BackgroundMonogenean 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.ResultsUsing 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.ConclusionsThe 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.Electronic supplementary materialThe online version of this article (10.1186/s12864-018-4893-5) contains supplementary material, which is available to authorized users.

Amplicon sequencing on a High Throughput Sequencing (HTS) platform (custom barcoding) was used to detect and characterise myxosporean communities in environmental DNA samples from marine and freshwater environments and in faeces of animals that may serve as hosts or whose prey may host myxosporean infections. A diversity of myxozoans in filtered water samples and in faeces of piscivores (otters and great cormorants) was detected, demonstrating the suitability of lineage specific amplicons for characterising otherwise difficult to sample parasite communities. The importance of using the approach was highlighted by the lack of myxosporean detection using commonly employed, broadly-targeted eukaryote primers. These results suggest that, despite being frequently present in eDNA samples, myxozoans have been generally overlooked in 'eukaryote-wide' surveys. Lineage-specific primers in contrast detected 107 OTUs that were assigned to both the "freshwater" and "marine" myxosporean lineages. Only 7% of these OTUs clustered with sequences in GenBank, providing evidence for substantial undescribed myxosporean diversity. Many new OTUs, including those found in otter faeces, clustered with a clade of myxosporeans previously characterized by sequences from invertebrate hosts and water samples only. Because myxozoan species identification is highly reliant on molecular signatures, lineage-specific amplicon sequencing offers an effective and non-destructive means of improving our knowledge of myxozoan diversity. In addition, the analysis of myxozoan DNA in faeces of piscivores offers a potentially efficient method of sampling for diversity and revealing life cycles as piscivore activities may integrate myxozoan infections in fish over relatively broad spatial scales. *Graphical Abstract (for review) Highlights eDNA reveals diversity across the myxosporean phylogeny in water and faecal samples  A custom barcoding approach amplifies myxosporean SSU rDNA that is missed in 'eukaryote-wide' surveys  Piscivore activities may be useful in integrating myxozoan infections in prey over broad spatial scales  Recommendations for assessing the presence of myxozoans in eDNA are provided AbstractAmplicon sequencing on a High Throughput Sequencing (HTS) platform (custom barcoding) was used to detect and characterise myxosporean communities in environmental DNA samples from marine and freshwater environments and in faeces of animals that may serve as hosts or whose prey 25 may host myxosporean infections. A diversity of myxozoans in filtered water samples and in faeces of piscivores (otters and great cormorants) was detected, demonstrating the suitability of lineage specific amplicons for characterising otherwise difficult to sample parasite communities. The importance of using the approach was highlighted by the lack of myxosporean detection using commonly employed, broadly-targeted eukaryote primers. These results suggest that, despite being 30 frequently present in eDNA samples, myxozoans have been generally overlooked in 'euk...

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The living prokaryotic microbiome of the calcified geniculate (articulated) red alga, Corallina officinalis from the intertidal seashore is characterised for the first time based on the V6 hypervariable region of 16S rRNA. Results revealed an extraordinary diversity of bacteria associated with the microbiome. Thirty-five prokaryotic phyla were recovered, of which Proteobacteria, Cyanobacteria, Bacteroidetes, Actinobacteria, Planctomycetes, Acidobacteria, Verrucomicrobia, Firmicutes and Chloroflexi made up the core microbiome. Unclassified sequences made up 25% of sequences, suggesting insufficient sampling of the world's oceans/macroalgae. The greatest diversity in the microbiome was on the upper shore, followed by the lower shore then the middle shore, although the microbiome community composition did not vary between shore levels. The C. officinalis core microbiome was broadly similar in composition to those reported in the literature for crustose coralline algae (CCAs) and free-living rhodoliths. Differences in relative abundance of the phyla between the different types of calcified macroalgal species may relate to the intertidal versus subtidal habit of the taxa and functionality of the microbiome components. The results indicate that much work is needed to identify prokaryotic taxa, and to determine the nature of the relationship of the bacteria with the calcified host spatially, temporally and functionally.