title: Comparing High-throughput Platforms for Sequencing the V4 Region of SSU-rDNA in Environmental Microbial Eukaryotic Diversity Surveys.
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.
authors.affiliation: Department of Ecology, University of Kaiserslautern, D-67663, Kaiserslautern, Germany.
authors.forename: Frédéric
authors.initials: F
authors.lastname: Mahé
authors.forename: Jordan
authors.initials: J
authors.lastname: Mayor
authors.forename: John
authors.initials: J
authors.lastname: Bunge
authors.forename: Jingyun
authors.initials: J
authors.lastname: Chi
authors.forename: Tobias
authors.initials: T
authors.lastname: Siemensmeyer
authors.forename: Thorsten
authors.initials: T
authors.lastname: Stoeck
authors.forename: Benjamin
authors.initials: B
authors.lastname: Wahl
authors.forename: Tobias
authors.initials: T
authors.lastname: Paprotka
authors.forename: Sabine
authors.initials: S
authors.lastname: Filker
authors.forename: Micah
authors.initials: M
authors.lastname: Dunthorn
mesh_terms: D058448:Biota; D004783:Environmental Microbiology; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D012337:RNA, Ribosomal, 18S / Q000235:genetics*
chemical_list: D012337:RNA, Ribosomal, 18S
keywords: 454; Illumina; MiSeq; Roche; abundances; next-generation sequencing; pyrosequencing