The mitochondrial genome ofPolylabris halichoeres(Monogenea: Microcotylidae)

An insight into the functional genomics and species classification of Eudiplozoon nipponicum (Monogenea, Diplozoidae), a haematophagous parasite of the common carp Cyprinus carpio

BACKGROUND

Monogenea (Platyhelminthes, Neodermata) are the most species-rich class within the Neodermata superclass of primarily fish parasites. Despite their economic and ecological importance, monogenean research tends to focus on their morphological, phylogenetic, and population characteristics, while comprehensive omics analyses aimed at describing functionally important molecules are few and far between. We present a molecular characterisation of monogenean representative Eudiplozoon nipponicum, an obligate haematophagous parasite infecting the gills of the common carp. We report its nuclear and mitochondrial genomes, present a functional annotation of protein molecules relevant to the molecular and biochemical aspect of physiological processes involved in interactions with the fish hosts, and re-examinate the taxonomic position of Eudiplozoon species within the Diplozoidae family.

RESULTS

We have generated 50.81 Gbp of raw sequencing data (Illumina and Oxford Nanopore reads), bioinformatically processed, and de novo assembled them into a genome draft 0.94 Gbp long, consisting of 21,044 contigs (N50 = 87 kbp). The final assembly represents 57% of the estimated total genome size (~ 1.64 Gbp), whereby repetitive and low-complexity regions account for ~ 64% of the assembled length. In total, 36,626 predicted genes encode 33,031 proteins and homology-based annotation of protein-coding genes (PCGs) and proteins characterises 14,785 (44.76%) molecules. We have detected significant representation of functional proteins and known molecular functions. The numbers of peptidases and inhibitors (579 proteins), characterised GO terms (16,016 unique assigned GO terms), and identified KEGG Orthology (4,315 proteins) acting in 378 KEGG pathways demonstrate the variety of mechanisms by which the parasite interacts with hosts on a macromolecular level (immunomodulation, feeding, and development). Comparison between the newly assembled E. nipponicum mitochondrial genome (length of 17,038 bp) and other diplozoid monogeneans confirms the existence of two distinct Eudiplozoon species infecting different fish hosts: Cyprinus carpio and Carassius spp.

CONCLUSIONS

Although the amount of sequencing data and characterised molecules of monogenean parasites has recently increased, a better insight into their molecular biology is needed. The E. nipponicum nuclear genome presented here, currently the largest described genome of any monogenean parasite, represents a milestone in the study of monogeneans and their molecules but further omics research is needed to understand these parasites' biological nature.

Molecular (cox1), geographical, and host record investigation of monogeneans Mazocraes australis (Mazocraeidae), Polylabris sillaginae, and P. australiensis (Microcotylidae)

This study determines the occurrence and molecular characterisation of Monogenea from three commercially important Australian fish: Australian sardine Sardinops sagax (Jenyns), Australian anchovy Engraulis australis (White), and eastern school whiting Sillago flindersi McKay. Earlier studies have provided only morphological species identification, whereas this study combines both morphological and molecular methods. A total of 247 fish across 3 species, sourced from the New South Wales and Victorian coasts, were examined for Monogenea. A total of 187 monogenean parasites were recovered from the gills. The overall prevalence, mean intensity, and mean abundance were 34%, 2.23, and 0.78, respectively. The parasites were initially classified morphologically as three species across two families. Family Mazocraeidae was represented by Mazocraes australis Timi et al. J Parasitol 85:28-32, 1999, and family Microcotylidae by Polylabris sillaginae (Woolcock, Parasitology 28:79-91, 1936) Dillon, Hargis, and Harrises, 1983 and P. australiensis Hayward, 1996. Molecular identification of parasites was conducted through sequencing of the mitochondrial cytochrome c oxidase subunit 1 (cox1) gene. The fish hosts in the present study were also barcoded (mitochondrial cox1 gene) to confirm specific identities. There was no comparable cox1 sequence available in GenBank for the parasites found in the present study. However, the phylogenetic tree clustered the monogenean species identified in this study according to their familial groups of Mazocraeidae and Microcotylidae. The presence of M. australis on E. australis and S. sagax was confirmed in this study. Polylabris australiensis was only found on S. sagax but Si. flindersi was found to be a host for both Polylabris species. This study is the first to explore the mitochondrial cox1 genes of these three-monogenean species. These findings will serve as a foundation for future monogenean research in Australian waters and elsewhere.

