Changes in mitochondrial genetic codes as phylogenetic characters: two examples from the flatworms

Theama japonica sp. nov., an Interstitial Polyclad Flatworm Showing a Wide Distribution along Japanese Coasts

We establish a new interstitial polyclad species, Theama japonica sp. nov., based on specimens collected from coarse-sandy habitats in three Japanese main islands (Hokkaido, Honshu, and Shikoku) along the coasts of the Pacific Ocean and the Sea of Japan. Theama japonica is characterized by i) two pairs of cerebral eyespots and four to six precerebral eyespots; ii) eosinophilic secretion glands distributed in the distal half of the inner ventral part of the prostatic vesicle; iii) a conical penis papilla, bent up dorsally, with a sclerotized inner wall; iv) the prostatic sheath with an inner angular fold on the dorso-distal side; and v) the external cilia longer dorsally than ventrally. Partial sequences of the cytochrome c oxidase subunit I (COI) gene from 20 specimens collected at eight localities along Japanese coasts represented 19 haplotypes. The uncorrected p-distances among these COI haplotypes fell within intraspecific variations observed in other polyclads. A network analysis based on these COI haplotypes suggested a geographically non-cohesive genetic structure of the species, possibly indicating the species' high dispersibility. Molecular phylogenetic analyses based on a concatenated dataset of 18S and 28S rDNA sequences showed T. japonica formed a clade with other Theama species. The resulting tree also indicates that our new species is more closely related to Theama sp. from Colombia than species from Panama and Croatia.

Characterization of the complete mitochondrial genome of Plagiorchis multiglandularis (Digenea, Plagiorchiidae): Comparison with the members of Xiphidiatan species and phylogenetic implications

Plagiorchis multiglandularis Semenov, 1927 is a common fluke of birds and mammals, with significant impacts on animals and also human health. However, the systematics of Plagiorchiidae remain ambiguous. In the present study, the complete mitochondrial (mt) genome of P. multiglandularis cercariae was sequenced and compared with other digeneans in the order Xiphidiata. The complete circular mt genome of P. multiglandularis was 14,228 bp in length. The mitogenome contains 12 protein-coding genes and 22 transfer RNA genes. The 3' end of nad4L overlaps the 5' end of nad4 by 40 bp, while the atp8 gene is absent. Twenty-one transfer RNA genes transcribe products with conventional cloverleaf structures, while one transfer RNA gene has unpaired D-arms. Comparative analysis with related digenean trematodes revealed that A + T content of mt genome of P. multiglandularis was significantly higher among all the xiphidiatan trematodes. Phylogenetic analyses demonstrated that Plagiorchiidae formed a monophyletic branch, in which Plagiorchiidae are more closely related to Paragonimidae than Prosthogonimidae. Our data enhanced the Plagiorchis mt genome database and provides molecular resources for further studies of Plagiorchiidae taxonomy, population genetics and systematics.

Comparative Mitogenome Analyses Uncover Mitogenome Features and Phylogenetic Implications of the Parrotfishes (Perciformes: Scaridae)

In order to investigate the molecular evolution of mitogenomes among the family Scaridae, the complete mitogenome sequences of twelve parrotfish species were determined and compared with those of seven other parrotfish species. The comparative analysis revealed that the general features and organization of the mitogenome were similar among the 19 parrotfish species. The base composition was similar among the parrotfishes, with the exception of the genus Calotomus, which exhibited an unusual negative AT skew in the whole mitogenome. The PCGs showed similar codon usage, and all of them underwent a strong purifying selection. The gene rearrangement typical of the parrotfishes was detected, with the tRNAMet inserted between the tRNAIle and tRNAGln, and the tRNAGln was followed by a putative tRNAMet pseudogene. The parrotfish mitogenomes displayed conserved gene overlaps and secondary structure in most tRNA genes, while the non-coding intergenic spacers varied among species. Phylogenetic analysis based on the thirteen PCGs and two rRNAs strongly supported the hypothesis that the parrotfishes could be subdivided into two clades with distinct ecological adaptations. The early divergence of the sea grass and coral reef clades occurred in the late Oligocene, probably related to the expansion of sea grass habitat. Later diversification within the coral reef clade could be dated back to the Miocene, likely associated with the geomorphology alternation since the closing of the Tethys Ocean. This work provided fundamental molecular data that will be useful for species identification, conservation, and further studies on the evolution of parrotfishes.

Codetta: predicting the genetic code from nucleotide sequence

SUMMARY

Codetta is a Python program for predicting the genetic code table of an organism from nucleotide sequences. Codetta can analyze an arbitrary nucleotide sequence and needs no sequence annotation or taxonomic placement. The most likely amino acid decoding for each of the 64 codons is inferred from alignments of profile hidden Markov models of conserved proteins to the input sequence.

AVAILABILITY AND IMPLEMENTATION

Codetta 2.0 is implemented as a Python 3 program for MacOS and Linux and is available from http://eddylab.org/software/codetta/codetta2.tar.gz and at http://github.com/kshulgina/codetta.

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

Schistosomes in the Persian Gulf: novel molecular data, host associations, and life-cycle elucidations

Avian schistosomes, comprise a diverse and widespread group of trematodes known for their surprising ability to switch into new hosts and habitats. Despite the considerable research attention on avian schistosomes as causatives of the human cercarial dermatitis, less it is known about the diversity, geographical range and host associations of the marine representatives. Our molecular analyses inferred from cox1 and 28S DNA sequence data revealed presence of two schistosome species, Ornithobilharzia canaliculata (Rudolphi, 1819) Odhner, 1912 and a putative new species of Austrobilharzia Johnston, 1917. Molecular elucidation of the life-cycle of O. canaliculata was achieved for the first time via matching novel and published sequence data from adult and larval stages. This is the first record of Ornithobilharzia from the Persian Gulf and globally the first record of this genus in a potamidid snail host. Our study provides: (i) new host and distribution records for major etiological agents of cercarial dermatitis and contributes important information on host-parasite relationships; (ii) highlights the importance of the molecular systematics in the assessment of schistosome diversity; and (iii) calls for further surveys to reach a better understanding of the schistosome diversity and patterns of relationships among them, host associations, transmission strategies and distribution coverage.

Temnosewellia aff. vietnamensis (Platyhelminthes: Rhabdocoela: Temnocephalidae) associated with freshwater crabs from Kagoshima, southern Japan, with review of records of the genus from East to South Asian countries

Temnocephalids are ectosymbionts of various freshwater animals. A species tentatively identified as Temnosewellia aff. vietnamensis (Platyhelminthes: Rhabdocoela: Temnocephalidae) is reported based on materials collected from the body surface of the freshwater crabs Eriocheir japonica (Brachyura: Varunidae) and Geothelphusa exigua (Potamidae) in Kagoshima, southern Japan. The temnocephalid is characterized as follows: the cirrus composed of a cone-shaped shaft and a cylindrical introvert 42-77 μm long; the introvert covered with approximately 30 vertical rows of fine sharp spines; the four seminal receptacles; and a long, curved oviduct with vaginal gland; a pair of gland cells (Haswell's cells) present anterior to the excretory ampullae. Bayesian inference trees using partial nuclear 28S rDNA (28S) and mitochondrial cytochrome c oxidase subunit I (COI) genes supported that the specimens collected from both crab species are conspecific but these also showed the geographical variations among them on both 28S and COI. The previous records of the genus Temnosewellia in East to South Asian countries are assembled and shown on the map (fig.7, this paper).

