Parallel tagged sequencing on the 454 platform

Nature Protocols
Matthias MeyerMichael Hofreiter

Abstract

Parallel tagged sequencing (PTS) is a molecular barcoding method designed to adapt the recently developed high-throughput 454 parallel sequencing technology for use with multiple samples. Unlike other barcoding methods, PTS can be applied to any type of double-stranded DNA (dsDNA) sample, including shotgun DNA libraries and pools of PCR products, and requires no amplification or gel purification steps. The method relies on attaching sample-specific barcoding adapters, which include sequence tags and a restriction site, to blunt-end repaired DNA samples by ligation and strand-displacement. After pooling multiple barcoded samples, molecules without sequence tags are effectively excluded from sequencing by dephosphorylation and restriction digestion, and using the tag sequences, the source of each DNA sequence can be traced. This protocol allows for sequencing 300 or more complete mitochondrial genomes on a single 454 GS FLX run, or twenty-five 6-kb plasmid sequences on only one 16th plate region. Most of the reactions can be performed in a multichannel setup on 96-well reaction plates, allowing for processing up to several hundreds of samples in a few days.

References

Dec 1, 1977·Proceedings of the National Academy of Sciences of the United States of America·F SangerA R Coulson
Nov 25, 1995·Nucleic Acids Research·M M DeAngelisT L Hawkins
Jul 1, 1996·Nucleic Acids Research·S J AhnJ R Emanuel
Jul 14, 1998·Nature Biotechnology·D S Tawfik, A D Griffiths
Aug 25, 2001·Science·A L RocaS J O'Brien
Dec 1, 2004·Annual Review of Genetics·Svante PääboMichael Hofreiter
Jan 28, 2005·Nature·E HoskinsonThomas M Haard
May 7, 2005·Proceedings. Biological Sciences·Eske Willerslev, Alan Cooper
Aug 2, 2005·Nature·Marcel MarguliesJonathan M Rothberg
Dec 13, 2005·Nature·Kerstin Lindblad-TohEric S Lander
Dec 22, 2005·Science·Hendrik PoinarStephan C Schuster
Jan 10, 2006·Science·Warren E JohnsonStephen J O'Brien
Jul 25, 2006·Infection and Immunity·Dirk HofreuterJorge E Galán
Aug 22, 2006·Nucleic Acids Research·Clark M HendersonMichael T Howard
Aug 29, 2006·BMC Plant Biology·Michael J MooreDouglas E Soltis
Oct 24, 2006·Current Opinion in Genetics & Development·David R Bentley
Oct 28, 2006·BMC Genomics·Thomas WickerNils Stein
Jun 20, 2007·Nucleic Acids Research·Christian HoffmannFrederic D Bushman
Jul 31, 2007·Genome Biology·S M HuseDavid Mark Welch
Aug 3, 2007·Nucleic Acids Research·Matthias MeyerMichael Hofreiter
Sep 15, 2007·Nucleic Acids Research·Clyde A Hutchison