Redescription, complete mitochondrial genome and phylogenetic relationships of Hexostoma thynni (Delaroche, 1811) Rafinesque, 1815 (Monogenea, Hexostomatidae)

Specimens of Hexostoma thynni (Delaroche, 1811) Rafinesque, 1815 were collected from their type-host, the bluefin tuna Thunnus thynnus, caught off Algeria, i.e. close to the type-locality, off Mallorca, which is also in the Mediterranean. The species is briefly redescribed and compared to previous descriptions, under the same name or as its synonym Plagiopeltis duplicata Diesing, 1858, to ascertain identity of specimens. The three genera within the Hexostomatidae (Hexostoma Rafinesque, 1815, Neohexostoma Price, 1961 and Homostoma Unnithan, 1965) are briefly discussed, with comments on the fragility of characters used to distinguish them. Using next-generation sequencing, the complete mitogenome and the cluster of ribosomal genes (SSU, LSU, ITS1, ITS2, 5.8S) were obtained. The mitogenome is 14,649 bp long and codes for 12 protein-coding genes, 2 ribosomal RNA genes and 22 transfer RNA genes; its size is similar to other mitogenomes obtained from polyopisthocotylean monogeneans. A phylogeny based on concatenated mitogenome protein-coding genes from nine species of polyopisthocotylean monogeneans produced a tree in which the Hexostomatidae H. thynni was associated with other Mazocraeidea, such as Chauhaneidae and Diclidophoridae. This invalidates the hypothesis of Boeger & Kritsky (1993) of Hexostomatidae as sister-group to the Mazocraeidea and suggests the demise of the suborder Hexostomatinea Boeger & Kritsky, 1993. We insist on the usefulness of depositing parts of specimens used for molecular analyses, prepared on permanent slides, in a curated collection.

The complete mitochondrial genomes of Paradiplozoon yarkandense and Paradiplozoon homoion confirm that Diplozoidae evolve at an elevated rate

BACKGROUND

Diplozoidae are monogenean (Monogenea: Polyopisthocotylea) fish parasites characterised by a unique life history: two larvae permanently fuse into an X-shaped "Siamese" organism. Taxonomy and phylogeny of Diplozoidae and Polyopisthocotylea remain unresolved due to the unavailability of molecular markers with sufficiently high resolution. Mitogenomes may be a suitable candidate, but there are currently only 12 available for the Polyopisthocotylea (three for Diplozoidae). The only available study of diplozoid mitogenomes found unique base composition patterns and elevated evolution rates in comparison with other Monogenean mitogenomes.

METHODS

To further explore their evolution and generate molecular data for evolutionary studies, we sequenced the complete mitogenomes of two Diplozoidae species, Paradiplozoon homoion and Paradiplozoon yarkandense, and conducted a number of comparative mitogenomic analyses with other polyopisthocotyleans.

RESULTS

We found further evidence that mitogenomes of Diplozoidae evolve at a unique, elevated rate, which was reflected in their exceptionally long branches, large sizes, unique base composition, skews, and very low gene sequence similarity levels between the two newly sequenced species. They also exhibited remarkably large overlaps between some genes. Phylogenetic analysis of Polyopisthocotylea resolved all major taxa as monophyletic, and Mazocraeidea was split into two major clades: (Diplozoidae) + (all four remaining families: Diclidophoridae, Chauhaneidae, Mazocraeidae and Microcotylidae). It also provided further confirmation that the genus Paradiplozoon is paraphyletic and requires a taxonomic revision, so the two species may have to be renamed Indodiplozoon homoion and Diplozoon yarkandense comb. nov.

CONCLUSIONS

Although our findings indicate that mitogenomes may be a promising tool for resolving the phylogeny of Polyopisthocotylea, elevated evolutionary rates of Diplozoidae may cause phylogenetic artefacts, so future studies should pay caution to this problem. Furthermore, as the reason for their elevated evolution remains unknown, Diplozoidae are a remarkably interesting lineage for other types of evolutionary mitogenomic studies.