Different phylogenomic methods support monophyly of enigmatic 'Mesozoa' (Dicyemida + Orthonectida, Lophotrochozoa)

Dicyemids and orthonectids were traditionally classified in a group called Mesozoa, but their placement in a single clade has been contested and their position(s) within Metazoa is uncertain. Here, we assembled a comprehensive matrix of Lophotrochozoa (Metazoa) and investigated the position of Dicyemida (= Rhombozoa) and Orthonectida, employing multiple phylogenomic approaches. We sequenced seven new transcriptomes and one draft genome from dicyemids (Dicyema, Dicyemennea) and two transcriptomes from orthonectids (Rhopalura). Using these and published data, we assembled and analysed contamination-filtered datasets with up to 987 genes. Our results recover Mesozoa monophyletic and as a close relative of Platyhelminthes or Gnathifera. Because of the tendency of the long-branch mesozoans to group with other long-branch taxa in our analyses, we explored the impact of approaches purported to help alleviate long-branch attraction (e.g. taxon removal, coalescent inference, gene targeting). None of these were able to break the association of Orthonectida with Dicyemida in the maximum-likelihood trees. Contrastingly, the Bayesian analysis and site-specific frequency model in maximum-likelihood did not recover a monophyletic Mesozoa (but only when using a specific 50 gene matrix). The classic hypothesis on monophyletic Mesozoa is possibly reborn and should be further tested.

Expansion of Cyclophyllidea Biodiversity in Rodents of Qinghai-Tibet Plateau and the "Out of Qinghai-Tibet Plateau" Hypothesis of Cyclophyllideans

The Cyclophyllidea comprises the most species-rich order of tapeworms (Platyhelminthes, Cestoda) and includes species with some of the most severe health impact on wildlife, livestock, and humans. We collected seven Cyclophyllidea specimens from rodents in Qinghai-Tibet Plateau (QTP) and its surrounding mountain systems, of which four specimens in QTP were unsequenced, representing “putative new species.” Their complete mitochondrial (mt) genomes were sequenced and annotated. Phylogenetic reconstruction of partial 28S rDNA, cox1 and nad1 datasets provided high bootstrap frequency support for the categorization of three “putative new species,” assigning each, respectively, to the genera Mesocestoides, Paranoplocephala, and Mosgovoyia, and revealing that some species and families in these three datasets, which contain 291 species from nine families, may require taxonomic revision. The partial 18S rDNA phylogeny of 29 species from Taeniidae provided high bootstrap frequency support for the categorization of the “putative new species” in the genus Hydatigera. Combined with the current investigation, the other three known Taeniidae species found in this study were Taenia caixuepengi, T. crassiceps, and Versteria mustelae and may be widely distributed in western China. Estimates of divergence time based on cox1 + nad1 fragment and mt protein-coding genes (PCGs) showed that the differentiation rate of Cyclophyllidea species was strongly associated with the rate of change in the biogeographic scenarios, likely caused by the uplift of the QTP; i.e., species differentiation of Cyclophyllidea might be driven by host-parasite co-evolution caused by the uplift of QTP. We propose an “out of QTP” hypothesis for the radiation of these cyclophyllidean tapeworms.

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.

A computational screen for alternative genetic codes in over 250,000 genomes

The genetic code has been proposed to be a ‘frozen accident,’ but the discovery of alternative genetic codes over the past four decades has shown that it can evolve to some degree. Since most examples were found anecdotally, it is difficult to draw general conclusions about the evolutionary trajectories of codon reassignment and why some codons are affected more frequently. To fill in the diversity of genetic codes, we developed Codetta, a computational method to predict the amino acid decoding of each codon from nucleotide sequence data. We surveyed the genetic code usage of over 250,000 bacterial and archaeal genome sequences in GenBank and discovered five new reassignments of arginine codons (AGG, CGA, and CGG), representing the first sense codon changes in bacteria. In a clade of uncultivated Bacilli, the reassignment of AGG to become the dominant methionine codon likely evolved by a change in the amino acid charging of an arginine tRNA. The reassignments of CGA and/or CGG were found in genomes with low GC content, an evolutionary force that likely helped drive these codons to low frequency and enable their reassignment.

All life forms rely on a ‘code’ to translate their genetic information into proteins. This code relies on limited permutations of three nucleotides – the building blocks that form DNA and other types of genetic information. Each ‘triplet’ of nucleotides – or codon – encodes a specific amino acid, the basic component of proteins. Reading the sequence of codons in the right order will let the cell know which amino acid to assemble next on a growing protein. For instance, the codon CGG – formed of the nucleotides guanine (G) and cytosine (C) – codes for the amino acid arginine. From bacteria to humans, most life forms rely on the same genetic code. Yet certain organisms have evolved to use slightly different codes, where one or several codons have an altered meaning.

To better understand how alternative genetic codes have evolved, Shulgina and Eddy set out to find more organisms featuring these altered codons, creating a new software called Codetta that can analyze the genome of a microorganism and predict the genetic code it uses. Codetta was then used to sift through the genetic information of 250,000 microorganisms. This was made possible by the sequencing, in recent years, of the genomes of hundreds of thousands of bacteria and other microorganisms – including many never studied before.

These analyses revealed five groups of bacteria with alternative genetic codes, all of which had changes in the codons that code for arginine. Amongst these, four had genomes with a low proportion of guanine and cytosine nucleotides. This may have made some guanine and cytosine-rich arginine codons very rare in these organisms and, therefore, easier to be reassigned to encode another amino acid.

The work by Shulgina and Eddy demonstrates that Codetta is a new, useful tool that scientists can use to understand how genetic codes evolve. In addition, it can also help to ensure the accuracy of widely used protein databases, which assume which genetic code organisms use to predict protein sequences from their genomes.

Molecular and morphological characterisation of Diplostomum phoxini (Faust, 1918) with a revised classification and an updated nomenclature of the species-level lineages of Diplostomum (Digenea: Diplostomidae) sequenced worldwide

We characterised morphologically and molecularly Diplostomum phoxini (Faust, 1918) based on cercarial isolates from the snail Ampullaceana balthica (L.) (Gastropoda: Lymnaeidae) and metacercariae from the Eurasian minnow, Phoxinus phoxinus (L.) (Cypriniformes: Leuciscidae), and provided molecular evidence for the identification of the snail intermediate host. Phylogenetic analyses based on the cytochrome c oxidase subunit 1 (cox1) gene depicted 44 molecularly characterised species and genetically distinct lineages of Diplostomum, and resulted in: (i) a re-identification/re-classification of 98 isolates plus D. baeri sampled in North America; (ii) re-definition of the composition of the D. baeri species complex which now includes nine molecularly characterised species/lineages; (iii) re-definition of the composition of the D. mergi species complex which now includes seven molecularly characterised species/lineages; and (iv) an updated nomenclature for the molecularly characterised species-level lineages of Diplostomum.

