BACKGROUND: Monogenean flatworms are the main ectoparasites of fishes. Representatives of the species-rich families Gyrodactylidae and Dactylogyridae, especially those infecting cichlid fishes and clariid catfishes, are important parasites in African aquaculture, even more so due to the massive anthropogenic translocation of their hosts worldwide. Several questions on their evolution, such as the phylogenetic position of Macrogyrodactylus and the highly speciose Gyrodactylus, remain unresolved with available molecular markers. Also, diagnostics and population-level research would benefit from the development of higher-resolution genetic markers. We aim to offer genetic resources for work on African monogeneans by providing mitogenomic data of four species (two belonging to Gyrodactylidae, two to Dactylogyridae), and analysing their gene sequences and gene order from a phylogenetic perspective. RESULTS: Using Illumina technology, the first four mitochondrial genomes of African monogeneans were assembled and annotated for the cichlid parasites Gyrodactylus nyanzae, Cichlidogyrus halli, Cichlidogyrus mbirizei (near-complete mitogenome) and the catfish parasite Macrogyrodactylus karibae (near-complete mitogenome). Complete nuclear ribosomal operons were also retrieved, as molecular vouchers. The start codon TTG is new for Gyrodactylus and for Dactylogyridae, as is the incomplete stop codon TA for Dactylogyridae. Especially the nad2 gene is promising for primer development. Gene order was identical for protein-coding genes and differed between the African representatives of these families only in a tRNA gene transposition. A mitochondrial phylogeny based on an alignment of nearly 12,500 bp including 12 protein-coding and two ribosomal RNA genes confirms that the Neotropical oviparous Aglaiogyrodactylus forficulatus takes a sister group position with respect to the other gyrodactylids, instead of the supposedly 'primitive' African Macrogyrodactylus. Inclusion of the African Gyrodactylus nyanzae confirms the paraphyly of Gyrodactylus. The position of the African dactylogyrid Cichlidogyrus is unresolved, although gene order suggests it is closely related to marine ancyrocephalines. CONCLUSIONS: The amount of mitogenomic data available for gyrodactylids and dactylogyrids is increased by roughly one-third. Our study underscores the potential of mitochondrial genes and gene order in flatworm phylogenetics, and of next-generation sequencing for marker development for these non-model helminths for which few primers are available.

Centre for Environmental Sciences Research Group Zoology Biodiversity and Toxicology Hasselt University Agoralaan Gebouw D B 3590 Diepenbeek Belgium Biology Department Royal Museum for Central Africa Leuvensesteenweg 13 B 3080 Tervuren Belgium

Department of Botany and Zoology Faculty of Science Masaryk University Kotlářská 2 CZ 611 37 Brno Czech Republic Zoology Unit Finnish Museum of Natural History University of Helsinki P O Box 17 FI 00014 Helsinki Finland Centre for Environmental Sciences Research Group Zoology Biodiversity and Toxicology Hasselt University Agoralaan Gebouw D B 3590 Diepenbeek Belgium Laboratory of Biodiversity and Evolutionary Genomics Department of Biology University of Leuven Ch Deberiotstraat 32 B 3000 Leuven Belgium Biology Department Royal Museum for Central Africa Leuvensesteenweg 13 B 3080 Tervuren Belgium

Department of Life Sciences Natural History Museum Cromwell Road London SW7 5BD UK

Laboratory of Biodiversity and Evolutionary Genomics Department of Biology University of Leuven Ch Deberiotstraat 32 B 3000 Leuven Belgium Biology Department Royal Museum for Central Africa Leuvensesteenweg 13 B 3080 Tervuren Belgium

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