Novel molecular data for monogenean parasites of sparid fishes in the Mediterranean and a molecular phylogeny of the Microcotylidae Taschenberg, 1879

During a study of the monogeneans of four sparid fishes (Diplodus vulgaris, Pagellus bogaraveo, Pagrus pagrus and Sparus aurata) from the Western Mediterranean off Algeria, a large collection of parasites was characterised molecularly (28S rRNA and cox1 genes). A total of 46 partial sequences (23 for each gene) were generated from 38 isolates of monogeneans which included four species (Atrispinum acarne, Microcotyle erythrini (sensu stricto), Sparicotyle chrysophrii and Prostatomicrocotylinae gen. sp.) of the family Microcotylidae, two putative species of the family Capsalidae (Encotyllabe spp.), and one species (Choricotyle chrysophryi) of the family Diclidophoridae. Our study provides (i) the first molecular data for the Capsalidae in the Mediterranean; (ii) the first record of a member of the Prostatomicrocotylinae in the Mediterranean and in a sparid fish (D. vulgaris); (iii) the first cox1 sequences for A. acarne; (iv) the second record of M. erythrini (s.s.) from P. pagrus; and (v) the second confirmed by molecular data record of S. chrysophrii in wild populations of S. aurata. The first phylogenetic hypotheses for the family Microcotylidae developed here, revealed the monophyly of the subfamily Prostatomicrocotylinae and the genus Microcotyle but the relationships among the subfamilies were still largely unresolved with the best represented subfamily Microcotylinae being polyphyletic. Our results highlight the importance of molecular methods in the assessment of monogenean diversity and the need for a thorough taxon-sampling approach to increase the accuracy of phylogenetic reconstruction of the relationships of the large and taxonomically complex polyopisthocotylean family Microcotylidae.

Heteromicrocotyla polyorchis Unnithan, 1961 (Monogenea: Heteromicrocotylidae), a gill parasite of the yellow-spotted trevally, Carangoides fulvoguttatus (Carangidae) from Saudi Arabia: Morphology and phylogeny

Little information for parasitic infections of Carangoides fulvoguttatus was recorded. The present study was intended to investigate the gill parasite Heteromicrocotyla polyorchis of this fish and to provide a full morphological description and clarify its taxonomic status through phylogenetic analysis of the 28S rRNA gene region. A total of sixty fish specimens have been collected from the studied area (the Red Sea in Jeddah Province, Saudi Arabia) and gills were isolated and examined for identification of parasites. Using light electron microscopy, the recovered monogenean parasite's morphology was exhaustively characterized and described. Microscope examinations found that this parasite species represent Heteromicrocotyla polyorchis, and it could be distinguished from congeners of the same genus by armed genital atrium and cirrus sac, follicular post-ovarian testes, unique shape and number of clamps on both haptor sides, and the dorsally curved tip of the male copulatory organ. Morphological features were combined with molecular analysis of the 28S rRNA gene region. The selected gene for the isolated Heteromicrocotyla species was analyzed using appropriate primers to assist in phylogeny with those in the GenBank database. The present monogenean species was characterized by unique genetic sequences that were analyzed and deposited in the GenBank for the first time under the accession number MW406473. Phylogenetic analyses reported that the maximum identity between the current Heteromicrocotyla species and taxa of Heteromicrocotylidae was between 91.42 and 92.09% and confirmed its taxonomic status in this family with a well-distinct clade. The present study supported the second report of H. polyorchis as carangid fish ectoparasites and investigates the first appearance in C. fulvoguttatus inhabiting Saudi Arabia.

Taxonomic revision of Microcotyle caudata Goto, 1894 parasitic on gills of sebastids (Scorpaeniformes: Sebastidae), with a description of Microcotyle kasago n. sp. (Monogenea: Microcotylidae) from off Japan

Two species of microcotylid monogeneans, Microcotyle caudata Goto, 1894 and Microcotyle sebastisci Yamaguti, 1958, have been reported from fishes of the Sebastes inermis species complex and Sebastiscus marmoratus (Cuvier) (Scorpaeniformes: Sebastidae). So far, these parasite species have been distinguished by the size of the eggs and the number of testes, but based on morphological evidence including re-examination of the type-specimens and topotypes and molecular analysis, we consider M. sebastisci to be a junior synonym of M. caudata. As a result, M. caudata exhibits a wide host range, seven species from three genera and two families. A new species, Microcotyle kasago n. sp., is described based on material from S. marmoratus and differentiated from other congeners by means of morphological and molecular analysis.

Bivagina Pagrosomi Murray (1931) (Monogenea: Polyopisthocotylea), a Microcotylid Infecting the Gills of the Gilt-head Sea Bream Sparus Aurata (Sparidae) from the Red Sea: Morphology and Phylogeny

Introduction

Monogenea is a class of ectoparasitic flatworms on the skin, gills, or fins of fish. Microcotylidae is a family of polyopisthocotylean monogeneans parasitising only marine fishes. This work describes and taxonomically determines a microcotylid polyopisthocotylean monogenean in an important fish in Saudi aquaculture.