Genetic Evolution and Implications of the Mitochondrial Genomes of Two Newly Identified Taenia spp. in Rodents From Qinghai-Tibet Plateau

The larva of Taeniidae species can infect a wide range of mammals, causing major public health and food safety hazards worldwide. The Qinghai-Tibet Plateau (QTP), a biodiversity hotspot, is home to many species of rodents, which act as the critical intermediate hosts of many Taeniidae species. In this study, we identified two new larvae of Taenia spp., named T. caixuepengi and T. tianguangfui, collected from the plateau pika (Ochotona curzoniae) and the Qinghai vole (Neodon fuscus), respectively, in QTP, and their mitochondrial genomes were sequenced and annotated. Phylogenetic trees based on the mitochondrial genome showed that T. caixuepengi has the closest genetic relationship with T. pisiformis, while T. tianguangfui was contained in a monophyletic group with T. crassiceps, T. twitchelli, and T. martis. Biogeographic scenarios analysis based on split time speculated that the speciation of T. caixuepengi (∼5.49 Mya) is due to host switching caused by the evolution of its intermediate host. Although the reason for T. tianguangfui (∼13.11 Mya) speciation is not clear, the analysis suggests that it should be infective to a variety of other rodents following the evolutionary divergence time of its intermediate host and the range of intermediate hosts of its genetically close species. This study confirms the species diversity of Taeniidae in the QTP, and speculates that the uplift of the QTP has not only a profound impact on the biodiversity of plants and animals, but also that of parasites.

Another blow to the conserved gene order in Annelida: Evidence from mitochondrial genomes of the calcareous tubeworm genus Hydroides

Mitochondrial genomes are frequently applied in phylogenetic and evolutionary studies across metazoans, yet they are still poorly represented in many groups of invertebrates, including annelids. Here, we report ten mitochondrial genomes from the annelid genus Hydroides (Serpulidae) and compare them with all available annelid mitogenomes. We detected all 13 protein coding genes in Hydroides spp., including the atp8 which was reported as a missing gene in the Christmas Tree worm Spirobranchus giganteus, another annelid of the family Serpulidae. All available mitochondrial genomes of Hydroides show a highly positive GC skew combined with a highly negative AT skew - a feature consistent with that found only in the mitogenome of S. giganteus. In addition, amino acid sequences of the 13 protein-coding genes showed a high genetic distance between the Hydroides clade and S. giganteus, suggesting a fast rate of mitochondrial sequence evolution in Serpulidae. The gene order of protein-coding genes within Hydroides exhibited extensive rearrangements at species level, and were different from the arrangement patterns of other annelids, including S. giganteus. Phylogenetic analyses based on protein-coding genes recovered Hydroides as a monophyletic group sister to Spirobranchus with a long branch, and sister to the fan worm Sabellidae. Yet the Serpulidae + Sabellidae clade was unexpectedly grouped with Sipuncula, suggesting that mitochondrial genomes alone are insufficient to resolve the phylogenetic position of Serpulidae within Annelida due to its high base substitution rates. Overall, our study revealed a high variability in the gene order arrangement of mitochondrial genomes within Serpulidae, provided evidence to question the conserved pattern of the mitochondrial gene order in Annelida and called for caution when applying mitochondrial genes to infer their phylogenetic relationships.

Nanopore Sequencing Resolves Elusive Long Tandem-Repeat Regions in Mitochondrial Genomes

Long non-coding, tandem-repetitive regions in mitochondrial (mt) genomes of many metazoans have been notoriously difficult to characterise accurately using conventional sequencing methods. Here, we show how the use of a third-generation (long-read) sequencing and informatic approach can overcome this problem. We employed Oxford Nanopore technology to sequence genomic DNAs from a pool of adult worms of the carcinogenic parasite, Schistosoma haematobium, and used an informatic workflow to define the complete mt non-coding region(s). Using long-read data of high coverage, we defined six dominant mt genomes of 33.4 kb to 22.6 kb. Although no variation was detected in the order or lengths of the protein-coding genes, there was marked length (18.5 kb to 7.6 kb) and structural variation in the non-coding region, raising questions about the evolution and function of what might be a control region that regulates mt transcription and/or replication. The discovery here of the largest tandem-repetitive, non-coding region (18.5 kb) in a metazoan organism also raises a question about the completeness of some of the mt genomes of animals reported to date, and stimulates further explorations using a Nanopore-informatic workflow.

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.

Three new species of acanthocephalans (Palaeacanthocephala) from marine fishes collected off the East Coast of South Africa

Three new species of acanthocephalans are described from marine fishes collected in Sodwana Bay, South Africa: Rhadinorhynchus gerberi n. sp. from Trachinotus botla (Shaw), Pararhadinorhynchus sodwanensis n. sp. from Pomadasys furcatus (Bloch et Schneider) and Transvena pichelinae n. sp. from Thalassoma purpureum (Forsskål). Transvena pichelinae n. sp. differs from the single existing species of the genus Transvena annulospinosa Pichelin et Cribb, 2001, by the lower number of longitudinal rows of hooks (10-12 vs 12-14, respectively) and fewer hooks in a row (5 vs 6-8), shorter blades of anterior hooks (55-63 vs 98), more posterior location of the ganglion (close to the posterior margin of the proboscis receptacle vs mid-level of the proboscis receptacle) and smaller eggs (50-58 × 13 µm vs 62-66 × 13-19 µm). Pararhadinorhynchus sodwanensis n. sp. differs from all known species of the genus by a combination of characters. It closely resembles unidentified species Pararhadinorhynchus sp. sensu Weaver and Smales (2014) in the presence of a similar number of longitudinal rows of hooks on the proboscis (16-18 vs 18) and hooks in a row (11-13 vs 13-14), but differs in the position of the lemnisci (extend to the level of the posterior end of the proboscis receptacle or slightly posterior vs extend to the mid-level of the receptacle), length of the proboscis receptacle (910-1180 µm vs 1,460 µm) and cement glands (870-880 µm vs 335-350 µm). Rhadinorhynchus gerberi n. sp. is distinguishable from all its congeners by a single field of 19-26 irregular circular rows of the tegumental spines on the anterior part of the trunk, 10 longitudinal rows of hooks on the proboscis with 29-32 hooks in each row, subterminal genital pore in both sexes, and distinct separation of the opening of the genital pore from the posterior edge of the trunk (240-480 μm) in females. Sequences for the 18S rDNA, 28S rDNA and cox1 genes were generated to molecularly characterise the species and assess their phylogenetic position. This study provides the first report based on molecular evidence for the presence of species of Transvena Pichelin et Cribb, 2001 and Pararhadinorhynchus Johnston et Edmonds, 1947 in African coastal fishes.

Phylogenetic studies on three Helicotylenchus species based on 28S rDNA and mtCOI sequence data

To facilitate the process of spiral nematode species delineation, populations of Helicotylenchus canadensis, H. pseudorobustus, and H. varicaudatus deriving from various locations and diverse natural and anthropogenic environments from Poland were investigated and characterized. For the first time, 28S rDNA sequences are reported for H. canadensis and H. varicaudatus, whereas new mtCOI sequences were acquired for all three analyzed species. A Bayesian phylogenetic analysis of the 28S rDNA fragments revealed that H. canadensis and H. varicaudatus are members of a clade that is a sister group to all other Helicotylenchus species; however, the closest known sister group to H. canadensis is H. vulgaris type A. Both 28S rDNA- and mtCOI-based phylogenetic results suggest that this clade excludes H. pseudorobustus, whose most recent common ancestor with the former species was inferred to be the ancestor of all Helicotylenchus species. Moreover, within the mtCOI sequences obtained from H. pseudorobustus, unlike from the other two, a simultaneous presence of TAG and TAA codons was identified. This may indicate mitochondrial genetic code alterations or other genomic rearrangements in H. pseudorobustus.

