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

TY - JOUR

T1 - Genetic barcoding of dark-spored myxomycetes (Amoebozoa)

T2 - identification, evaluation and application of a sequence similarity threshold for species differentiation in NGS studies

AU - Dahl, Mathilde Borg

AU - Brejnrod, Asker Daniel

AU - Unterseher, Martin

AU - Hoppe, Thomas

AU - Feng, Yun

AU - Novozhilov, Yuri

AU - Sørensen, Søren Johannes

AU - Schnittler, Martin

N1 - © 2017 John Wiley & Sons Ltd.

PY - 2018/3

Y1 - 2018/3

N2 - 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.

AB - 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.

U2 - 10.1111/1755-0998.12725

DO - 10.1111/1755-0998.12725

M3 - Journal article

C2 - 29024429

SN - 1755-098X

VL - 18

SP - 306

EP - 318

JO - Molecular Ecology Resources

JF - Molecular Ecology Resources

IS - 2

ER -