Material and Methods

Thirty gilt-head sea bream captured alive from the Red Sea of Saudi Arabia were examined for monogenean infection. Worms were described morphologically and morphometrically by light microscopy and multiple sequence alignments and phylogenetic trees were also constructed after maximum likelihood analysis of the 28S rRNA sequences.

Results

Seventeen fish were infected by a monogenean parasite in the gill lamellae. It showed a bilobed anterior extremity, two rows of numerous unequal clamps of microcotylid type, and paired muscular vaginae crowned by differently sized spines. The vaginal number and its relative armature suggested the species’ affiliation to group D; the parasite possessed large, muscular vaginae with a full corona of spines over almost the entire width resembling Bivagina pagrosomi Murray (1931). The molecular analysis of the parasite 28s rRNA revealed 97% homology with B. pagrosomi (AJ577461.1).

Conclusion

The results confirmed the taxonomic status of the parasite recorded. On the basis of morphology and molecular data, we consider that several conclusions on the systematic status of microcotylids from Red Sea fishes in Saudi Arabia should be discussed.

Towards the resolution of the Microcotyle erythrini species complex: description of Microcotyle isyebi n. sp. (Monogenea, Microcotylidae) from Boops boops (Teleostei, Sparidae) off the Algerian coast

The monogenean Microcotyle erythrini is atypical because it has been recorded from several fish host species in the Mediterranean Sea and Atlantic Ocean, in contrast to many species which are considered strictly specific. This could indicate a true lack of specificity or that several cryptic species are involved. This paper is a partial attempt to solve this problem. Specimens of a monogenean resembling M. erythrini were collected from bogues, Boops boops, caught off Algeria. A comparison with published descriptions and with museum specimens of M. erythrini did not yield any clear morphological difference. However, sequences of cytochrome c oxidase subunit I (COI) differed by 16.3% from that of M. erythrini (from GenBank, material collected from the type-host Pagellus erythrinus), indicating that the species was different. The species from B. boops is therefore described here as Microcotyle isyebi n. sp. and differential diagnoses with Microcotyle species from the Mediterranean and from sparids are provided. These results suggest that a molecular re-evaluation of other M. erythrini-like specimens from various fish hosts could reveal the existence of additional parasite biodiversity.

Microcotyle visa n. sp. (Monogenea: Microcotylidae), a gill parasite of Pagrus caeruleostictus (Valenciennes) (Teleostei: Sparidae) off the Algerian coast, Western Mediterranean

Parasite biodiversity of fish of the southern part of the Mediterranean sea is still incompletely explored. We describe here Microcotyle visa n. sp. from the gill filaments of the bluespotted seabream Pagrus caeruleostictus (Valenciennes) (Sparidae) collected off the Algerian coast. The identity of fish hosts was confirmed by barcoding. Microcotyle visa n. sp. is herein described and illustrated. Analysis of the cox1 gene of the monogeneans revealed minor intraspecific variation (1.4%), an order of magnitude lower than the distance between this species and other Microcotyle species (10-15 %). Microcotyle visa n. sp. is distinguished from Microcotyle erythrini van Beneden & Hesse, 1863, a congener infesting sparids, on the basis of morphological (size of clamps, number of testes) and molecular (cox1) differences. This is the fourth member of the genus known to parasitise a sparid host. A species of Paramicrocotyle sp. included in the molecular analysis was nested within a robust Microcotyle + Paramicrocotyle clade; in the absence of demonstrated molecular and morphological differences, we consider that Paramicrocotyle Caballero & Bravo-Hollis, 1972 is a junior synonym of Microcotyle van Beneden & Hesse, 1863 and transfer two species of Paramicrocotyle as Microcotyle danielcarrioni (Martinez & Barrantes, 1977) n. comb. and Microcotyle moyanoi (Villalba & Fernandes, 1986) n. comb.

Mitochondrial genomes of two diplectanids (Platyhelminthes: Monogenea) expose paraphyly of the order Dactylogyridea and extensive tRNA gene rearrangements

BACKGROUND

Recent mitochondrial phylogenomics studies have reported a sister-group relationship of the orders Capsalidea and Dactylogyridea, which is inconsistent with previous morphology- and molecular-based phylogenies. As Dactylogyridea mitochondrial genomes (mitogenomes) are currently represented by only one family, to improve the phylogenetic resolution, we sequenced and characterized two dactylogyridean parasites, Lamellodiscus spari and Lepidotrema longipenis, belonging to a non-represented family Diplectanidae.

