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

The genetic variation of mitochondrial sequences and pathological differences of Echinococcus multilocularis strains from different continents

Alveolar echinococcosis is a lethal zoonotic disease caused by the fox tapeworm Echinococcus multilocularis. The parasite is widely distributed in the Northern Hemisphere and exhibits low genetic diversity among populations. To compare the differences among four E. multilocularis strains from different geographical locations, namely, Alaska (EM-AK), Japan (EM-JP), Xinjiang (EM-XJ), and Ningxia (EM-NX), their complete mitochondrial (mt) sequences were compared, and their induced pathological lesions were analyzed in mouse models. The complete mt sequence of EM-AK resulted in 0.84%-0.86% variation as compared with the other strains, which had a lower variation. Phylogenetic analysis and parsimony network indicated that EM-AK resulted in 30,000 years of evolutionary distance from the other three strains. EM-AK induced more pathological damage than the other three strains, which was likely to induce more host cell infiltration and acute granuloma in the liver. More importantly, EM-AK produced more protoscoleces than the other three strains, which may impact the transmission dynamics of the parasite. Given the geographical location of four strains, which is far from each other, and also the pathological differences, the strains of E. multilocularis are likely models for addressing the relationship and interfacial immune response between the host and the helminth.IMPORTANCEEchinococcus multilocularis is the causative agent of alveolar echinococcosis, which is considered the most serious parasitic disease in the Northern Hemisphere. There are many genotypes, but the pathogenic and mitochondria sequence and differences are still unclear. Therefore, this study showed both pathological and genetic differences between the four strains of E. multilocularis. EM-AK induced more severe immune responses and especially induced more host cell infiltration, which resulted in more severe granuloma in the liver. EM-JP has metacestode lesions morphologically closer to those of E. granulosus with clear cyst fluid. However, this strain produced much fewer protoscoleces (PSCs). Genetically, EM-AK is more distant from other strains.

Complete mitochondrial genomes of Dactylogyrus crucifer and Dactylogyrus zandti reveal distinct patterns of codon usage within Dactylogyrus

Monogeneans of the genus Dactylogyrus Diesing, 1850, the largest genus in the family Dactylogyridae, mostly parasitize the gills of cyprinoid hosts; however, only 3 Dactylogyrus' mitochondrial genomes (mitogenomes) are studied so far. The aim of this research is to extend our understanding of the mitogenomes of Dactylogyrus. We sequenced the mitogenomes of D. crucifer and D. zandti isolated from Rutilus rutilus and Abramis brama orientalis in northwest China, and then we compared these mitogenomes with other monogeneans. We used Illumina NovaSeq to sequence the entire mitochondrial genomes of D. crucifer and D. zandti and characterized the mitogenomes to understand the gene structure, gene identity, the secondary structures of the 22 tRNA genes, and relative synonymous codon usage. We used the analytic Bayesian Information and Maximum Likelihood methods to determine their associated phylogenetic trees. The mitogenomes of D. crucifer and D. zandti were 14,403 and 18,584 bp, respectively. Organization and positioning of these genes were in accordance with Dactylogyrus lamellatus and Dactylogyrus tuba. The nucleotide composition of Dactylogyridae was different from other families of Monogenea, and the A+T count of genus Dactylogyrus (54 - 58.4 %) was lower than other genus species of the family Dactylogyridea (63.9 - 78.4 %) in protein-coding genes. Dactylogyrus members displayed a codon usage bias. The relative synonymous codon used by Dactylogyrus was not conserved and was lower than other monogeneans. The codon use patterns of closely-related species isolated from closely-related hosts were identical. Phylogenetic analyses using mitogenomic dataset produced Dactylogyrus isolated from host subfamily Leuciscinae formed a sister-group. Our results contributed significantly to an increased database of mitogenomes, more than 50 %, for Dactylogyrus that may help future studies of mitochondrial genes and codon uses for the analysis of monogenean phylogenetics.