Dicyemida and Orthonectida: Two Stories of Body Plan Simplification

Two enigmatic groups of morphologically simple parasites of invertebrates, the Dicyemida (syn. Rhombozoa) and the Orthonectida, since the 19th century have been usually considered as two classes of the phylum Mesozoa. Early molecular evidence suggested their relationship within the Spiralia (=Lophotrochozoa), however, high rates of dicyemid and orthonectid sequence evolution led to contradicting phylogeny reconstructions. Genomic data for orthonectids revealed that they are highly simplified spiralians and possess a reduced set of genes involved in metazoan development and body patterning. Acquiring genomic data for dicyemids, however, remains a challenge due to complex genome rearrangements including chromatin diminution and generation of extrachromosomal circular DNAs, which are reported to occur during the development of somatic cells. We performed genomic sequencing of one species of Dicyema, and obtained transcriptomic data for two Dicyema spp. Homeodomain (homeobox) transcription factors, G-protein-coupled receptors, and many other protein families have undergone a massive reduction in dicyemids compared to other animals. There is also apparent reduction of the bilaterian gene complements encoding components of the neuromuscular systems. We constructed and analyzed a large dataset of predicted orthologous proteins from three species of Dicyema and a set of spiralian animals including the newly sequenced genome of the orthonectid Intoshia linei. Bayesian analyses recovered the orthonectid lineage within the Annelida. In contrast, dicyemids form a separate clade with weak affinity to the Rouphozoa (Platyhelminthes plus Gastrotricha) or (Entoprocta plus Cycliophora) suggesting that the historically proposed Mesozoa is a polyphyletic taxon. Thus, dramatic simplification of body plans in dicyemids and orthonectids, as well as their intricate life cycles that combine metagenesis and heterogony, evolved independently in these two lineages.

A taxonomic review and revisions of Microstomidae (Platyhelminthes: Macrostomorpha)

Microstomidae (Platyhelminthes: Macrostomorpha) diversity has been almost entirely ignored within recent years, likely due to inconsistent and often old taxonomic literature and a general rarity of sexually mature collected specimens. Herein, we reconstruct the phylogenetic relationships of the group using both previously published and new 18S and CO1 gene sequences. We present some taxonomic revisions of Microstomidae and further describe 8 new species of Microstomum based on both molecular and morphological evidence. Finally, we briefly review the morphological taxonomy of each species and provide a key to aid in future research and identification that is not dependent on reproductive morphology. Our goal is to clarify the taxonomy and facilitate future research into an otherwise very understudied group of tiny (but important) flatworms.

Species of Lepidapedon Stafford, 1904 (Digenea: Lepidapedidae) from deep-sea fishes in the Western Mediterranean: molecular and morphological evidence

The species diversity of Lepidapedon Stafford, 1904 (Lepidapediae) in the Western Mediterranean was assessed based on samples from five deep-sea gadiform fishes collected between the Balearic Islands and the Catalonian coast of Spain: Lepidion lepidion (Risso) and Mora moro (Risso) (both Moridae); Coelorinchus mediterraneus Iwamoto & Ungaro and Trachyrincus scabrus (Rafinesque) (both Macrouridae); and Phycis blennoides (Brünnich) (Phycidae). Integration of morphological and molecular evidence (28S rRNA gene and the mitochondrial nad1 gene) revealed that the deep-sea fishes in the Western Mediterranean share two species of Lepidapedon. Lepidapedon desclersae Bray & Gibson, 1995 was recovered in all five fish species of three families [Moridae (L. lepidion and M. moro); Macrouridae (C. mediterraneus and T. scabrus); and Phycidae (P. blennoides)] and L. guevarai Lopez-Roman & Maillard, 1973 was recovered in three fish species of three families [Phycidae (P. blennoides); Macrouridae (T. scabrus); and Moridae (L. lepidion)]. Therefore, both species are considered to be euryxenic but restricted to gadiforms. The voucher material for the two species from different fish hosts is described in detail and the host-related variability based on the morphometric data is assessed.

Mitogenomics Reveals a Novel Genetic Code in Hemichordata

The diverse array of codon reassignments demonstrate that the genetic code is not universal in nature. Exploring mechanisms underlying codon reassignment is critical for understanding the evolution of the genetic code during translation. Hemichordata, comprising worm-like Enteropneusta and colonial filter-feeding Pterobranchia, is the sister taxon of echinoderms and is more distantly related to chordates. However, only a few hemichordate mitochondrial genomes have been sequenced, hindering our understanding of mitochondrial genome evolution within Deuterostomia. In this study, we sequenced four mitochondrial genomes and two transcriptomes, including representatives of both major hemichordate lineages and analyzed together with public available data. Contrary to the current understanding of the mitochondrial genetic code in hemichordates, our comparative analyses suggest that UAA encodes Tyr instead of a "Stop" codon in the pterobranch lineage Cephalodiscidae. We also predict that AAA encodes Lys in pterobranch and enteropneust mitochondrial genomes, contradicting the previous assumption that hemichordates share the same genetic code with echinoderms for which AAA encodes Asn. Thus, we propose a new mitochondrial genetic code for Cephalodiscus and a revised code for enteropneusts. Moreover, our phylogenetic analyses are largely consistent with previous phylogenomic studies. The only exception is the phylogenetic position of the enteropneust Stereobalanus, whose placement as sister to all other described enteropneusts. With broader taxonomic sampling, we provide evidence that evolution of mitochondrial gene order and genetic codes in Hemichordata are more dynamic than previously thought and these findings provide insights into mitochondrial genome evolution within this clade.

A cross-talk on compositional dynamics and codon usage patterns of mitochondrial CYB gene in Echinodermata

Codon usage bias (CUB) refers to a phenomenon in which some synonymous codons are used in mature mRNA at a higher frequency than other members codifying the same amino acid. CUB is mainly determined by mutation pressure and natural selection. We used bioinformatic tools to analyze the protein coding sequences of mitochondrial CYB gene in different classes of Echinodermata to understand the patterns of codon usage. The ENC values of CYB gene in five different classes of Echinodermata were 41.64, 30.33, 43.63, 41.11, and 41.33, which suggested that the CUB of this gene was low. The relative synonymous codon usage (RSCU) values showed that the patterns of over-represented and under-represented codons were different among different classes. Correspondence analysis indicated that the plots of CYB gene were different across classes, suggesting that the pattern of codon usage was also different among five classes under study. Highly significant correlation (p < .01) between overall nucleotide composition and its 3rd codon position indicated that both mutational pressure and natural selection had an influence on the codon usage bias of CYB gene. Furthermore, PR-2 bias plot analysis showed that both mutation pressure and natural selection might have affected the pattern of codon usage in CYB gene of Echinodermata.

Morphological and molecular evidence for synonymy of Corynosoma obtuscens Lincicome, 1943 with Corynosoma australe Johnston, 1937 (Acanthocephala: Polymorphidae)

Corynosoma obtuscens Lincicome, 1943 (Acanthocephala: Polymorphidae) is synonymised with Corynosoma australe Johnston, 1937 based on combined morphological and molecular evidence. Morphological comparison of C. obtuscens (24 males and 27 females) collected from a California sea lion Zalophus californianus (Lesson) in California, USA, with the type-specimens of C. obtuscens and C. australe, and with published data on C. australe collected from different hosts and regions showed no significant differences. The levels of genetic divergence in the cox1 sequences obtained from C. obtuscens from a California sea lion in the present study and C. australe from otariid seals from Argentina and penguins from Brazil ranged between 1.4-1.6% and was considered to represent intraspecific variability. Additionally, cox1 sequences were generated for Andracantha phalacrocoracis (Yamaguti, 1939), Corynosoma semerme (Forssell, 1904), C. strumosum (Rudolphi, 1802), C. validum Van Cleave, 1953 and C. villosum Van Cleave, 1953. Our results revealed inconsistency in the identification of material used as a source of the previously published sequence data for C. obtuscens and C. magdaleni Montreuil, 1958.