RESULTS

The L. longipenis mitogenome (15,433 bp) contains the standard 36 flatworm mitochondrial genes (atp8 is absent), whereas we failed to detect trnS1, trnC and trnG in L. spari (14,614 bp). Both mitogenomes exhibit unique gene orders (among the Monogenea), with a number of tRNA rearrangements. Both long non-coding regions contain a number of different (partially overlapping) repeat sequences. Intriguingly, these include putative tRNA pseudogenes in a tandem array (17 trnV pseudogenes in L. longipenis, 13 trnY pseudogenes in L. spari). Combined nucleotide diversity, non-synonymous/synonymous substitutions ratio and average sequence identity analyses consistently showed that nad2, nad5 and nad4 were the most variable PCGs, whereas cox1, cox2 and cytb were the most conserved. Phylogenomic analysis showed that the newly sequenced species of the family Diplectanidae formed a sister-group with the Dactylogyridae + Capsalidae clade. Thus Dactylogyridea (represented by the Diplectanidae and Dactylogyridae) was rendered paraphyletic (with high statistical support) by the nested Capsalidea (represented by the Capsalidae) clade.

CONCLUSIONS

Our results show that nad2, nad5 and nad4 (fast-evolving) would be better candidates than cox1 (slow-evolving) for species identification and population genetics studies in the Diplectanidae. The unique gene order pattern further suggests discontinuous evolution of mitogenomic gene order arrangement in the Class Monogenea. This first report of paraphyly of the Dactylogyridea highlights the need to generate more molecular data for monogenean parasites, in order to be able to clarify their relationships using large datasets, as single-gene markers appear to provide a phylogenetic resolution which is too low for the task.

Sequencing of the complete mitochondrial genome of a fish-parasitic flatworm Paratetraonchoides inermis (Platyhelminthes: Monogenea): tRNA gene arrangement reshuffling and implications for phylogeny

BACKGROUND

Paratetraonchoides inermis (Monogenea: Tetraonchoididae) is a flatworm parasitising the gills of uranoscopid fishes. Its morphological characteristics are ambiguous, and molecular data have never been used to study its phylogenetic relationships, which makes its taxonomic classification controversial. Also, several decades of unsuccessful attempts to resolve the relationships within the Monogenea present a strong indication that morphological datasets may not be robust enough to be used to infer evolutionary histories. As the use of molecular data is currently severely limited by their scarcity, we have sequenced and characterized the complete mitochondrial (mt) genome of P. inermis. To investigate its phylogenetic position, we performed phylogenetic analyses using Bayesian inference and maximum likelihood approaches using concatenated amino acid sequences of all 12 protein-coding genes on a dataset containing all available monogenean mt genomes.

RESULTS

The circular mt genome of P. inermis (14,654 bp) contains the standard 36 genes: 22 tRNAs, two rRNAs, 12 protein-encoding genes (PCGs; Atp8 is missing) and a major non-coding region (mNCR). All genes are transcribed from the same strand. The A + T content of the whole genome (82.6%), as well as its elements, is the highest reported among the monogeneans thus far. Three tRNA-like cloverleaf structures were found in mNCR. Several results of the phylogenomic analysis are in disagreement with previously proposed relationships: instead of being closely related to the Gyrodactylidea, Tetraonchidea exhibit a phylogenetic affinity with the Dactylogyridea + Capsalidea clade; and the order Capsalidea is neither basal within the subclass Monopisthocotylea, nor groups with the Gyrodactylidea, but instead forms a sister clade with the Dactylogyridea. The mt genome of P. inermis exhibits a unique gene order, with an extensive reorganization of tRNAs. Monogenea exhibit exceptional gene order plasticity within the Neodermata.

CONCLUSIONS

This study shows that gene order within monopisthocotylid mt genomes is evolving at uneven rates, which creates misleading evolutionary signals. Furthermore, our results indicate that all previous attempts to resolve the evolutionary history of the Monogenea may have produced at least partially erroneous relationships. This further corroborates the necessity to generate more molecular data for this group of parasitic animals.

The mitochondrial genome of the egg-laying flatworm Aglaiogyrodactylus forficulatus (Platyhelminthes: Monogenoidea)

BACKGROUND

The rather species-poor oviparous gyrodactylids are restricted to South America. It was suggested that they have a basal position within the otherwise viviparous Gyrodactylidae. Accordingly, it was proposed that the species-rich viviparous gyrodactylids diversified and dispersed from there.