The complete mitochondrial genome of Gyrodactylus pseudorasborae (Platyhelminthes: Monogenea) with a phylogeny of Gyrodactylidae parasites

BACKGROUND

Gyrodactylus von Nordmann, 1832, a genus of viviparous parasites within the family Gyrodactylidae, contains one of the largest nominal species in the world. Gyrodactylus pseudorasborae Ondračková, Seifertová & Tkachenko, 2023 widely distributed in Europe and China, although its mitochondrial genome remains unclear. This study aims to sequence the mitogenome of G.pseudorasborae and clarify its phylogenetic relationship within the Gyrodactylidea. The mitochondrial genome of G. pseudorasborae was amplified in six parts from a single parasite, sequenced using primer walking, annotated and analyzed using bioinformatic tools.

RESULTS

The mitochondrial genome of G. pseudorasborae is 14,189 bp in length, containing 12 protein-coding genes (PCGs), 22 transfer RNA genes (tRNAs), two ribosomal RNA genes (rRNAs), and two major non-coding regions (NCR: NC1 and NC2). The overall A + T content of the mitogenome is 73.1%, a medium content compared with all reported mitochondrial genomes of monogeneans. The mitogenome of G. pseudorasborae presents a clear bias in nucleotide composition with a negative AT skew and a positive GC skew except for NCR. All tRNAs have the typical cloverleaf secondary structure except for tRNACys, tRNASer1, and tRNASer2, which lack the dihydrouridine (DHU) arm. Furthermore, one repetitive non-coding region of 32 bp repeats occurred in the NC1 region with poly-T stretch, stem-loop structure, and TAn motif. The gene order is identical to the mitochondrial genomes reported from other Gyrodactylus species except Gyrodactylus nyanzae Paperna, 1973 and Gyrodactylus sp. FZ-2021. Phylogenetic analyses show that G. pseudorasborae and Gyrodactylus parvae You, Easy & Cone, 2008 cluster together with high nodal support based on 12 PCGs sequences and amino acid sequences, Gyrodactylidae forms independent monophyletic clade within Gyrodactylidea.

CONCLUSION

Both the mitochondrial genome and phylogenetic analyses support G. pseudorasborae is a member of the genus Gyrodactylus and Gyrodactylidae forms an independent monophyletic clade within Gyrodactylidea. Furthermore, the mitochondrial genome of G. pseudorasborae is the shortest in the Gyrodactylidea species compared with size differences in NCR.

Aberrant Mitochondrial tRNA Genes Appear Frequently in Animal Evolution

Mitochondrial tRNAs have acquired a diverse portfolio of aberrant structures throughout metazoan evolution. With the availability of more than 12,500 mitogenome sequences, it is essential to compile a comprehensive overview of the pattern changes with regard to mitochondrial tRNA repertoire and structural variations. This, of course, requires reanalysis of the sequence data of more than 250,000 mitochondrial tRNAs with a uniform workflow. Here, we report our results on the complete reannotation of all mitogenomes available in the RefSeq database by September 2022 using mitos2. Based on the individual cases of mitochondrial tRNA variants reported throughout the literature, our data pinpoint the respective hotspots of change, i.e. Acanthocephala (Lophotrochozoa), Nematoda, Acariformes, and Araneae (Arthropoda). Less dramatic deviations of mitochondrial tRNAs from the norm are observed throughout many other clades. Loss of arms in animal mitochondrial tRNA clearly is a phenomenon that occurred independently many times, not limited to a small number of specific clades. The summary data here provide a starting point for systematic investigations into the detailed evolutionary processes of structural reduction and loss of mitochondrial tRNAs as well as a resource for further improvements of annotation workflows for mitochondrial tRNA annotation.

