Computational protocol: Hidden diversity of Acoelomorpha revealed through metabarcoding

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Protocol publication

[…] Clustered operational taxonomic units (OTUs) were obtained from public repositories or directly from the authors. The reference tree was constructed from 255 acoelomorph 18S rDNA GenBank sequences (from herein RefTree). Alignment was carried out using the E-INS-I option from MAFFT v. 7.271 [] and manually trimmed. The maximum-likelihood (ML) tree was built using RAxML v. 8.0.0 [] considering a GTR-GAMMA substitution model. Nodal support was obtained through 1000 bootstrap replicates. We selected the OTUs through RAxML-EPA [] and chose those whose abundance was greater than 10 reads.A final ML tree using both the RefTree sequences and our OTUs was inferred using RAxML [], with the same conditions as above. A Bayesian tree was built using MrBayes v. 3.2.6 [] using a GTR + I + Γ model of evolution. Pplacer v. 1.1 [] was used to perform a phylogenetic placement of the OTUs into the RefTree. Novelty blast percentages were obtained running a blastn 2.2.31 [] against our curated Acoelomorpha-GenBank database.A more detailed description of Materials and Methods can be found in the electronic supplementary material. […]

Pipeline specifications

Software tools MAFFT, RAxML, MrBayes, Pplacer, BLASTN
Application Phylogenetics