Citations

Apr 6, 2012·TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik·Muhammet SakirogluE Charles Brummer
Feb 6, 2013·Applied Microbiology and Biotechnology·Sarunyou WongwilaiwalinVerawat Champreda
Jul 19, 2011·Journal of Laboratory Automation·Rosalee S Rasmussen Hellberg, Michael T Morrissey
Aug 25, 2011·Molecular Therapy : the Journal of the American Society of Gene Therapy·Annette DeichmannGerard Wagemaker
Nov 10, 2009·Nature Biotechnology·Daniel E Zak, Alan Aderem
Mar 17, 2011·Nature Communications·Ellen D GunnarsdóttirMark Stoneking
Aug 25, 2011·Nature Communications·Sebastian LippoldMichael Hofreiter
Mar 21, 2009·Nature Protocols·Rebecca V ThurberForest Rohwer
Jul 2, 2011·Nature Protocols·Wieteke A M HoeijmakersHendrik G Stunnenberg
Jul 24, 2013·Proceedings of the National Academy of Sciences of the United States of America·Ravi KoppoluThorsten Schnurbusch
Jun 19, 2009·Briefings in Functional Genomics & Proteomics·Paul J Hurd, Christopher J Nelson
Oct 18, 2011·Genome Biology and Evolution·Seth M BybeeKeith A Crandall
Nov 25, 2011·Genome Biology and Evolution·Ehsan KayalDennis V Lavrov
Oct 25, 2011·Nucleic Acids Research·Martin KircherMatthias Meyer
Nov 17, 2010·Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences·Kees van Oers, Jakob C Mueller
Jan 14, 2010·Genome Research·John E PoolRasmus Nielsen
Dec 15, 2010·Genome Research·Ellen D GunnarsdóttirMark Stoneking
Sep 6, 2011·Applied and Environmental Microbiology·David BerryAlexander Loy
Oct 14, 2009·BMC Bioinformatics·Xin ZhouJoshua S Yuan
Mar 12, 2011·BMC Evolutionary Biology·Julia T VilstrupM Thomas P Gilbert
Aug 23, 2012·BMC Evolutionary Biology·Yi-Chiao ChanLinda Vigilant
Dec 26, 2008·BMC Evolutionary Biology·Carles Lalueza-FoxJohannes Krause
May 4, 2010·BMC Genetics·Larissa M WilliamsMarjorie F Oleksiak
Feb 24, 2010·BMC Genomics·Juan I Montoya-BurgosIlham Bahechar
Sep 13, 2013·BMC Microbiology·Jing LiMark Stoneking
Oct 18, 2011·BMC Research Notes·Stefan TaudienMatthias Platzer
Nov 8, 2012·PLoS Computational Biology·Art F Y PoonP Richard Harrigan
Jan 13, 2010·PloS One·Lance B PriceRonald H Gray
Mar 17, 2011·PloS One·Mårten NeimanAfshin Ahmadian
Jul 13, 2011·PloS One·Anne FischerSvante Pääbo
Aug 23, 2011·PloS One·Ivan NasidzeMark Stoneking
Jul 23, 2013·PloS One·Knut FinstermeierChristian Roos
Apr 9, 2014·PloS One·Naraporn SomboonnaSissades Tongsima
Apr 3, 2010·BioTechniques·Tatyana AzhikinaEugene Sverdlov
Jan 21, 2014·Functional & Integrative Genomics·Marianna PasquarielloEnrico Francia
Nov 20, 2013·TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik·Samantha BaldwinJohn McCallum
Jan 3, 2014·The British Journal of Nutrition·Kristian DalySoraya P Shirazi-Beechey
Jun 2, 2014·Molecular Biology and Evolution·Kieren J MitchellAlan Cooper
Mar 24, 2012·Current Opinion in Virology·John L MokiliBas E Dutilh
Dec 27, 2011·Molecular Phylogenetics and Evolution·John E McCormackRobb T Brumfield
May 3, 2011·Trends in Ecology & Evolution·Mark de BruynMichael Hofreiter
May 12, 2010·Forensic Science International. Genetics·B BrenigE Schütz
Sep 19, 2009·Molecular Phylogenetics and Evolution·A B ZhangC-D Zhu
Aug 25, 2009·Clinica Chimica Acta; International Journal of Clinical Chemistry·Maniesh van der VaartPiet J Pretorius
Feb 10, 2009·Trends in Ecology & Evolution·Antonis Rokas, Patrick Abbot