Genome Rearrangement Analysis : Cut and Join Genome Rearrangements and Gene Cluster Preserving Approaches

Genome rearrangements are mutations that change the gene content of a genome or the arrangement of the genes on a genome. Several years of research on genome rearrangements have established different algorithmic approaches for solving some fundamental problems in comparative genomics based on gene order information. This review summarizes the literature on genome rearrangement analysis along two lines of research. The first line considers rearrangement models that are particularly well suited for a theoretical analysis. These models use rearrangement operations that cut chromosomes into fragments and then join the fragments into new chromosomes. The second line works with rearrangement models that reflect several biologically motivated constraints, e.g., the constraint that gene clusters have to be preserved. In this chapter, the border between algorithmically "easy" and "hard" rearrangement problems is sketched and a brief review is given on the available software tools for genome rearrangement analysis.

Mitochondrial genes are involved in the fertility transformation of the thermosensitive male-sterile line YS3038 in wheat

Heterosis can improve the stress resistance, quality, and yield of crops, and the male sterility of wheat can be utilized to accelerate the breeding process of hybrid. To determine whether mitochondrial genes are involved in the fertility of K-type cytoplasmic male-sterile (CMS) line and the YS-type thermosensitive male-sterile (TMS) line in wheat, we sequenced and assembled the mitochondrial genomes of K519A, 519B, and YS3038 by next-generation sequencing (NGS). The non-synonymous mutations were analyzed, and the first-generation sequencing was conducted to verify the non-synonymous mutation sites. Furthermore, the expression patterns of genes with non-synonymous mutations were analyzed. Finally, the candidate genes were silenced by barley stripe mosaic virus-induced gene silencing (BSMV-VIGS) to test the functions of the candidate genes. The results revealed that the mitochondrial genomes of K519A, 519B, and YS3038 were 420,543, 433,560, and 452,567 bp in length, respectively. Besides, 33, 31, and 37 protein-coding genes were identified in K519A, 519B, and YS3038, respectively. There were 14 protein-coding genes and 83 open reading frame (ORF) sequences that differed between K519A and 519B and 10 protein-coding genes and 122 ORF sequences that differed between K519A and YS3038. At the binucleate stage, seven genes (nad6, ORF256, ORF216, ORF138, atp6, nad3, and cox1) were downregulated in K519A compared with 519B, and 10 genes (nad6, atp6, cox3, atp8, nad3, cox1, rps3, ORF216, ORF138, and ORF224) were downregulated in YS3038 compared with K519A. Besides, six genes (nad6, ORF138, cox3, cox1, rps3, and ORF224) were downregulated under fertile conditions relative to sterile conditions in YS3038. Gene silencing analysis showed that the silencing of cox1 significantly reduced the seed setting rate of YS3038, indicating that the cox1 gene may be involved in the fertility transformation of YS3038.

Supplementary Information

The online version contains supplementary material available at 10.1007/s11032-021-01252-x.

Contrasting Host-Parasite Population Structure: Morphology and Mitogenomics of a Parasitic Flatworm on Pelagic Deepwater Cichlid Fishes from Lake Tanganyika

Little phylogeographic structure is presumed for highly mobile species in pelagic zones. Lake Tanganyika is a unique ecosystem with a speciose and largely endemic fauna famous for its remarkable evolutionary history. In bathybatine cichlid fishes, the pattern of lake-wide population differentiation differs among species. We assessed the congruence between the phylogeographic structure of bathybatine cichlids and their parasitic flatworm Cichlidogyrus casuarinus to test the magnifying glass hypothesis. Additionally, we evaluated the use of a PoolSeq approach to study intraspecific variation in dactylogyrid monogeneans. The lake-wide population structure of C. casuarinus ex Hemibates stenosoma was assessed based on a portion of the cox1 gene combined with morphological characterisation. Additionally, intraspecific mitogenomic variation among 80 parasite samples from one spatially constrained metapopulation was assessed using shotgun NGS. While no clear geographic genetic structure was detected in parasites, both geographic and host-related phenotypic variation was apparent. The incongruence with the genetic north-south gradient observed in H. stenosoma may be explained by the broad host range of this flatworm including eupelagic bathybatine host species that form panmictic populations across the lake. In addition, we present the first parasite mitogenome from Lake Tanganyika and propose a methodological framework for studying the intraspecific mitogenomic variation of dactylogyrid monogeneans.

