10.5061/DRYAD.JV77V
Borg Dahl, Mathilde
University of Greifswald
Brjenrod, Asker D.
Russian Academy of Sciences
Unterseher, Martin
University of Greifswald
Hoppe, Thomas
University of Greifswald
Feng, Yun
University of Greifswald
Novozhilov, Yuri
Russian Academy of Sciences
Sørensen, Søren J.
University of Copenhagen
Schnittler, Martin
University of Greifswald
Brejnrod, Asker D.
University of Copenhagen
Data from: Genetic barcoding of dark-spored myxomycetes
(Amoebozoa)—Identification, evaluation and application of a sequence
similarity threshold for species differentiation in NGS studies
Dryad
dataset
2017
myxomycetes
2017-10-10T18:52:53Z
2017-10-10T18:52:53Z
en
https://doi.org/10.1111/1755-0998.12725
352386446 bytes
1
CC0 1.0 Universal (CC0 1.0) Public Domain Dedication
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.
502-705_S22_L001_R2_001Raw data, forward reads502-705_S22_L001_R2_001Raw
data, reverse reads502705mapA mapping file to describe the barcode
combinations for demultiplexing.cau demultiplexing scriptDemultiplexing
script for the caucasus data. Requires uparse 7 and biopieces
installed.cau.pypost-processing of caucasus data after
demultiplexingpost-processing of caucasus data after demultiplexing.
Requires uparse 7 including support scripts and NCBI
blastpost-process.shcau_demultiplexedDemultiplexed fastq files produced by
cau_fastq.pycau_demultiplexed_trimmedDemultiplexed fastq files with
barcodes removed.cau_fastqScript for preprocessing raw miseq output
data.S6_Scripts_ResubmissionSupplementary S6 from the manuscript. Contains
scripts and commandlines necessary for reproducing the conclusions of the
manuscriptREADMEREADME file for the
dataDatabase_MAFFT_incl_outlier_20170725The database of Myxomycete
sequences described in the paper.