Comparative analyses within Gyrodactylus (Platyhelminthes: Monogenea) mitochondrial genomes and conserved polymerase chain reaction primers for gyrodactylid mitochondrial DNA

Supplemental description of Gyrodactylus pseudorasborae (Gyrodactylidae) parasitic on topmouth gudgeon Pseudorasbora parva (Cyprinidae) in South China

Based on morphology and ITS sequence data, we identify and supplementally describe Gyrodactylus pseudorasborae Ondračková, Seifertová & Tkachenko, 2023 on the fins of topmouth gudgeon (Pseudoraspora parva) from freshwaters of southern China. The highest similarity (99.57% and 99.47%) to G. pseudorasborae suggested they were the same species. Prevalence and mean intensity were 45% and 2.3, respectively. The gyrodactylid species morphologically resembled G. pseudorasborae recorded from the same host species P. parva in Czech Republic, Ukraine, and Central China. But there were slight morphological differences in the shape and size of the marginal hook. Comparisons of marginal hook sickles of various Gyrodactylus species suggested that G. pseudorasborae and G. parvae were members of the G. wageneri-group. A molecular phylogeny of G. pseudorasborae with related species is presented and discussed within the context of the mechanism of local evolution of these sister species.

The First Two Complete Mitochondrial Genomes for the Subfamily Meligethinae (Coleoptera: Nitidulidae) and Implications for the Higher Phylogeny of Nitidulidae

The phylogenetic status of the family Nitidulidae and its sister group relationship remain controversial. Also, the status of the subfamily Meligethinae is not fully understood, and previous studies have been mainly based on morphology, molecular fragments, and biological habits, rather than the analysis of the complete mitochondrial genome. Up to now, there has been no complete mitochondrial genome report of Meligethinae. In this study, the complete mitochondrial genomes of Meligethinus tschungseni and Brassicogethes affinis (both from China) were provided, and they were compared with the existing complete mitochondrial genomes of Nitidulidae. The phylogenetic analysis among 20 species of Coleoptera was reconstructed via PhyloBayes analysis and Maximum likelihood (ML) analysis, respectively. The results showed that the full lengths of Meligethinus tschungseni and Brassicogethes affinis were 15,783 bp and 16,622 bp, and the AT contents were 77% and 76.7%, respectively. Each complete mitochondrial genome contains 13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNAs), 2 ribosomal RNA genes (rRNAs), and a control region (A + T-rich region). All the PCGs begin with the standard start codon ATN (ATA, ATT, ATG, ATC). All the PCGs terminate with a complete terminal codon, TAA or TAG, except cox1, cox2, nad4, and nad5, which terminate with a single T. Furthermore, all the tRNAs have a typical clover-leaf secondary structure except trnS1, whose DHU arm is missing in both species. The two newly sequenced species have different numbers and lengths of tandem repeat regions in their control regions. Based on the genetic distance and Ka/Ks analysis, nad6 showed a higher variability and faster evolutionary rate. Based on the available complete mitochondrial genomes, the results showed that the four subfamilies (Nitidulinae, Meligethinae, Carpophilinae, Epuraeinae) of Nitidulidae formed a monophyletic group and further supported the sister group relationship of Nitidulidae + Kateretidae. In addition, the taxonomic status of Meligethinae and the sister group relationship between Meligethinae and Nitidulinae (the latter as currently circumscribed) were also preliminarily explored.

A Mitochondrial Genome Phylogeny of Cleridae (Coleoptera, Cleroidea)

The predaceous beetle family Cleridae includes a large and widely distributed rapid radiation, which is vital for the ecosystem. Despite its important role, a number of problems remain to be solved regarding the phylogenetic inter-relationships, the timing of divergence, and the mitochondrial biology. Mitochondrial genomes have been widely used to reconstruct phylogenies of various insect groups, but never introduced to Cleridae until now. Here, we generated 18 mitochondrial genomes to address these issues, which are all novel to the family. In addition to phylogenomic analysis, we have leveraged our new sources to study the mitochondrial biology in terms of nucleotide composition, codon usage and substitutional rate, to understand how these vital cellular components may have contributed to the divergence of the Cleridae. Our results recovered Korynetinae sister to the remaining clerids, and the calde of Clerinae+Hydnocerinae is indicated more related to Tillinae. A time-calibrated phylogeny estimated the earliest divergence time of Cleridae was soon after the origin of the family, not later than 160.18 Mya (95% HPD: 158.18–162.07 Mya) during the mid-Jurassic. This is the first mitochondrial genome-based phylogenetic study of the Cleridae that covers nearly all subfamily members, which provides an alternative evidence for reconstructing the phylogenetic relationships.