The first mitochondrial genomes of endosymbiotic rhabdocoels illustrate evolutionary relaxation of atp8 and genome plasticity in flatworms

The first three mitochondrial (mt) genomes of endosymbiotic turbellarian flatworms are characterised for the rhabdocoels Graffilla buccinicola, Syndesmis echinorum and S. kurakaikina. Interspecific comparison of the three newly obtained sequences and the only previously characterised rhabdocoel, the free-living species Bothromesostoma personatum, reveals high mt genomic variability, including numerous rearrangements. The first intrageneric comparison within rhabdocoels shows that gene order is not fully conserved even between congeneric species. Atp8, until recently assumed absent in flatworms, was putatively annotated in two sequences. Selection pressure was tested in a phylogenetic framework and is shown to be significantly relaxed in this and another protein-coding gene: cox1. If present, atp8 appears highly derived in platyhelminths and its functionality needs to be addressed in future research. Our findings for the first time allude to a large degree of undiscovered (mt) genomic plasticity in rhabdocoels. It merits further attention whether this variation is correlated with a symbiotic lifestyle. Our results illustrate that this phenomenon is widespread in flatworms as a whole and not exclusive to the better-studied neodermatans.

Mitochondrial Genomes of Two Thaparocleidus Species (Platyhelminthes: Monogenea) Reveal the First rRNA Gene Rearrangement among the Neodermata

Phylogenetic framework for the closely related Ancylodiscoidinae and Ancyrocephalinae subfamilies remains contentious. As this issue was never studied using a large molecular marker, we sequenced the first two Ancylodiscoidinae mitogenomes: Thaparocleidus asoti and Thaparocleidus varicus. Both mitogenomes had two non-coding regions (NCRs) that contained a number of repetitive hairpin-forming elements (RHE). Due to these, the mitogenome of T. asoti (16,074 bp) is the longest among the Monogenea; especially large is its major NCR, with 3500 bp, approximately 1500 bp of which could not be sequenced (thus, the total mitogenome size is ≈ 17,600 bp). Although RHEs have been identified in other monopisthocotyleans, they appear to be independently derived in different taxa. The presence of RHEs may have contributed to the high gene order rearrangement rate observed in the two mitogenomes, including the first report of a transposition of rRNA genes within the Neodermata. Phylogenetic analyses using mitogenomic dataset produced Dactylogyrinae embedded within the Ancyrocephalinae (paraphyly), whereas Ancylodiscoidinae formed a sister-group with them. This was also supported by the gene order analysis. 28S rDNA dataset produced polyphyletic Dactylogyridae and Ancyrocephalinae. The phylogeny of the two subfamilies shall have to be further evaluated with more data.

Homoplasy or plesiomorphy? Reconstruction of the evolutionary history of mitochondrial gene order rearrangements in the subphylum Neodermata

Recent mitogenomic studies have exposed a gene order (GO) shared by two classes, four orders and 31 species ('common GO') within the flatworm subphylum Neodermata. There are two possible hypotheses for this phenomenon: convergent evolution (homoplasy) or shared ancestry (plesiomorphy). To test those, we conducted a meta-analysis on all available mitogenomes to infer the evolutionary history of GO in Neodermata. To improve the resolution, we added a newly sequenced mitogenome that exhibited the common GO, Euryhaliotrema johni (Ancyrocephalinae), to the dataset. Phylogenetic analyses conducted on two datasets (nucleotides of all 36 genes and amino acid sequences of 12 protein coding genes) and four algorithms (MrBayes, RAxML, IQ-TREE and PhyloBayes) produced topology instability towards the tips, so ancestral GO reconstructions were conducted using TreeREx and MLGO programs using all eight obtained topologies, plus three unique topologies from previous studies. The results consistently supported the second hypothesis, resolving the common GO as a plesiomorphic ancestral GO for Neodermata, Cestoda, Monopisthocotylea, Cestoda + Trematoda and Cestoda + Trematoda + Monopisthocotylea. This allowed us to trace the evolutionary GO scenarios from each common ancestor to its descendants amongst the Monogenea and Cestoda classes, and propose that the common GO was most likely retained throughout all of the common ancestors, leading to the extant species possessing the common GO. Neodermatan phylogeny inferred from GOs was largely incongruent with all 11 topologies described above, but it did support the mitogenomic dataset in resolving Polyopisthocotylea as the earliest neodermatan branch. Although highly derived GOs might be of some use in resolving isolated taxonomic and phylogenetic uncertainties, we conclude that, due to the discontinuous nature of their evolution, they tend to produce artefactual phylogenetic relationships, which makes them unsuitable for phylogenetic reconstruction in Neodermata. Wider and denser sampling of neodermatan mitogenomic sequences will be needed to infer the evolutionary pathways leading to the observed diversity of GOs with confidence.

