Problematic barcoding in flatworms: A case-study on monogeneans and rhabdocoels (Platyhelminthes)

Abstract

Some taxonomic groups are less amenable to mitochondrial DNA barcoding than others. Due to the paucity of molecular information of understudied groups and the huge molecular diversity within flatworms, primer design has been hampered. Indeed, all attempts to develop universal flatworm-specific COI markers have failed so far. We demonstrate how high molecular variability and contamination problems limit the possibilities for barcoding using standard COI-based protocols in flatworms. As a consequence, molecular identification methods often rely on other widely applicable markers. In the case of Monogenea, a very diverse group of platyhelminth parasites, and Rhabdocoela, representing one-fourth of all free-living flatworm taxa, this has led to a relatively high availability of nuclear ITS and 18S/28S rDNA sequences on GenBank. In a comparison of the effectiveness in species assignment we conclude that mitochondrial and nuclear ribosomal markers perform equally well. In case intraspecific information is needed, rDNA sequences can guide the selection of the appropriate (i.e. taxon-specific) COI primers if available.

The first multi-gene phylogeny of the Macrostomorpha sheds light on the evolution of sexual and asexual reproduction in basal Platyhelminthes

“…Due to difficulties in COI amplification for certain macrostomorphan clades (genera Psammomacrostomum and Haplopharynx), we used the partial 28S rDNA as a barcode gene. In doing so, we follow the argument of Vanhove et al (2013) that 28S rDNA is equally useful in providing a first phylogenetic placement of flatworm species. Within the Macrostomorpha, both genes provide good phylogenetic resolution as 51% of the 28S and 62% of the COI regions are parsimony informative.…”

Reduced host-specificity in a parasite infecting non-littoral Lake Tanganyika cichlids evidenced by intraspecific morphological and genetic diversity

“…Genetic species identification of parasites was performed using three nuclear markers (28 S rDNA, 18 S rDNA, ITS-1) generally considered as suitable for monogenean species level determination5859. The length of the successfully sequenced 28 S rDNA fragment ranged from 641 to 747 base pairs (bp).…”

“…Nuclear rDNA regions are considered to be suitable markers for species-level identification of monogeneans5962. They have been used to show that allegedly generalist Cichlidogyrus species might actually comprise a complex of cryptic species, which are more host-specific than previously assumed28.…”

“…Considering COI is the fastest evolving marker currently available for these monogeneans59, it was used to investigate the intraspecific variability of C. casuarinus in our study. Although the characterisation of C. casuarinus as an intermediate generalist species is well supported by ribosomal DNA, morphometric analyses of haptoral elements showed intraspecific variation, which was linked to host species.…”

Finding Them Before They Find Us: Informatics, Parasites, and Environments in Accelerating Climate Change

“…Barcoding alone, however, is inadequate for documenting and assessing parasite diversity; among some groups of flatworms, for example, barcoding applications remain challenging (Vanhove et al, 2013). There are 2 reasons for this inadequacy.…”