Tag jumps illuminated - reducing sequence-to-sample misidentifications in metabarcoding studies

Molecular Ecology Resources
Ida Baerholm SchnellM Thomas P Gilbert

Abstract

Metabarcoding of environmental samples on second-generation sequencing platforms has rapidly become a valuable tool for ecological studies. A fundamental assumption of this approach is the reliance on being able to track tagged amplicons back to the samples from which they originated. In this study, we address the problem of sequences in metabarcoding sequencing outputs with false combinations of used tags (tag jumps). Unless these sequences can be identified and excluded from downstream analyses, tag jumps creating sequences with false, but already used tag combinations, can cause incorrect assignment of sequences to samples and artificially inflate diversity. In this study, we document and investigate tag jumping in metabarcoding studies on Illumina sequencing platforms by amplifying mixed-template extracts obtained from bat droppings and leech gut contents with tagged generic arthropod and mammal primers, respectively. We found that an average of 2.6% and 2.1% of sequences had tag combinations, which could be explained by tag jumping in the leech and bat diet study, respectively. We suggest that tag jumping can happen during blunt-ending of pools of tagged amplicons during library build and as a consequence of chimera format...Continue Reading

References

Apr 11, 1990·Nucleic Acids Research·A MeyerhansS Wain-Hobson
Jan 1, 1996·Molecular Biology and Evolution·P G Taylor
May 30, 1998·Nucleic Acids Research·M S JudoC Wilson
Apr 17, 2003·Journal of Biotechnology·Michihiko NakanoAkira Mizuno
Aug 2, 2005·Nature·Marcel MarguliesJonathan M Rothberg
Apr 11, 2008·Biology Letters·Gentile Francesco FicetolaPierre Taberlet
Sep 4, 2008·Journal of Cell Communication and Signaling·Laure Rittié, Bernard Perbal
Mar 26, 2009·Molecular Ecology·Bruce E DeagleSimon N Jarman
Jul 2, 2009·Journal of Agricultural and Food Chemistry·Anthony PegardFrançois Pompanon
Dec 19, 2009·Proceedings of the National Academy of Sciences of the United States of America·James HaileEske Willerslev
Jun 3, 2010·Cold Spring Harbor Protocols·Matthias Meyer, Martin Kircher
Aug 17, 2010·Bioinformatics·Robert C Edgar
Feb 1, 2011·BMC Bioinformatics·Christopher QuincePeter J Turnbaugh
Mar 25, 2011·Molecular Ecology Resources·Matt R K ZealeGareth Jones
Jan 1, 2009·Molecular Ecology Resources·Alice ValentiniPierre Taberlet
May 14, 2011·Molecular Ecology Resources·J H SønstebøC Brochmann
Jun 28, 2011·Bioinformatics·Robert C EdgarRob Knight
Oct 25, 2011·Nucleic Acids Research·Martin KircherMatthias Meyer
Nov 19, 2011·Molecular Ecology·Lucie ZingerThomas Pommier
Dec 17, 2011·Molecular Ecology·Francois PompanonPierre Taberlet
Apr 11, 2012·Molecular Ecology·Pierre TaberletLoren H Rieseberg
Apr 11, 2012·Molecular Ecology·Eric CoissacNicolas Puillandre
Apr 11, 2012·Molecular Ecology·Pierre TaberletEske Willerslev
Jul 4, 2012·BMC Research Notes·Stinus Lindgreen
Jan 29, 2013·Molecular Ecology Resources·R BlaalidH Kauserud
Dec 5, 2013·Conservation Biology : the Journal of the Society for Conservation Biology·Chad B WilseyNathan H Schumaker
Dec 11, 2013·Molecular Ecology·Rakel BlaalidPernille B Eidesen
Jan 3, 2014·Molecular Ecology·Synnøve BotnenHåvard Kauserud

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Citations

Oct 20, 2015·Molecular Ecology·Alice ValentiniTony Dejean
Aug 11, 2015·Molecular Ecology Resources·Alvaro SebastianJacek Radwan
Nov 21, 2015·Molecular Ecology·Jesse A PortRyan P Kelly
Nov 13, 2015·Environmental Science & Technology·Elvira MächlerFlorian Altermatt
Jun 3, 2015·Molecular Ecology Resources·Nathan T EvansDavid M Lodge
Mar 12, 2016·BMC Ecology·Thomas SauvageSuzanne Fredericq
Oct 28, 2016·Genome Génome / Conseil National De Recherches Canada·Anaïs Lacoursière-RousselLouis Bernatchez
Feb 9, 2017·Genome Génome / Conseil National De Recherches Canada·Joanna R Freeland
Apr 4, 2017·The New Phytologist·Laura ParducciMikkel Winther Pedersen
Apr 26, 2017·PloS One·Elizabeth A AndruszkiewiczAlexandria B Boehm
Mar 28, 2018·BMC Genomics·Paul D N HebertEvgeny V Zakharov
Feb 20, 2018·Molecular Ecology Resources·Timothy J DivollJoy M O'Keefe
Nov 1, 2017·Nature Communications·Tobias Guldberg FrøslevAnders Johannes Hansen
Apr 20, 2018·Molecular Ecology Resources·Kristine BohmannM Thomas P Gilbert
Sep 19, 2017·Molecular Ecology·Kristy DeinerLouis Bernatchez
Jul 17, 2018·Molecular Ecology Resources·Taylor M WilcoxMichael K Schwartz
Apr 23, 2017·Applied and Environmental Microbiology·Carles CastañoJosé Antonio Bonet
Nov 9, 2016·MSystems·Maxime GalanJean-François Cosson
Dec 27, 2018·MicrobiologyOpen·Andreas MakiolaTravis R Glare
Oct 26, 2018·Molecular Ecology Resources·Antton AlberdiMarcus Thomas Pius Gilbert
Mar 1, 2019·Scientific Reports·Isabel CanteraSébastien Brosse
Apr 10, 2019·Molecular Ecology Resources·Vera M A ZizkaFlorian Leese
Apr 2, 2019·Molecular Ecology·Matthieu LerayAndrew J Brooks

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