Comparing High‐throughput Platforms for Sequencing the V4 Region of SSU‐rDNA in Environmental Microbial Eukaryotic Diversity Surveys |
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| Authors: | Frédéric Mahé Jordan Mayor John Bunge Jingyun Chi Tobias Siemensmeyer Thorsten Stoeck Benjamin Wahl Tobias Paprotka Sabine Filker Micah Dunthorn |
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| Affiliation: | 1. Department of Ecology, University of Kaiserslautern, Kaiserslautern, Germany;2. Department of Forest Ecology and Management, Swedish University of Agricultural Sciences, Ume?, Sweden;3. Department of Statistical Science, Cornell University, Ithaca, New York, USA;4. GATC Biotech AG, European Genome and Diagnostics Centre, Konstanz, Germany |
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| Abstract: | High‐throughput sequencing platforms are continuing to increase resulting read lengths, which is allowing for a deeper and more accurate depiction of environmental microbial diversity. With the nascent Reagent Kit v3, Illumina MiSeq now has the ability to sequence the eukaryotic hyper‐variable V4 region of the SSU‐rDNA locus with paired‐end reads. Using DNA collected from soils with analyses of strictly‐ and nearly identical amplicons, here we ask how the new Illumina MiSeq data compares with what we can obtain with Roche/454 GS FLX with regard to quantity and quality, presence and absence, and abundance perspectives. We show that there is an easy qualitative transition from the Roche/454 to the Illumina MiSeq platforms. The ease of this transition is more nuanced quantitatively for low‐abundant amplicons, although estimates of abundances are known to also vary within platforms. |
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| Keywords: | 454 abundances Illumina MiSeq next‐generation sequencing pyrosequencing Roche |
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