The mitochondrial genomes of the mesozoans Intoshia linei, Dicyema sp. and Dicyema japonicum

The Dicyemida and Orthonectida are two groups of tiny, simple, vermiform parasites that have historically been united in a group named the Mesozoa. Both Dicyemida and Orthonectida have just two cell layers and appear to lack any defined tissues. They were initially thought to be evolutionary intermediates between protozoans and metazoans but more recent analyses indicate that they are protostomian metazoans that have undergone secondary simplification from a complex ancestor. Here we describe the first almost complete mitochondrial genome sequence from an orthonectid, Intoshia linei, and describe nine and eight mitochondrial protein-coding genes from Dicyema sp. and Dicyema japonicum, respectively. The 14,247 base pair long I. linei sequence has typical metazoan gene content, but is exceptionally AT-rich, and has a unique gene order. The data we have analysed from the Dicyemida provide very limited support for the suggestion that dicyemid mitochondrial genes are found on discrete mini-circles, as opposed to the large circular mitochondrial genomes that are typical of the Metazoa. The cox1 gene from dicyemid species has a series of conserved, in-frame deletions that is unique to this lineage. Using cox1 genes from across the genus Dicyema, we report the first internal phylogeny of this group.

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.

Orthonectids Are Highly Degenerate Annelid Worms

The animal groups of Orthonectida and Dicyemida are tiny, extremely simple, vermiform endoparasites of various marine animals and have been linked in the Mesozoa (Figure 1). The Orthonectida (Figures 1A and 1B) have a few hundred cells, including a nervous system of just ten cells [2], and the Dicyemida (Figure 1C) are even simpler, with ∼40 cells [3]. They are classic "Problematica" [4]-the name Mesozoa suggests an evolutionary position intermediate between Protozoa and Metazoa (animals) [5] and implies that their simplicity is a primitive state, but molecular data have shown they are members of Lophotrochozoa within Bilateria [6-9], which means that they derive from a more complex ancestor. Their precise affinities remain uncertain, however, and it is disputed whether they even constitute a clade. Ascertaining their affinities is complicated by the very fast evolution observed in their genes, potentially leading to the common systematic error of long-branch attraction (LBA) [10]. Here, we use mitochondrial and nuclear gene sequence data and show that both dicyemids and orthonectids are members of the Lophotrochozoa. Carefully addressing the effects of unequal rates of evolution, we show that the Mesozoa is polyphyletic. While the precise position of dicyemids remains unresolved within Lophotrochozoa, we identify orthonectids as members of the phylum Annelida. This result reveals one of the most extreme cases of body-plan simplification in the animal kingdom; our finding makes sense of an annelid-like cuticle in orthonectids [2] and suggests that the circular muscle cells repeated along their body [11] may be segmental in origin.

Tour around the globe: The case of invasive tapeworm Atractolytocestus huronensis (Cestoda: Caryophyllidea), a parasite of common carp

The monozoic tapeworm Atractolytocestus huronensis Anthony, 1958 (Cestoda: Caryophyllidea), an intestinal parasite of the common carp, is characterized by its invasive character and potential to colonize new territories. It was initially described from North America and has also been found in several European countries. The most recent findings of A. huronensis originated from China and South Africa; however, no data on genetic relationships of these populations were available. The current study provides the first molecular characterisation of A. huronensis from South Africa and China using a partial sequence of mitochondrial cytochrome c oxidase subunit 1 (cox1) and a complete ribosomal ITS2 spacer. Ribosomal and mitochondrial data were applied for phylogenetic analyses in order to assess the genetic interrelationships among global A. huronensis populations. Divergent intragenomic copies of ribosomal ITS2 were detected in all analysed specimens; the structure and frequency of the ITS2 variants of tapeworms from China and South Africa corresponded with the data on ITS2 paralogues observed previously in A. huronensis from Slovakia, the United States and the United Kingdom. The phylogenetic analysis of cox1 indicated that A. huronensis exist in two slightly differentiated clusters; one cluster was supported by all phylogenetic approaches (NJ, ML, BI) and was represented by samples from China, the USA and the UK. A second cluster was represented by tapeworms from continental Europe (Slovakia, Hungary, Romania, Croatia) and South Africa. Haplotype network analysis revealed that the highest population diversity occurs in China. The results provide useful pilot information about the interrelationships of A. huronensis on four continents and indicate that China, or the eastern Palaearctic, served as the original source population for the global expansion of this invasive tapeworm. Data on the origin and distribution of the common carp, the only specific host of A. huronensis, are also discussed.

Probing recalcitrant problems in polyclad evolution and systematics with novel mitochondrial genome resources

For their apparent morphological simplicity, the Platyhelminthes or "flatworms" are a diverse clade found in a broad range of habitats. Their body plans have however made them difficult to robustly classify. Molecular evidence is only beginning to uncover the true evolutionary history of this clade. Here we present nine novel mitochondrial genomes from the still undersampled orders Polycladida and Rhabdocoela, assembled from short Illumina reads. In particular we present for the first time in the literature the mitochondrial sequence of a Rhabdocoel, Bothromesostoma personatum (Typhloplanidae, Mesostominae). The novel mitochondrial genomes examined generally contained the 36 genes expected in the Platyhelminthes, with all possessing 12 of the 13 protein-coding genes normally found in metazoan mitochondrial genomes (ATP8 being absent from all Platyhelminth mtDNA sequenced to date), along with two ribosomal RNA genes. The majority presented possess 22 transfer RNA genes, and a single tRNA gene was absent from two of the nine assembled genomes. By comparison of mitochondrial gene order and phylogenetic analysis of the protein coding and ribosomal RNA genes contained within these sequences with those of previously sequenced species we are able to gain a firm molecular phylogeny for the inter-relationships within this clade. Our phylogenetic reconstructions, using both nucleotide and amino acid sequences under several models and both Bayesian and Maximum Likelihood methods, strongly support the monophyly of Polycladida, and the monophyly of Acotylea and Cotylea within that clade. They also allow us to speculate on the early emergence of Macrostomida, the monophyly of a "Turbellarian-like" clade, the placement of Rhabditophora, and that of Platyhelminthes relative to the Lophotrochozoa (=Spiralia). The data presented here therefore represent a significant advance in our understanding of platyhelminth phylogeny, and will form the basis of a range of future research in the still-disputed classifications within this taxon.

Exploring the diversity of Diplostomum (Digenea: Diplostomidae) in fishes from the River Danube using mitochondrial DNA barcodes

BACKGROUND

Metacercariae of Diplostomum are important fish pathogens, but reliable data on their diversity in natural fish populations are virtually lacking. This study was conducted to explore the species diversity and host-parasite association patterns of Diplostomum spp. in a large riverine system in Europe, using molecular and morphological data.

