Have only a small percentage of archived specimen-based Proportion of uploaded reads carry minimal taxonomic information, limiting their utility to comparative biology. More importantly,ĭatabases such as GenBank have become the de facto repositoriesįor environmental sequencing data. Information, and must deal with issues of variable read length and * E-mail: is confronted with enormous volumes of sequence
The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.Ĭompeting Interests: The authors have declared that no competing interests exist. Genomics (University of Pretoria), the Tree Protection Co-operative Program (TPCP) and the DST/NRF Centre of Excellence in Tree Health Biotechnology (CTHB). Unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.įunding: The authors would like to acknowledge the University of Pretoria postdoctoral fellowship for funding to MK. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits Received FebruAccepted OctoPublished December 16, 2013Ĭopyright: ß 2013 Kemler et al. doi:10.1371/journal.pone.0081718Įditor: Jack Anthony Gilbert, Argonne National Laboratory, United States of America
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(2013) Ion Torrent PGM as Tool for Fungal Community Analysis: A Case Study ofĮndophytes in Eucalyptus grandis Reveals High Taxonomic Diversity. Pitfalls in subsequent data analyses when using a technology with relatively short read lengths.Ĭitation: Kemler M, Garnas J, Wingfield MJ, Gryzenhout M, Pillay K-A, et al. Sequencing is an ideal strategy for environmental sequencing of fungal communities. The study demonstrates that semiconductor The community was dominated by Ascomycota, and particularly byįamilies in the Dothidiomycetes that harbor well-known plant pathogens. Database filte ring had a small, but statistically significant, effect on theĪssignment of sequences to reference sequences. 48įamilies between least and most stringent filters). Marginal effect on the identified family numbers, whereas different sequence quality filters had a large effect (89 vs. Sequence similarity cutoff values only had a The results, namely different sequence quality parameter settings, different sequence similarity cutoffs for clustering andįiltering of databases for removal of sequences with incomplete taxonomy. We determined the impact of various analysis parameters on the interpretation of
RNA of the endophytic community of the economically important tree, Eucalyptus grandis, from South Africa using the Ion In this study we sequenced the internal transcribed spacer 1 (ITS1) nuclear encoded ribosomal
One of the promising new technologies, namely semiconductor sequencing, has thus far not been used inįungal diversity assessments. The developments in next generation sequencing technologies are, however, starting to reveal the true extent ofįungal diversity. This is especially true for endophytic communities of fungi living in healthy plant The Kingdom Fungi adds substantially to the diversity of life, but due to their cryptic morphology and lifestyle, tremendousĭiversity, paucity of formally described specimens, and the difficulty in isolating environmental strains into culture, fungalĬommunities are difficult to characterize.
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Wingfield1, Marieka Gryzenhout3, Kerry-Anne Pillay1,ġ Department of Genetics, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa, 2 Department of Zoology andĮntomology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa, 3 Department of Plant Sciences, University of the Free Martin Kemler1*, Jeff Garnas2, Michael J. Ion Torrent PGM as Tool for Fungal Community Analysis:Ī Case Study of Endophytes in Eucalyptus grandis
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