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.

Three new Diplozoidae mitogenomes expose unusual compositional biases within the Monogenea class: implications for phylogenetic studies

BACKGROUND

As the topologies produced by previous molecular and morphological studies were contradictory and unstable (polytomy), evolutionary relationships within the Diplozoidae family and the Monogenea class (controversial relationships among the Discocotylinea, Microcotylinea and Gastrocotylinea suborders) remain unresolved. Complete mitogenomes carry a relatively large amount of information, sufficient to provide a much higher phylogenetic resolution than traditionally used morphological traits and/or single molecular markers. However, their implementation is hampered by the scarcity of available monogenean mitogenomes. Therefore, we sequenced and characterized mitogenomes belonging to three Diplozoidae family species, and conducted comparative genomic and phylogenomic analyses for the entire Monogenea class.

RESULTS

Taxonomic identification was inconclusive, so two of the species were identified merely to the genus level. The complete mitogenomes of Sindiplozoon sp. and Eudiplozoon sp. are 14,334 bp and 15,239 bp in size, respectively. Paradiplozoon opsariichthydis (15,385 bp) is incomplete: an approximately 2000 bp-long gap within a non-coding region could not be sequenced. Each genome contains the standard 36 genes (atp8 is missing). G + T content and the degree of GC- and AT-skews of these three mitogenome (and their individual elements) were higher than in other monogeneans. nad2, atp6 and nad6 were the most variable PCGs, whereas cox1, nad1 and cytb were the most conserved. Mitochondrial phylogenomics analysis, conducted using concatenated amino acid sequences of all PCGs, indicates that evolutionary relationships of the three genera are: (Eudiplozoon, (Paradiplozoon, Sindiplozoon)); and of the three suborders: (Discocotylinea, (Microcotylinea, Gastrocotylinea)). These intergeneric relationships were also supported by the skewness and principal component analyses.

CONCLUSIONS

Our results show that nad2, atp6 and nad6 (fast-evolving) would be better candidates than cox1 (slow-evolving) for species identification and population genetics studies in Diplozoidae. Nucleotide bias and codon and amino acid usage patterns of the three diplozoid mitogenomes are more similar to cestodes and trematodes than to other monogenean flatworms. This unusual mutational bias was reflected in disproportionately long branches in the phylogram. Our study offsets the scarcity of molecular data for the subclass Polyopisthocotylea to some extent, and might provide important new insights into the evolutionary history of the three genera and three suborders.

The first next-generation sequencing approach to the mitochondrial phylogeny of African monogenean parasites (Platyhelminthes: Gyrodactylidae and Dactylogyridae)

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.

