Ion Torrent PGM as tool for fungal community analysis: a case study of endophytes in Eucalyptus grandis reveals high taxonomic diversity

PloS One
Martin KemlerBernard Slippers

Abstract

The Kingdom Fungi adds substantially to the diversity of life, but due to their cryptic morphology and lifestyle, tremendous diversity, paucity of formally described specimens, and the difficulty in isolating environmental strains into culture, fungal communities are difficult to characterize. This is especially true for endophytic communities of fungi living in healthy plant tissue. The developments in next generation sequencing technologies are, however, starting to reveal the true extent of fungal diversity. One of the promising new technologies, namely semiconductor sequencing, has thus far not been used in fungal diversity assessments. In this study we sequenced the internal transcribed spacer 1 (ITS1) nuclear encoded ribosomal RNA of the endophytic community of the economically important tree, Eucalyptus grandis, from South Africa using the Ion Torrent Personal Genome Machine (PGM). We determined the impact of various analysis parameters on the interpretation of the results, namely different sequence quality parameter settings, different sequence similarity cutoffs for clustering and filtering of databases for removal of sequences with incomplete taxonomy. Sequence similarity cutoff values only had a marginal effect on th...Continue Reading

References

Oct 5, 1990·Journal of Molecular Biology·S F AltschulD J Lipman
Jun 12, 2002·Current Opinion in Microbiology·Vigdis Torsvik, Lise Øvreås
Jul 24, 2002·Nucleic Acids Research·Kazutaka KatohTakashi Miyata
Feb 7, 2003·Nature·Charles E Mitchell, Alison G Power
Apr 2, 2004·Nature·Kerstin Lindblad-Toh
Jan 22, 2005·Nucleic Acids Research·Kazutaka KatohTakashi Miyata
Jan 15, 2008·Applied and Environmental Microbiology·K Eric WommackJacques Ravel
May 21, 2008·Studies in Mycology·Pedro W CrousJohannes Z Groenewald
Aug 30, 2008·Molecular Biology and Evolution·Uwe K Simon, Michael Weiss
Mar 3, 2010·PLoS Computational Biology·John C WooleyIddo Friedberg
Mar 4, 2010·Persoonia·P W CrousM J Wingfield
Mar 20, 2010·Izvestiia Akademii nauk. Seriia biologicheskaia·O V IsaevaI Iu Chernov
Mar 20, 2010·Environmental Microbiology·Susan M HuseMitchell L Sogin
Apr 13, 2010·Nature Methods·J Gregory CaporasoRob Knight
Apr 23, 2010·The New Phytologist·Kessy AbarenkovUrmas Kõljalg
Jul 10, 2010·Proceedings of the National Academy of Sciences of the United States of America·Anthony S AmendThomas D Bruns
Jan 1, 2009·Journal of Computer Science and Technology·John C Wooley, Yuzhen Ye
Aug 17, 2010·Bioinformatics·Robert C Edgar
May 20, 2011·Molecular Ecology Resources·Travis C Glenn
Jul 22, 2011·Nature·Jonathan M RothbergJames Bustillo
Jul 28, 2012·Proceedings of the National Academy of Sciences of the United States of America·Naupaka B Zimmerman, Peter M Vitousek
Aug 2, 2012·Journal of Microbiological Methods·Andrew S WhiteleyAnthony O'Donnell
Apr 18, 2013·PLoS Computational Biology·Lauren M BraggGene W Tyson

❮ Previous
Next ❯

Citations

Jun 11, 2015·Fungal Biology·Seonju MarincowitzMichael J Wingfield
Jun 7, 2015·Annual Review of Phytopathology·Pedro W CrousMichael J Wingfield
Dec 17, 2014·Microbial Ecology·Marco PautassoOttmar Holdenrieder
Sep 15, 2016·Frontiers in Microbiology·Teng YangHaiyan Chu
Nov 9, 2016·AoB Plants·Treena I BurgessMichael J Wingfield
Mar 21, 2017·Fungal Biology·Bernard SlippersMichael John Wingfield
Dec 3, 2015·Environmental Microbiology·Teng YangHaiyan Chu
Jun 21, 2018·Phytopathology·Émilie D TremblayGuillaume J Bilodeau
Oct 13, 2018·Molecular Plant Pathology·Janneke AylwardMichael J Wingfield
May 29, 2020·Journal of Integrative Bioinformatics·Irene MartorelliFons J Verbeek
Apr 22, 2017·FEMS Microbiology Reviews·Chloe E HuseyinPauline D Scanlan
Apr 20, 2019·Frontiers in Plant Science·Sanushka NaidooCaryn N Oates
Jan 1, 2018·Mycological Progress·Elisa BanchiLucia Muggia
Jan 22, 2020·Current Microbiology·Mosimanegape JongmanMalick Bill
Dec 19, 2020·Microbiological Research·Pedro Avelino Maia de AndradeFernando Dini Andreote

❮ Previous
Next ❯

Methods Mentioned

BETA
Ion
chips
PCR
electrophoresis

Software Mentioned

uclust
IonTorrent
QIIME
BLAST
MAFFT
Ion Torrent
454
Mothur
R

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.