METHODS

The mitochondrial genome of Aglaiogyrodactylus forficulatus was bioinformatically assembled from next-generation illumina MiSeq sequencing reads, annotated, and compared to previously published mitochondrial genomes of other monogenoidean flatworm species.

RESULTS

The mitochondrial genome of A. forficulatus consists of 14,371 bp with an average A + T content of 75.12 %. All expected 12 protein coding, 22 tRNA, and 2 rRNA genes were identified. Furthermore, there were two repetitive non-coding regions essentially consisting of 88 bp and 233 bp repeats, respectively. Maximum Likelihood analyses placed the mitochondrial genome of A. forficulatus in a well-supported clade together with the viviparous Gyrodactylidae species. The gene order differs in comparison to that of other monogenoidean species, with rearrangements mainly affecting tRNA genes. In comparison to Paragyrodactylus variegatus, four gene order rearrangements, i.e. three transpositions and one complex tandem-duplication-random-loss event, were detected.

CONCLUSION

Mitochondrial genome sequence analyses support a basal position of the oviparous A. forficulatus within Gyrodactylidae, and a sister group relationship of the oviparous and viviparous forms.

The complete mitochondrial genome of Neobenedenia melleni (Platyhelminthes: Monogenea): mitochondrial gene content, arrangement and composition compared with two Benedenia species

The complete mitochondrial (mt) genome sequences of Neobenedenia melleni were determined and compared with those of Benedenia seriolae and B. hoshinai. This circular genome comprises 13,270 bp and includes all 36 typical mt genes found in flatworms. Total AT content of N. melleni is 75.9 %. ATG is the most common start codon, while nad4L is initiated by GTG. All protein-coding genes are predicted to terminate with TAG and TAA. N. melleni has the trnR with a TCG anticodon, which is the same to B. seriolae but different from B. hoshinai (ACG). The mt gene arrangement of N. melleni is similar to that of B. seriolae and B. hoshinai with the exception of three translocations (trnF, trnT and trnG). The overlapped region between nad4L and nad4 was found in the N. melleni mt genome, which was also reported for the published Gyrodactylus species, but it was not found in those of B. seriolae and B. hoshinai, which are non-coding regions instead. The present study provides useful molecular characters for species or strain identification and systematic studies of this parasite.

The complete mitochondrial genome of Tetrancistrum nebulosi (Monogenea: Ancyrocephalidae)

The first complete mitochondrial (mt) genome of Ancyrocephalidae is reported herein. The mt genome of Tetrancistrum nebulosi was 13,392 bp in length containing 12 protein-coding genes (lacking atp8), 22 tRNA genes and 2 rRNA genes. The longest non-coding region was located between nad5 and trnG, and the A + T content was 72.4%. All tRNAs had the typical clover-leaf secondary structure except for trnS1((AGN)), trnR, trnF and trnQ. The rrnL and rrnS subunits were separated by trnC, as documented in the monopisthocotylean groups (Benedenia and Gyrodactylus species), while they were adjacent to each other in the polyopisthocotylean species (Microcotyle sebastis, Polylabris halichoeres and Pseudochauhanea macrorchis).

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

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 complete mitochondrial genome of Pseudochauhanea macrorchis (Monogenea: Chauhaneidae) revealed a highly repetitive region and a gene rearrangement hot spot in Polyopisthocotylea

The complete mitochondrial genome of Pseudochauhanea macrorchis was determined and compared with other monogenean mitochondrial genomes from GenBank. The circular genome was 15,031 bp in length and encoded 36 genes (12 protein-coding genes, two ribosomal RNAs, and 22 transfer RNAs) typically found in flatworms. Structures of the mitochondrial genome were mostly concordant with that known for Microcotyle sebastis and Polylabris halichoeres, but also contained two noted features-a gene rearrangement hot spot and the highly repetitive region (HRR) in major non-coding region (NCR). The gene rearrangement hot spot located between the cox3 and nad5 genes, including a cluster of tRNA genes, nad6 gene and one major NCR. The HRR seemed to be a unique feature of the polyopisthocotylean mitochondrial genomes. In conclusion, the present study provided new molecular data for future studies of the comparative mitochondrial genomics and also served as a resource of markers for the studies of species populations and monogenean phylogenetics.