Data from: Genetic barcoding of dark-spored myxomycetes (Amoebozoa)—Identification, evaluation and application of a sequence similarity threshold for species differentiation in NGS studies

Unicellular, eukaryotic organisms (protists) play a key role in soil food
webs as major predators of microorganisms. However, due to the
polyphyletic nature of protists, no single universal barcode can be
established for this group, and the structure of many protistean
communities remains unresolved. Plasmodial slime moulds (Myxogastria or
Myxomycetes) stand out among protists by their formation of fruit bodies,
which allow for a morphological species concept. By Sanger sequencing of a
large collection of morphospecies, this study presents the largest
database to date of dark-spored myxomycetes and evaluate a partial 18S SSU
gene marker for species annotation. We identify and discuss the use of an
intraspecific sequence similarity threshold of 99.1% for species
differentiation (OTU picking) in environmental PCR studies (ePCR) and
estimate a hidden diversity of putative species, exceeding those of
described morphospecies by 99%. When applying the identified threshold to
an ePCR data set (including sequences from both NGS and cloning), we find
64 OTUs of which 21.9% had a direct match (>99.1% similarity) to
the database and the remaining had on average 90.2 ± 0.8% similarity to
their best match, thus thought to represent undiscovered diversity of
dark-spored myxomycetes.