METHODS

Twenty-eight species of fish of nine families were sampled in the River Danube at Nyergesújfalu in Hungary in 2012 and Štúrovo in Slovakia in 2015. Isolates of Diplostomum spp. were characterised morphologically and molecularly. Partial sequences of the 'barcode' region of the cytochrome c oxidase subunit 1 (cox1) and complete sequences of the nicotinamide adenine dinucleotide dehydrogenase subunit 3 (nad3) mitochondrial genes were amplified for 76 and 30 isolates, respectively. The partial cox1 sequences were used for molecular identification of the isolates and an assessment of haplotype diversity and possible host-associated structuring of the most prevalent parasite species. New primers were designed for amplification of the mitochondrial nad3 gene.

RESULTS

Only lens-infecting Diplostomum spp. were recovered in 16 fish species of five families. Barcoding of representative isolates provided molecular identification for three species/species-level genetic lineages, D. spathaceum, D. pseudospathaceum and 'D. mergi Lineage 2', and three single isolates potentially representing distinct species. Molecular data helped to elucidate partially the life-cycle of 'D. mergi Lineage 2'. Many of the haplotypes of D. spathaceum (16 in total), D. pseudospathaceum (15 in total) and 'D. mergi Lineage 2' (7 in total) were shared by a number of fish hosts and there was no indication of genetic structuring associated with the second intermediate host. The most frequent Diplostomum spp. exhibited a low host-specificity, predominantly infecting a wide range of cyprinid fishes, but also species of distant fish families such as the Acipenseridae, Lotidae, Percidae and Siluridae. The nad3 gene exhibited distinctly higher levels of interspecific divergence in comparison with the cox1 gene.

CONCLUSIONS

This first exploration of the species diversity and host ranges of Diplostomum spp., in natural fish populations in the River Danube, provided novel molecular, morphological and host-use data which will advance further ecological studies on the distribution and host ranges of these important fish parasites in Europe. Our results also indicate that the nad3 gene is a good candidate marker for multi-gene approaches to systematic estimates within the genus.

From mammals back to birds: Host-switch of the acanthocephalan Corynosoma australe from pinnipeds to the Magellanic penguin Spheniscus magellanicus

Trophically-transmitted parasites are regularly exposed to potential new hosts through food web interactions. Successful colonization, or switching, to novel hosts, occur readily when ‘donor’ and ‘target’ hosts are phylogenetically related, whereas switching between distantly related hosts is rare and may result from stochastic factors (i.e. rare favourable mutations). This study investigates a host-switching event between a marine acanthocephalan specific to pinnipeds that is apparently able to reproduce in Magellanic penguins Spheniscus magellanicus from Brazil. Detailed analysis of morphological and morphometrical data from acanthocephalans from penguins indicates that they belong to Corynosoma australe Johnston, 1937. Partial fragments of the 28S rRNA and mitochondrial cox1 genes were amplified from isolates from penguins and two pinniped species (i.e. South American sea lion Otaria flavescens and South American fur seal Arctocephalus australis) to confirm this identification. Infection parameters clearly differ between penguins and the two pinniped species, which were significantly lower in S. magellanicus. The sex ratio of C. australe also differed between penguins and pinnipeds; in S. magellanicus was strongly biased against males, while in pinnipeds it was close to 1:1. Females of C. australe from O. flavescens were smaller than those from S. magellanicus and A. australis. However, fecundity (i.e. the proportion of fully developed eggs) was lower and more variable in females collected from S. magellanicus. At first glance, the occurrence of reproductive individuals of C. australe in Magellanic penguins could be interpreted as an adaptive colonization of a novel avian host through favourable mutations. However, it could also be considered, perhaps more likely, as an example of ecological fitting through the use of a plesimorphic (host) resource, since the ancestors of Corynosoma infected aquatic birds.

The mitochondrial genomes of the acoelomorph worms Paratomella rubra, Isodiametra pulchra and Archaphanostoma ylvae

Acoels are small, ubiquitous - but understudied - marine worms with a very simple body plan. Their internal phylogeny is still not fully resolved, and the position of their proposed phylum Xenacoelomorpha remains debated. Here we describe mitochondrial genome sequences from the acoels Paratomella rubra and Isodiametra pulchra, and the complete mitochondrial genome of the acoel Archaphanostoma ylvae. The P. rubra and A. ylvae sequences are typical for metazoans in size and gene content. The larger I. pulchra  mitochondrial genome contains both ribosomal genes, 21 tRNAs, but only 11 protein-coding genes. We find evidence suggesting a duplicated sequence in the I. pulchra mitochondrial genome. The P. rubra, I. pulchra and A. ylvae mitochondria have a unique genome organisation in comparison to other metazoan mitochondrial genomes. We found a large degree of protein-coding gene and tRNA overlap with little non-coding sequence in the compact P. rubra genome. Conversely, the A. ylvae and I. pulchra genomes have many long non-coding sequences between genes, likely driving genome size expansion in the latter. Phylogenetic trees inferred from mitochondrial genes retrieve Xenacoelomorpha as an early branching taxon in the deuterostomes. Sequence divergence analysis between P. rubra sampled in England and Spain indicates cryptic diversity.

No evidence for strong cytonuclear conflict over sex allocation in a simultaneously hermaphroditic flatworm

Background

Cytoplasmic sex allocation distorters, which arise from cytonuclear conflict over the optimal investment into male versus female reproductive function, are some of the best-researched examples for genomic conflict. Among hermaphrodites, many such distorters have been found in plants, while, to our knowledge, none have been clearly documented in animals.

Methods

Here we provide a quantitative test for cytonuclear conflict over sex allocation in the simultaneously hermaphroditic flatworm Macrostomum lignano. We used a quantitative genetic breeding design, employing pair-wise crosses of 2 × 15 independent inbred lines, to partition the phenotypic variance in several traits (including sex allocation) into its nuclear and cytoplasmic components.

Results

Although the nuclear genetic background had a significant effect on all traits analyzed, we found significant cytoplasmic genetic variation only for ovary size, there explaining just 4.1% of the variance. A subsequent statistical power analysis showed that the experimental design had considerable power to detect cytonuclear interactions.

Conclusion

We conclude that there were no strong effects of cytonuclear conflict in the studied populations, possibly because the usually compact mitochondrial genomes in animals have a lower evolvability than the large mitochondrial genomes in plants or because the sampled populations currently do not harbor variation at putative distorter and/or the restorer loci.

Electronic supplementary material

The online version of this article (doi:10.1186/s12862-017-0952-9) contains supplementary material, which is available to authorized users.

