GM Blattner FR The complete genome sequence of Escherichia coli DH10B: insights into the biology of a laboratory workhorseJ Bacteriol2008 1425972606
Not in our library10.1128/jb.01695-07
34.
Nagarajan N Pop M Parametric complexity of sequence assembly: theory and applications to next generation sequencingJ Comput Biol2009 14897908
Not in our library10.1089/cmb.2009.0005
35.
Interactive metagenomic visualization in a Web browser · 2011
No notice
36.
Pacific Biosciences Launches the PacBio(R) RS II Sequencing Systemhttp://investor.pacificbiosciences.com/releasedetail.cfm?ReleaseID=755828
Not in our library
37.
Salzberg SL Phillippy AM Zimin A Puiu D Magoc T Koren S Treangen TJ Schatz MC Delcher AL Roberts M GAGE: A critical evaluation of genome assemblies and assembly algorithmsGenome Res2012 14557567
Not in our library10.1101/gr.131383.111
38.
Magoc T Pabinger S Canzar S Liu X Su Q Puiu D Tallon LJ Salzberg SL GAGE-B: an evaluation of genome assemblers for bacterial organismsBioinformatics2013 1417181725
Not in our library10.1093/bioinformatics/btt273
39.
Margulies M Egholm M Altman WE Attiya S Bader JS Bemben LA Berka J Braverman MS Chen YJ Chen Z Dewell SB Du L Fierro JM Gomes XV Godwin BC He W Helgesen S Ho CH Irzyk GP Jando SC Alenquer ML Jarvie TP Jirage KB Kim JB Knight JR Lanza JR Leamon JH Lefkowitz SM Lei M Li J Genome sequencing in microfabricated high-density picolitre reactorsNature2005 14376380
Not in our library10.1038/nature03959
40.
Bentley DR Balasubramanian S Swerdlow HP Smith GP Milton J Brown CG Hall KP Evers DJ Barnes CL Bignell HR Boutell JM Bryant J Carter RJ Keira Cheetham R Cox AJ Ellis DJ Flatbush MR Gormley NA Humphray SJ Irving LJ Karbelashvili MS Kirk SM Li H Liu X Maisinger KS Murray LJ Obradovic B Ost T Parkinson ML Pratt MR Accurate whole human genome sequencing using reversible terminator chemistryNature2008 145359
Not in our library10.1038/nature07517

All 60 references

Cited by papers we hold 16

HiCanu: accurate assembly of segmental duplications, satellites, and allelic variants from high-fidelity long reads · 2020
No notice
Evaluation of strategies for the assembly of diverse bacterial genomes using MinION long-read sequencing · 2019
No notice
Improved reference genome for the domestic horse increases assembly contiguity and composition · 2018
Corrected
Comprehensive benchmarking and ensemble approaches for metagenomic classifiers · 2017
Corrected
Scaffolding of long read assemblies using long range contact information · 2017
No notice
Advantages of genome sequencing by long-read sequencer using SMRT technology in medical area · 2017
No notice
Canu: scalable and accurate long-read assembly via adaptive k -mer weighting and repeat separation · 2017
No notice
Contiguous and accurate de novo assembly of metazoan genomes with modest long read coverage · 2016
No notice
Oxford Nanopore MinION Sequencing and Genome Assembly · 2016
No notice
The channel catfish genome sequence provides insights into the evolution of scale formation in teleosts · 2016
No notice
Denoising DNA deep sequencing data—high-throughput sequencing errors and their correction · 2015
No notice
Next-generation sequencing (NGS) for assessment of microbial water quality: current progress, challenges, and future opportunities · 2015
No notice
The Harvest suite for rapid core-genome alignment and visualization of thousands of intraspecific microbial genomes · 2014
No notice
Illumina TruSeq Synthetic Long-Reads Empower De Novo Assembly and Resolve Complex, Highly-Repetitive Transposable Elements · 2014
No notice
SSPACE-LongRead: scaffolding bacterial draft genomes using long read sequence information · 2014
No notice
Long-read, whole-genome shotgun sequence data for five model organisms · 2014
No notice

Reads

Read by people on this page

None yet.

Checked or read by AI through naulon

None yet.

A person counts once a day per paper. We keep no cookie and no address: a reader is a hash that changes every day. Any month under five reads shows no number.

Are you an author?

Is this your paper?

Claim it to add your note and be paid when agents cite it. Free.