Introducing ribosomal tandem repeat barcoding for fungi

Molecular Ecology Resources
Christian WurzbacherR Henrik Nilsson

Abstract

Sequence comparison and analysis of the various ribosomal genetic markers are the dominant molecular methods for identification and description of fungi. However, new environmental fungal lineages known only from DNA data reveal significant gaps in our sampling of the fungal kingdom in terms of both taxonomy and marker coverage in the reference sequence databases. To facilitate the integration of reference data from all of the ribosomal markers, we present three sets of general primers that allow for amplification of the complete ribosomal operon from the ribosomal tandem repeats. The primers cover all ribosomal markers: ETS, SSU, ITS1, 5.8S, ITS2, LSU and IGS. We coupled these primers successfully with third-generation sequencing (PacBio and Nanopore sequencing) to showcase our approach on authentic fungal herbarium specimens (Basidiomycota), aquatic chytrids (Chytridiomycota) and a poorly understood lineage of early diverging fungi (Nephridiophagidae). In particular, we were able to generate high-quality reference data with Nanopore sequencing in a high-throughput manner, showing that the generation of reference data can be achieved on a regular desktop computer without the involvement of any large-scale sequencing facility. ...Continue Reading

References

Dec 1, 1991·The Quarterly Review of Biology·D M Hillis, M T Dixon
Jun 1, 1990·Proceedings of the National Academy of Sciences of the United States of America·C R WoeseM L Wheelis
Feb 27, 2004·Nucleic Acids Research·Wolfgang LudwigKarl-Heinz Schleifer
Oct 11, 2005·Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences·Mark BlaxterEyualem Abebe
Oct 20, 2006·Nature·Timothy Y JamesRytas Vilgalys
May 10, 2007·Mycologia·Merlin M WhiteJunta Sugiyama
Sep 1, 2009·Fungal Genetics and Biology : FG & B·Kerry O'DonnellBrice A J Sarver
Jun 24, 2010·Nucleic Acids Research·Kevin J TraversStephen W Turner
Jul 20, 2010·BMC Genomics·Gentile Francesco FicetolaFrançois Pompanon
Aug 17, 2010·Bioinformatics·Robert C Edgar
Aug 10, 2011·BMC Genomics·Nabil-Fareed AlikhanScott A Beatson
Mar 29, 2012·Proceedings of the National Academy of Sciences of the United States of America·Conrad L SchochUNKNOWN Fungal Barcoding Consortium Author List
Jan 19, 2013·Molecular Biology and Evolution·Kazutaka Katoh, Daron M Standley
Oct 12, 2013·Molecular Ecology·Urmas KõljalgKarl-Henrik Larsson
Nov 30, 2013·Nucleic Acids Research·James R ColeJames M Tiedje
Apr 16, 2014·PloS One·Christian WurzbacherHans-Peter Grossart
Jan 28, 2015·Environmental Microbiology Reports·Seiji IshidaMaiko Kagami
May 23, 2015·Science·Colomban de VargasEric Karsenti
Feb 10, 2016·The ISME Journal·Esther SingerTanja Woyke
Jun 17, 2016·International Journal of Systematic and Evolutionary Microbiology·Gaëtan BurgaudSerge Casaregola
Apr 9, 2017·Microbiome·Leho TedersooTimothy Y James
Apr 22, 2017·The ISME Journal·Christian WurzbacherSari Peura
Jun 27, 2017·Journal of Biotechnology·Frank Oliver GlöcknerWolfgang Ludwig
Jul 29, 2017·Microbiology Spectrum·David L Hawksworth, Robert Lücking
Sep 15, 2017·The New Phytologist·Leho TedersooSten Anslan
Apr 20, 2018·Molecular Ecology Resources·Amrita SrivathsanRudolf Meier
Aug 15, 2018·Molecular Ecology Resources·Felix HeegerMichael T Monaghan

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Citations

Jul 11, 2019·Environmental Microbiology·Katarína ŠoltysFlavia Pinzari
Jun 21, 2019·Environmental Microbiology Reports·Leho Tedersoo, Sten Anslan
Dec 12, 2019·Molecular Ecology Resources·Shawn R NarumBenjamin Sibbett
Mar 16, 2019·Nature Reviews. Microbiology·Hans-Peter GrossartKeilor Rojas-Jimenez
Oct 2, 2019·Journal of Fungi·Amir ArastehfarTeun Boekhout
Nov 18, 2018·Nature Reviews. Microbiology·R Henrik NilssonLeho Tedersoo
Jan 8, 2020·BMC Evolutionary Biology·Michael BradshawSteven D Leavitt
Nov 17, 2020·Frontiers in Microbiology·Matthias HessKateřina Fliegerová
Oct 30, 2020·Journal of Fungi·Cene Gostinčar
Nov 15, 2020·International Journal of Molecular Sciences·Dominika G MalarczykMagdalena Frąc
Feb 20, 2021·World Journal of Microbiology & Biotechnology·Prassan ChoudharyAnil Kumar Saxena
Feb 19, 2021·Ecology and Evolution·Kristoffer SahlinStefan Prost
May 19, 2021·Emerging Topics in Life Sciences·Rob OgdenStefan Prost
Jun 17, 2021·Applied and Environmental Microbiology·Leho TedersooBenjamin Callahan
Aug 25, 2021·The Science of the Total Environment·Lin ZangRui Zhang

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