Sep 1, 2009·Molecular Ecology Resources·Albano Beja-PereiraGordon Luikart
Mar 26, 2009·Molecular Ecology·K Mathias Wegner
May 9, 2012·Environmental Microbiology·Sara BeierStefan Bertilsson
Jul 28, 2011·Molecular Ecology Resources·Coralie BertheauChristian Stauffer
Apr 5, 2011·Molecular Ecology Resources·Peter Wandeler, Glauco Camenisch
Feb 6, 2013·Molecular Ecology·John E McCormack, Brant C Faircloth
Nov 7, 2012·Environmental Microbiology·Zhao-Qi SongWen-Jun Li
Oct 19, 2011·Environmental Microbiology·Renee J SmithJames G Mitchell
May 14, 2011·Molecular Ecology Resources·M R GarvinA J Gharrett
May 14, 2011·Molecular Ecology Resources·Maja P GremingerPeter Wandeler
Mar 1, 2010·Molecular Ecology Resources·W Babik
Oct 21, 2009·Human Mutation·Astrid A OutFrederik J Hes
May 21, 2010·BioEssays : News and Reviews in Molecular, Cellular and Developmental Biology·Martin Kircher, Janet Kelso
May 15, 2010·Molecular Ecology·Robert C ThomsonJarrett R Johnson
Sep 18, 2010·Microbiology·Monica ContrerasMaria G Dominguez-Bello
Mar 11, 2015·Molecular Ecology·S Elizabeth AlterMichael Hofreiter
Oct 25, 2011·Current Biology : CB·Heather R L LernerRobert C Fleischer
May 7, 2013·Molecular Phylogenetics and Evolution·Suat Hui YeohWilliam J Foley
Jun 20, 2014·Journal of Environmental Management·Thanaporn LaothanachareonVerawat Champreda
Dec 24, 2014·Journal of Human Evolution·Andrew S BurrellChristina M Bergey
Dec 25, 2012·American Journal of Human Genetics·Michael MuellerTimothy J Aitman
Mar 13, 2014·Proceedings of the National Academy of Sciences of the United States of America·Sandra WildeJoachim Burger
May 29, 2013·FEMS Microbiology Ecology·Sotirios VasileiadisMarco Trevisan
Apr 24, 2013·FEMS Microbiology Ecology·Qiuyuan HuangHailiang Dong
Mar 27, 2016·Genome Biology and Evolution·Shotaro HiraseWataru Iwasaki
Sep 28, 2016·Bioscience, Biotechnology, and Biochemistry·Honglada ThoetkiattikulVerawat Champreda
Sep 9, 2010·Acta Biochimica Et Biophysica Sinica·Yuhua ZhouXiaokui Guo
Oct 15, 2010·Mycologia·Ari JumpponenJohn Blair
Jul 18, 2012·Mycologia·Justine KarstJason D Hoeksema
Apr 28, 2017·Scientific Data·Sebastian BeierMartin Mascher
Mar 4, 2017·Nature Communications·Martina UnterländerJoachim Burger
Jun 7, 2012·Transfusion Medicine and Hemotherapy : Offizielles Organ Der Deutschen Gesellschaft Fur̈ Transfusionsmedizin Und Immunham̈atologie·Christian GabrielJohannes Pröll
Jan 1, 2013·Genetics & Epigenetics·Amanda K WyattChristine L Jasoni
Jun 18, 2011·Journal of Pediatric Gastroenterology and Nutrition·Vi GohDavid Dimmock
Oct 11, 2008·Nature Biotechnology·Jay Shendure, Hanlee Ji
Feb 28, 2009·Clinical Chemistry·Karl V VoelkerdingJacob D Durtschi
Apr 5, 2013·The American Journal of Clinical Nutrition·Hui-Min ChenJing-Yuan Fang
Oct 13, 2016·Mitochondrial DNA. Part A. DNA Mapping, Sequencing, and Analysis·Hongliang ChuTongyan Zhao
Jul 21, 2020·BioMed Research International·Yanwu ChenQiong Xie
Apr 10, 2017·Archives of Microbiology·Naraporn SomboonnaSissades Tongsima
Aug 23, 2017·PeerJ·Naraporn SomboonnaSissades Tongsima
Aug 16, 2017·Nature Ecology & Evolution·Eva Egelyng SigsgaardPhilip Francis Thomsen

Related Concepts

DNA, Mitochondrial
Episomes
Sequence Tagged Sites
Sequence Determinations, DNA
Genome, Mitochondrial

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