Characterization of the complete mitochondrial genomes from Polycladida (Platyhelminthes) using next-generation sequencing

• We provide three complete mitochondrial genomes of Polycladida (Platyhelminthes).
• Our analysis reveals a great diversity of gene orders within Platyhelminthes.
• The phylogenetic analyses strongly supported the monophyly of Polycladida.
• The results suggest the monophyly of the two suborders within Polycladida: Acotylea and Cotylea.

The complete mitochondrial genomes of three polycladids, the acotylean Hoploplana elisabelloi and the cotyleans Enchiridium sp. and Prosthiostomum siphunculus have been assembled with high coverage from Illumina sequencing data. The mt genomes contain 36 genes including 12 of the 13 protein-coding genes characteristic for metazoan mitochondrial genomes, two ribosomal RNA genes, and 22 transfer RNA genes. Gene annotation, gene order, genetic code, start and stop codons and codon bias have been identified. In comparison with the well investigated parasitic Neodermata, our analysis reveals a great diversity of gene orders within Polycladida and Platyhelminthes in general. By analyzing representative genomes of the main groups of Platyhelminthes we explored the phylogenetic relationships of this group. The phylogenetic analyses strongly supported the monophyly of Polycladida, and based on a small taxon sampling suggest the monophyly of Acotylea and Cotylea.