Spermiogenesis and spermatozoon ultrastructure in basal polyopisthocotylean monogeneans, Hexabothriidae and Chimaericolidae, and their significance for the phylogeny of the Monogenea

Sperm ultrastructure provides morphological characters useful for understanding phylogeny; no study was available for two basal branches of the Polyopisthocotylea, the Chimaericolidea and Diclybothriidea. We describe here spermiogenesis and sperm in Chimaericola leptogaster (Chimaericolidae) and Rajonchocotyle emarginata (Hexabothriidae), and sperm in Callorhynchocotyle callorhynchi (Hexabothriidae). Spermiogenesis in C. leptogaster and R. emarginata shows the usual pattern of most Polyopisthocotylea with typical zones of differentiation and proximo-distal fusion of the flagella. In all three species, the structure of the spermatozoon is biflagellate, with two incorporated trepaxonematan 9 + "1" axonemes and a posterior nucleus. However, unexpected structures were also seen. An alleged synapomorphy of the Polyopisthocotylea is the presence of a continuous row of longitudinal microtubules in the nuclear region. The sperm of C. leptogaster has a posterior part with a single axoneme, and the part with the nucleus is devoid of the continuous row of microtubules. The spermatozoon of R. emarginata has an anterior region with membrane ornamentation, and posterior lateral microtubules are absent. The spermatozoon of C. callorhynchi has transverse sections with only dorsal and ventral microtubules, and its posterior part shows flat sections containing a single axoneme and the nucleus. These findings have important implications for phylogeny and for the definition of synapomorphies in the Neodermata. We point out a series of discrepancies between actual data and interpretation of character states in the matrix of a phylogeny of the Monogenea. Our main conclusion is that the synapomorphy "lateral microtubules in the principal region of the spermatozoon" does not define the Polyopisthocotylea but is restricted to the Mazocraeidea.

Genome Rearrangement Analysis: Cut and Join Genome Rearrangements and Gene Cluster Preserving Approaches

Genome rearrangements are mutations that change the gene content of a genome or the arrangement of the genes on a genome. Several years of research on genome rearrangements have established different algorithmic approaches for solving some fundamental problems in comparative genomics based on gene order information. This review summarizes the literature on genome rearrangement analysis along two lines of research. The first line considers rearrangement models that are particularly well suited for a theoretical analysis. These models use rearrangement operations that cut chromosomes into fragments and then join the fragments into new chromosomes. The second line works with rearrangement models that reflect several biologically motivated constraints, e.g., the constraint that gene clusters have to be preserved. In this chapter, the border between algorithmically "easy" and "hard" rearrangement problems is sketched and a brief review is given on the available software tools for genome rearrangement analysis.

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.

Sequencing, characterization and phylogenomics of the complete mitochondrial genome of Dactylogyrus lamellatus (Monogenea: Dactylogyridae)

Despite the worldwide distribution and pathogenicity of monogenean parasites belonging to the largest helminth genus, Dactylogyrus, there are no complete Dactylogyrinae (subfamily) mitogenomes published to date. In order to fill this knowledge gap, we have sequenced and characterized the complete mitogenome of Dactylogyrus lamellatus, a common parasite on the gills of grass carp (Ctenopharyngodon idella). The circular mitogenome is 15,187 bp in size, containing the standard 22 tRNA genes, 2 rRNA genes, 12 protein-encoding genes and a long non-coding region (NCR). There are two highly repetitive regions in the NCR. We have used concatenated nucleotide sequences of all 36 genes to perform the phylogenetic analysis using Bayesian inference and maximum likelihood approaches. As expected, the two dactylogyrids, D. lamellatus (Dactylogyrinae) and Tetrancistrum nebulosi (Ancyrocephalinae), were closely related to each other. These two formed a sister group with Capsalidae, and this cluster finally formed a further sister group with Gyrodactylidae. Phylogenetic affinity between Dactylogyrinae and Ancyrocephalinae was further confirmed by the similarity in their gene arrangement. The sequencing of the first Dactylogyrinae, along with a more suitable selection of outgroups, has enabled us to infer a much better phylogenetic resolution than recent mitogenomic studies. However, as many lineages of the class Monogenea remain underrepresented or not represented at all, a much larger number of mitogenome sequences will have to be available in order to infer the evolutionary relationships among the monogeneans fully, and with certainty.