Molecular characterisation of four echinostomes (Digenea: Echinostomatidae) from birds in New Zealand, with descriptions of Echinostoma novaezealandense n. sp. and Echinoparyphium poulini n. sp

Morphological and molecular characterisation of echinostome specimens (Digenea: Echinostomatidae) recovered in one Anas platyrhynchos L. and one Cygnus atratus (Latham) (Anseriformes: Anatidae) from New Zealand revealed the presence of two known species, Echinostoma miyagawai Ishii, 1932 and Echinoparyphium ellisi (Johnston & Simpson, 1944) and two species new to science. Comparative morphological and phylogenetic analyses supported the distinct species status of Echinostoma novaezealandense n. sp. ex Branta canadensis (L.), A. platyrhynchos and C. atratus, and Echinoparyphium poulini n. sp. ex C. atratus. Echinostoma novaezealandense n. sp., a species of the "revolutum" species complex characterised by the possession of a head collar armed with 37 spines, keyed down to E. revolutum but was distinguished from the latter in having a much narrower body with almost parallel margins, longer oesophagus, wider cirrus-sac, larger seminal vesicle, much smaller ventral sucker, ovary, Mehlis' gland and testes, more anteriorly located ovary and testes, and distinctly smaller eggs (81-87 × 42-53 vs 106-136 × 55-70 µm). This new species appears similar to Echinostoma acuticauda Nicoll, 1914 described in Australia but differs in having a longer forebody, more posteriorly located ovary and testes, and much smaller eggs (81-87 × 42-53 vs 112-126 × 63-75 µm). Echinoparyphium poulini n. sp. is differentiated from the four species of Echinoparyphium possessing 37 collar spines considered valid as follows: from E. chinensis Ku, Li & Chu, 1964 in having a much smaller body, four (vs five) angle spines and simple seminal vesicle (vs bipartite); from E. schulzi Matevosyan, 1951 in having a less robust body at a comparable body length, much smaller ventral sucker, ovary and testes, and longer but narrower eggs (87-109 × 50-59 vs 70-85 × 60-84 µm); and from the two smaller forms, E. serratum Howell, 1968 and E. aconiatum Dietz, 1909, in a number of additional metrical features correlated with body size and especially in the possession of much larger collar spines. Partial fragments of the mitochondrial nad1 and 28S rRNA genes were amplified for representative isolates of the four species and analysed together with sequences for Echinostoma spp. and Echinoparyphium spp. available on GenBank. Phylogenetic analyses based on the mitochondrial nad1 gene revealed congruence between the molecular data and species identification/delineation based on morphology; this was corroborated by the 28S rDNA sequence data.

Morphology and molecules reveal the alien Posthodiplostomum centrarchi Hoffman, 1958 as the third species of Posthodiplostomum Dubois, 1936 (Digenea: Diplostomidae) in Europe

Metacercariae of two species of Posthodiplostomum Dubois, 1936 (Digenea: Diplostomidae) were subjected to morphological and molecular studies: P. brevicaudatum (von Nordmann, 1832) from Gasterosteus aculeatus (L.) (Gasterosteiformes: Gasterosteidae), Bulgaria (morphology, cox1 and ITS1-5.8S-ITS2) and Perca fluviatilis L. (Perciformes: Percidae), Czech Republic (morphology, cox1, ITS1-5.8S-ITS2 and 28S); and P. centrarchi Hoffman, 1958 from Lepomis gibbosus (L.) (Perciformes: Centrarchidae), Bulgaria (morphology, cox1 and ITS1-5.8S-ITS2) and Slovakia (cox1 and ITS1-5.8S-ITS2). In addition, cercariae of P. cuticola (von Nordmann, 1832) from Planorbis planorbis (L.) (Mollusca: Planorbidae), Lithuania (morphology and cox1) and metacercariae of Ornithodiplostomum scardinii (Schulman in Dubinin, 1952) from Scardinius erythrophthalmus (L.) (Cypriniformes: Cyprinidae), Czech Republic, were examined (morphology, cox1, ITS1-5.8S-ITS2 and 28S). These represent the first molecular data for species of Posthodiplostomum and Ornithodiplostomum Dubois, 1936 from the Palaearctic. Phylogenetic analyses based on cox1 and ITS1-5.8S-ITS2, using O. scardinii as the outgroup and including the three newly-sequenced Posthodiplostomum spp. from Europe and eight published unidentified (presumably species-level) lineages of Posthodiplostomum from Canada confirmed the distinct status of the three European species (contrary to the generally accepted opinion that only P. brevicaudatum and P. cuticola occur in the Palaearctic). The subspecies Posthodiplostomum minimum centrarchi Hoffmann, 1958, originally described from North America, is elevated to the species level as Posthodiplostomum centrarchi Hoffman, 1958. The undescribed "Posthodiplostomum sp. 3" of Locke et al. (2010) from centrarchid fishes in Canada has identical sequences with the European isolates of P. centrarchi and is recognised as belonging to the same species. The latter parasite, occurring in the alien pumpkinseed sunfish Lepomis gibbosus in Europe, is also supposed to be alien for this continent. It is speculated that it colonised Europe long ago and is currently widespread (recorded in Bulgaria, Slovakia and Spain); based on the cox1 sequence of an adult digenean isolate from the Ebro Delta, Spain, only the grey heron (Ardea cinerea L.) (Ciconiiformes: Ardeidae) is known to be its definitive host in Europe.

New approach to molecular characterization of Paramphistomum cervi and Carmyerius gregarius and comparative analyses with selected trematodes

The two ruminant parasites, Paramphistomum cervi and Carmyerius gregarius, were collected from fresh-slaughtered native cattle at local abattoirs in Sadat district, Menoufia province and identified morphologically, then molecularly by sequencing the nucleotides of 18S ribosomal RNA gene (18S rRNA). The nucleotide sequences of the two isolates were 456 (P. cervi) and 401 bases for (C. gregarius). The data were used along with those of several other helminth species from the GenBank to identify these two species genetically. The nucleotide sequences were aligned using multiple sequence alignments of nucleotides by Clustal W 12.1 V and construct their relationship. Neighbor-joining analytical method was used showing sister relationship between C. gregarius from Sadat district and Gastrodiscoides hominis (EF027096) with relative identity of (98%) due to the presence of single nucleotides polymorphisms (SNPs) in the form of indels as nine nucleotides positions. But when clustering of P. cervi Sadat isolate with Paramphistomoidea sp. S4 isolate P5 (GU735643), this relationship shows complete identity (99%) between them. The homology and diversity was done using Bayesian analyses in MrBayes v3.1. This work will give a useful guide for other researchers for the molecular taxonomic position of Paramphistomatidae spp. in Sadat district among the different species around the world.

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.

Non-Standard Genetic Codes Define New Concepts for Protein Engineering

The essential feature of the genetic code is the strict one-to-one correspondence between codons and amino acids. The canonical code consists of three stop codons and 61 sense codons that encode 20% of the amino acid repertoire observed in nature. It was originally designated as immutable and universal due to its conservation in most organisms, but sequencing of genes from the human mitochondrial genomes revealed deviations in codon assignments. Since then, alternative codes have been reported in both nuclear and mitochondrial genomes and genetic code engineering has become an important research field. Here, we review the most recent concepts arising from the study of natural non-standard genetic codes with special emphasis on codon re-assignment strategies that are relevant to engineering genetic code in the laboratory. Recent tools for synthetic biology and current attempts to engineer new codes for incorporation of non-standard amino acids are also reviewed in this article.