Complete mitochondrial genomes of four species of praying mantises (Dictyoptera, Mantidae) with ribosomal second structure, evolutionary and phylogenetic analyses

Praying mantises are distributed all over the world. Though some Mantodea mitogenomes have been reported, an evolutionary genomic and phylogenetic analysis study lacks the latest taxonomic system. In the present study, four new mitogenomes were sequenced and annotated. Deroplatys truncate, D. lobate, Amorphoscelis chinensis and Macromantis sp. belong to Deroplatyidae, Amorphoscelidae and Photinaidae family, respectively. Our results indicated that the ATP8 gene may be lost in D. truncate and D. lobata mt genome, and four tRNA genes have not been found in D. truncate, D. lobata and Macromantis sp. A dN/dS pair analysis was conducted and it was found that all genes have evolved under purifying selection. Furthermore, we tested the phylogenetic relationships between the eight families of the Mantodea, including 35 species of praying Mantis. Based on the complete mitochondrial genome data, it was also suggested as sister to Deroplatyidae + Mantidae, Metallyticus sp., the only representative of Metallyticidae, is sister to the remaining mantises. Our results support the taxonomic system of Schwarz and Roy and are consistent with previous studies.

Characterization of the First Complete Mitochondrial Genome of Cyphonocerinae (Coleoptera: Lampyridae) with Implications for Phylogeny and Evolution of Fireflies

Complete mitochondrial genomes are valuable resources for phylogenetics in insects. The Cyphonoceridae represents an important lineage of fireflies. However, no complete mitogenome is available until now. Here, the first complete mitochondrial genome from this subfamily was reported, with Cyphonocerus sanguineus klapperichi as a representative. The mitogenome of C. sanguineus klapperichi was conserved in the structure and comparable to that of others in size and A+T content. Nucleotide composition was A+T-biased, and all genes exhibited a positive AT-skew and negative GC-skew. Two types of tandem repeat sequence units were present in the control region (136 bp × 2; 171 bp × 2 + 9 bp). For reconstruction of Lampyridae's phylogeny, three different datasets were analyzed by both maximum likelihood (ML) and Bayesian inference (BI) methods. As a result, the same topology was produced by both ML analysis of 13 protein-coding genes and 2rRNA and BI analysis of 37 genes. The results indicated that Lampyridae, Lampyrinae, Luciolinae (excluding Emeia) were monophyletic, but Ototretinae was paraphyletic, of which Stenocladius was recovered as the sister taxon to all others, while Drilaster was more closely related to Cyphonocerinae; Phturinae + Emeia were included in a monophyletic clade, which comprised sister groups with Lampyridae. Vesta was deeply rooted in the Luciolinae.

Species delimitation of Gyrodactylus (Monogenea: Gyrodactylidae) infecting the southernmost cyprinids (Actinopterygii: Cyprinidae) in the New World

