Nanopore sequencing of long ribosomal DNA amplicons enables portable and simple biodiversity assessments with high phylogenetic resolution across broad taxonomic scale

GigaScience
Henrik KrehenwinkelStefan Prost

Abstract

In light of the current biodiversity crisis, DNA barcoding is developing into an essential tool to quantify state shifts in global ecosystems. Current barcoding protocols often rely on short amplicon sequences, which yield accurate identification of biological entities in a community but provide limited phylogenetic resolution across broad taxonomic scales. However, the phylogenetic structure of communities is an essential component of biodiversity. Consequently, a barcoding approach is required that unites robust taxonomic assignment power and high phylogenetic utility. A possible solution is offered by sequencing long ribosomal DNA (rDNA) amplicons on the MinION platform (Oxford Nanopore Technologies). Using a dataset of various animal and plant species, with a focus on arthropods, we assemble a pipeline for long rDNA barcode analysis and introduce a new software (MiniBar) to demultiplex dual indexed Nanopore reads. We find excellent phylogenetic and taxonomic resolution offered by long rDNA sequences across broad taxonomic scales. We highlight the simplicity of our approach by field barcoding with a miniaturized, mobile laboratory in a remote rainforest. We also test the utility of long rDNA amplicons for analysis of communi...Continue Reading

References

Dec 1, 1991·The Quarterly Review of Biology·D M Hillis, M T Dixon
Oct 5, 1990·Journal of Molecular Biology·S F AltschulD J Lipman
Feb 1, 1996·Applied and Environmental Microbiology·M T Suzuki, S J Giovannoni
Mar 10, 2000·Science·O E SalaD H Wall
Aug 29, 2001·Bioinformatics·J P Huelsenbeck, F Ronquist
Sep 4, 2003·Proceedings. Biological Sciences·Paul D N HebertJeremy R deWaard
Nov 11, 2003·Annales D'urologie·F Boukinda, G Nervetti
Nov 3, 2004·Proceedings of the National Academy of Sciences of the United States of America·Todd A Blackledge, Rosemary G Gillespie
Feb 20, 2007·Frontiers in Zoology·Rainer SonnenbergDiethard Tautz
May 20, 2009·Bioinformatics·Heng Li, Richard Durbin
Jun 10, 2009·Bioinformatics·Heng Li1000 Genome Project Data Processing Subgroup
Sep 14, 2011·Annual Review of Entomology·Gonzalo Giribet, Gregory D Edgecombe
Nov 22, 2011·Proceedings of the National Academy of Sciences of the United States of America·De-Zhu LiGuang-Wen Duan
Dec 17, 2011·American Journal of Botany·Shannon C K StraubAaron Liston
Feb 10, 2012·Molecular Biology and Evolution·Robert LanfearStephane Guindon
Mar 29, 2012·Proceedings of the National Academy of Sciences of the United States of America·Conrad L SchochFungal Barcoding Consortium Author List
Sep 19, 2012·Proceedings of the National Academy of Sciences of the United States of America·Cuong Q TangDiego Fontaneto
Oct 11, 2012·PloS One·Ryuji J Machida, Nancy Knowlton
Oct 18, 2013·Molecular Biology and Evolution·Koichiro TamuraSudhir Kumar
Nov 8, 2014·Science·Bernhard MisofXin Zhou
Apr 1, 2015·Nature Methods·Nicholas J Loman, Mick Watson
Feb 4, 2016·Nature·Joshua QuickMiles W Carroll
Apr 19, 2016·Evolutionary Applications·Rosemary G Gillespie
Nov 11, 2016·Nature·Axel Hochkirch
Jan 20, 2017·Genome Research·Robert VaserMile Šikic
Apr 30, 2017·Bioinformatics·Martin Šošic, Mile Šikic
Jun 24, 2017·Scientific Reports·Francesca GiordanoZemin Ning
Sep 15, 2017·The New Phytologist·Leho TedersooSten Anslan
Dec 17, 2017·Scientific Reports·Henrik KrehenwinkelRosemary G Gillespie
Feb 13, 2018·Nature Biotechnology·Miten JainMatthew Loose
Mar 17, 2018·Bioinformatics·Wouter De CosterChristine Van Broeckhoven
Apr 20, 2018·Molecular Ecology Resources·Amrita SrivathsanRudolf Meier
May 26, 2018·Molecular Ecology Resources·Ruth V NicholsBeth Shapiro
Aug 15, 2018·Molecular Ecology Resources·Felix HeegerMichael T Monaghan
Sep 22, 2018·Molecular Ecology Resources·Christian WurzbacherR Henrik Nilsson

Citations

Jul 11, 2019·Environmental Microbiology·Katarína ŠoltysFlavia Pinzari
Apr 17, 2020·PLoS Biology·Mrinalini WatsaStefan Prost
Jun 17, 2020·Molecular Ecology·Kristine BohmannM Thomas P Gilbert
Sep 30, 2020·Genes·Jia Jin Marc ChangDanwei Huang
Nov 5, 2020·Molecular Ecology·Paul A HohenloheOm P Rajora
Nov 17, 2020·Frontiers in Veterinary Science·Emeli TorssonOskar Karlsson Lindsjö
Feb 20, 2020·Computational and Structural Biotechnology Journal·Andres SantosJaime Martinez-Urtaza
Feb 9, 2021·Hydrobiologia·Maria BalsamoNiels W L Van Steenkiste
Jan 20, 2020·Trends in Ecology & Evolution·Jonas EberleBernhard Misof
Feb 19, 2021·Ecology and Evolution·Kristoffer SahlinStefan Prost
May 18, 2021·Emerging Topics in Life Sciences·Rob OgdenStefan Prost

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