The Complete Mitochondrial Genome of Delia antiqua and Its Implications in Dipteran Phylogenetics

Delia antiqua is a major underground agricultural pest widely distributed in Asia, Europe and North America. In this study, we sequenced and annotated the complete mitochondrial genome of this species, which is the first report of complete mitochondrial genome in the family Anthomyiidae. This genome is a double-stranded circular molecule with a length of 16,141 bp and an A+T content of 78.5%. It contains 37 genes (13 protein-coding genes, 22 tRNAs and 2 rRNAs) and a non-coding A+T rich region or control region. The mitochondrial genome of Delia antiqua presents a clear bias in nucleotide composition with a positive AT-skew and a negative GC-skew. All of the 13 protein-coding genes use ATN as an initiation codon except for the COI gene that starts with ATCA. Most protein-coding genes have complete termination codons but COII and ND5 that have the incomplete termination codon T. This bias is reflected in both codon usage and amino acid composition. The protein-coding genes in the D. antiqua mitochondrial genome prefer to use the codon UUA (Leu). All of the tRNAs have the typical clover-leaf structure, except for tRNA^Ser(AGN) that does not contain the dihydrouridine (DHU) arm like in many other insects. There are 7 mismatches with U-U in the tRNAs. The location and structure of the two rRNAs are conservative and stable when compared with other insects. The control region between 12S rRNA and tRNA^Ile has the highest A+T content of 93.7% in the D. antiqua mitochondrial genome. The control region includes three kinds of special regions, two highly conserved poly-T stretches, a (TA)_n stretch and several G(A)_nT structures considered important elements related to replication and transcription. The nucleotide sequences of 13 protein-coding genes are used to construct the phylogenetics of 26 representative Dipteran species. Both maximum likelihood and Bayesian inference analyses suggest a closer relationship of D. antiqua in Anthomyiidae with Calliphoridae, Calliphoridae is a paraphyly, and both Oestroidea and Muscoidea are polyphyletic.

Species of Apatemon Szidat, 1928 and Australapatemon Sudarikov, 1959 (Trematoda: Strigeidae) from New Zealand: linking and characterising life cycle stages with morphology and molecules

Species of Apatemon Szidat, 1928 and Australapatemon Sudarikov, 1959 are reported from New Zealand for the first time, and their life cycles are resolved using molecular sequence data (28S and ITS rDNA regions and mitochondrial COI). The metacercaria of Apatemon sp. 'jamiesoni' ex Gobiomorphus cotidianus and its cercaria ex Potamopyrgus antipodarum are described in detail. Its adult, found in Anas platyrhynchos and Phalacrocorax punctatus, is identified by molecular sequence data. Apatemon sp. 'jamiesoni' uses a different species of snail host, exhibits consistent differences in the genetic markers examined and its single described adult differs from known species so as to be considered distinct, but its formal description awaits additional adult specimens. Australapatemon niewiadomski n. sp. is described from Anas platyrhynchos. It is distinguished morphologically by the absence of a ringnapf and its overall smaller size compared to most other Australapatemon spp. except Au. magnacetabulum and Au. minor, which are smaller in nearly all features than the new species. Au. niewiadomski n. sp. metacercaria and its intermediate host (Barbronia weberi) are identified via matching of molecular sequence data. The status of Apatemon and Australapatemon as distinct genera is confirmed based on their respective monophyly, and genetic divergence between them is comparable to other well-established genera in the Strigeidae. The diagnosis of Australapatemon is emended. Life history data, accurate patterns of host specialisation and distribution, alongside concurrent molecular and morphological evidence would be useful for an integrative taxonomical approach towards the elucidation of species diversity in this group.

Ancient DNA sequence revealed by error-correcting codes

A previously described DNA sequence generator algorithm (DNA-SGA) using error-correcting codes has been employed as a computational tool to address the evolutionary pathway of the genetic code. The code-generated sequence alignment demonstrated that a residue mutation revealed by the code can be found in the same position in sequences of distantly related taxa. Furthermore, the code-generated sequences do not promote amino acid changes in the deviant genomes through codon reassignment. A Bayesian evolutionary analysis of both code-generated and homologous sequences of the Arabidopsis thaliana malate dehydrogenase gene indicates an approximately 1 MYA divergence time from the MDH code-generated sequence node to its paralogous sequences. The DNA-SGA helps to determine the plesiomorphic state of DNA sequences because a single nucleotide alteration often occurs in distantly related taxa and can be found in the alternative codon patterns of noncanonical genetic codes. As a consequence, the algorithm may reveal an earlier stage of the evolution of the standard code.

Complete mitochondrial genomes and nuclear ribosomal RNA operons of two species of Diplostomum (Platyhelminthes: Trematoda): a molecular resource for taxonomy and molecular epidemiology of important fish pathogens

BACKGROUND

The genus Diplostomum (Platyhelminthes: Trematoda: Diplostomidae) is a diverse group of freshwater parasites with complex life-cycles and global distribution. The larval stages are important pathogens causing eye fluke disease implicated in substantial impacts on natural fish populations and losses in aquaculture. However, the problematic species delimitation and difficulties in the identification of larval stages hamper the assessment of the distributional and host ranges of Diplostomum spp. and their transmission ecology.

METHODS

Total genomic DNA was isolated from adult worms and shotgun sequenced using Illumina MiSeq technology. Mitochondrial (mt) genomes and nuclear ribosomal RNA (rRNA) operons were assembled using established bioinformatic tools and fully annotated. Mt protein-coding genes and nuclear rRNA genes were subjected to phylogenetic analysis by maximum likelihood and the resulting topologies compared.

RESULTS

We characterised novel complete mt genomes and nuclear rRNA operons of two closely related species, Diplostomum spathaceum and D. pseudospathaceum. Comparative mt genome assessment revealed that the cox1 gene and its 'barcode' region used for molecular identification are the most conserved regions; instead, nad4 and nad5 genes were identified as most promising molecular diagnostic markers. Using the novel data, we provide the first genome wide estimation of the phylogenetic relationships of the order Diplostomida, one of the two fundamental lineages of the Digenea. Analyses of the mitogenomic data invariably recovered the Diplostomidae as a sister lineage of the order Plagiorchiida rather than as a basal lineage of the Diplostomida as inferred in rDNA phylogenies; this was concordant with the mt gene order of Diplostomum spp. exhibiting closer match to the conserved gene order of the Plagiorchiida.

CONCLUSIONS

Complete sequences of the mt genome and rRNA operon of two species of Diplostomum provide a valuable resource for novel genetic markers for species delineation and large-scale molecular epidemiology and disease ecology studies based on the most accessible life-cycle stages of eye flukes.

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

The Macrostomorpha-an early branching and species-rich clade of free-living flatworms-is attracting interest because it contains Macrostomum lignano, a versatile model organism increasingly used in evolutionary, developmental, and molecular biology. We elucidate the macrostomorphan molecular phylogeny inferred from both nuclear (18S and 28S rDNA) and mitochondrial (16S rDNA and COI) marker genes from 40 representatives. Although our phylogeny does not recover the Macrostomorpha as a statistically supported monophyletic grouping, it (i) confirms many taxa previously proposed based on morphological evidence, (ii) permits the first placement of many families and genera, and (iii) reveals a number of unexpected placements. Specifically, Myozona and Bradynectes are outside the three classic families (Macrostomidae, Microstomidae and Dolichomacrostomidae) and the asexually fissioning Myomacrostomum belongs to a new subfamily, the Myozonariinae nov. subfam. (Dolichomacrostomidae), rather than diverging early. While this represents the first evidence for asexuality among the Dolichomacrostomidae, we show that fissioning also occurs in another Myozonariinae, Myozonaria fissipara nov. sp. Together with the placement of the (also fissioning) Microstomidae, namely as the sister taxon of Dolichomacrostomidae, this suggests that fissioning is not basal within the Macrostomorpha, but rather restricted to the new taxon Dolichomicrostomida (Dolichomacrostomidae+Microstomidae). Furthermore, our phylogeny allows new insights into the evolution of the reproductive system, as ancestral state reconstructions reveal convergent evolution of gonads, and male and female genitalia. Finally, the convergent evolution of sperm storage organs in the female genitalia appears to be linked to the widespread occurrence of hypodermic insemination among the Macrostomorpha.