Atp8 is in the ground pattern of flatworm mitochondrial genomes

Background

To date, mitochondrial genomes of more than one hundred flatworms (Platyhelminthes) have been sequenced. They show a high degree of similarity and a strong taxonomic bias towards parasitic lineages. The mitochondrial gene atp8 has not been confidently annotated in any flatworm sequenced to date. However, sampling of free-living flatworm lineages is incomplete. We addressed this by sequencing the mitochondrial genomes of the two small-bodied (about 1 mm in length) free-living flatworms Stenostomum sthenum and Macrostomum lignano as the first representatives of the earliest branching flatworm taxa Catenulida and Macrostomorpha respectively.

Results

We have used high-throughput DNA and RNA sequence data and PCR to establish the mitochondrial genome sequences and gene orders of S. sthenum and M. lignano. The mitochondrial genome of S. sthenum is 16,944 bp long and includes a 1,884 bp long inverted repeat region containing the complete sequences of nad3, rrnS, and nine tRNA genes. The model flatworm M. lignano has the smallest known mitochondrial genome among free-living flatworms, with a length of 14,193 bp. The mitochondrial genome of M. lignano lacks duplicated genes, however, tandem repeats were detected in a non-coding region.

Mitochondrial gene order is poorly conserved in flatworms, only a single pair of adjacent ribosomal or protein-coding genes – nad4l-nad4 – was found in S. sthenum and M. lignano that also occurs in other published flatworm mitochondrial genomes. Unexpectedly, we unambiguously identified the full metazoan mitochondrial protein-coding gene complement including atp8 in S. sthenum and M. lignano. A subsequent search detected atp8 in all mitochondrial genomes of polyclad flatworms published to date, although the gene wasn’t previously annotated in these species.

Conclusions

Manual, but not automated genome annotation revealed the presence of atp8 in basally branching free-living flatworms, signifying both the importance of manual data curation and of diverse taxon sampling. We conclude that the loss of atp8 within flatworms is restricted to the parasitic taxon Neodermata.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-017-3807-2) contains supplementary material, which is available to authorized users.

Characterization of the complete mitochondrial genome of the cloacal tapeworm Cloacotaenia megalops (Cestoda: Hymenolepididae)

Background

The cloacal tapeworm Cloacotaenia megalops (Hymenolepididae) is one of the most common cestode parasites of domestic and wild ducks worldwide. However, limited information is available regarding its epidemiology, biology, genetics and systematics. This study provides characterisation of the complete mitochondrial (mt) genome of C. megalops.

Methods

The complete mt genome of C. megalops was obtained by long PCR, sequenced and annotated.

Results

The length of the entire mt genome of C. megalops is 13,887 bp; it contains 12 protein-coding, 2 ribosomal RNA and 22 transfer RNA genes, but lacks an atp8 gene. The mt gene arrangement of C. megalops is identical to that observed in Anoplocephala magna and A. perfoliata (Anoplocephalidae), Dipylidium caninum (Dipylidiidae) and Hymenolepis diminuta (Hymenolepididae), but differs from that reported in taeniids owing to the position shift between the tRNA (L1) and tRNA (S2) genes. The phylogenetic position of C. megalops was inferred using Maximum likelihood and Bayesian inference methods based on the concatenated amino acid data for 12 protein-coding genes. Phylogenetic trees showed that C. megalops is sister to Anoplocephala spp. (Anoplocephalidae) + Pseudanoplocephala crawfordi + Hymenolepis spp. (Hymenolepididae) indicating that the family Hymenolepididae is paraphyletic.

Conclusions

The complete mt genome of C. megalops is sequenced. Phylogenetic analyses provided an insight into the phylogenetic relationships among the families Anoplocephalidae, Hymenolepididae, Dipylidiidae and Taeniidae. This novel genomic information also provides the opportunity to develop useful genetic markers for studying the molecular epidemiology, biology, genetics and systematics of C. megalops.

Electronic supplementary material

The online version of this article (doi:10.1186/s13071-016-1782-0) contains supplementary material, which is available to authorized users.