The genus Gyrodactylus von Nordmann, 1832 represents one of the most diverse and widespread taxa within Monogenea, with approximately 500 species described worldwide. Thirty-three species of Gyrodactylus have been recorded in Mexico, and in the last two decades, at least 26 new species have been described mainly from freshwater fish families such as poeciliids, goodeids, profundulids, characids, and cichlids. In this study, we describe two new species of Gyrodactylus infecting freshwater cyprinids based on morphological and molecular characteristics. Gyrodactylus ticuchi n. sp. and Gyrodactylus tobala n. sp. were recovered from Notropis moralesi de Buen and N. imeldae Cortés, respectively, captured in five localities from the State of Oaxaca, Mexico. The new species differ slightly from their congeners in the morphology of the haptoral hard parts and the male copulatory organ. Sequences of the Internal Transcribed Spacers rDNA (ITS1-5.8S-ITS2), cytochrome oxidase subunit I (cox1), and the D2 + D3 domains of the large subunit (28S rDNA) were obtained from multiple specimens and analyzed using Maximum Likelihood (ML) and Bayesian Inference (BI). Phylogenetic hypotheses using ITS rDNA, cox1, and 28S rDNA genes recovered two new species of Gyrodactylus from N. moralesi and N. imeldae; we briefly discuss their phylogenetic relationship with other congeners. These gyrodactylids represent the first species described in species of Notropis from southern Mexico, the cyprinids exhibiting the southernmost distribution in the New World.

Phylogeography and demographic history of Gyrodactylus konovalovi (Monogenoidea: Gyrodactylidae), an ectoparasite on the East Asia Amur minnow (Cyprinidae) in Central China

Gyrodactylus konovalovi is an ectoparasite on the Amur minnow (Rhynchocypris lagowskii) that is widely distributed in the cold fresh waters of East Asia. In the present study, the phylogeography and demographic history of G. konovalovi and the distribution of its host in the Qinling Mountains are examined. A total of 79 individual parasites was sequenced for a 528 bp region of the mitochondrial NADH dehydrogenase subunit 5 (ND5) gene, and 25 haplotypes were obtained. The substitution rate (dN/dS) was 0.068 and indicated purifying selection. Haplotype diversity (h) and nucleotide diversity (π) varied widely in the Qinling Mountains. Phylogenetic trees based on Bayesian inference (BI), maximum likelihood (ML), and maximum parsimony (MP) methods and network analysis revealed that all haplotypes were consistently well-supported in three different lineages, indicating a significant geographic distribution pattern. There was a significant positive correlation between genetic differentiation (F st) and geographic distance. The results of mismatch distribution, neutrality test and Bayesian skyline plot analyses showed that whole populations underwent population contraction during the Pleistocene. Based on the molecular clock calibration, the most common ancestor was estimated to have emerged in the middle Pleistocene. Our study suggests for the first time that a clearly phylogeography of G. konovalovi was shaped by geological events and climate fluctuations, such as orogenesis, drainage capture changes, and vicariance, during the Pleistocene in the Qinling Mountains.

DNA detection of Gyrodactylus spp. in skin mucus of Nile tilapia Oreochromis niloticus

Monogeneans Gyrodactylus von Nordmann 1832, cause outbreaks of gyrodactylosis in aquaculture settings worldwide. Detection of Gyrodactylus spp. is based on the morphological identification of isolated parasites after fish necropsy. Contributing to the diagnosis of gyrodactylosis, in this study, a non-destructive PCR assay was standardized; the PCR was first performed using genomic DNA of Gyrodactylus spp. isolated from the surface of the Nile tilapia Oreochromis niloticus (Linnaeus 1758), and subsequently tested with mucus samples of infected and uninfected Nile tilapia fish. The primers (Ekgyro1) were designed from the ribosomal Internal Transcriber Spacer (ITS) RNA region (ITS1, 5.8S and ITS2 rRNA gene) of Gyrodactylus cichlidarum Paperna 1968. The positive control group included the DNA of 30 monogeneans Gyrodactylus spp. The heterologous control group included 75 monogeneans Cichlidogyrus Paperna 1960, 75 protozoans Ichthyophthirius multifiliis Fouquet 1876 and 75 Trichodina Ehrenberg 1830. PCR products of each parasite and from the external mucus samples (described as P and M respectively), were sequenced. The average DNA concentration of the ectoparasites was of 13.5 ng/μl. The PCR test had an analytical sensitivity of 0.0039 ng μl-1 of DNA of Gyrodactylus spp. No cross-reactions were observed with the heterologous group. The sensitivity and specificity of the PCR test were of 100% either with genomic DNA or with DNA from mucus samples. Six DNA consensus sequences with sizes ranging from 568 bp to 571 bp were obtained and the BLAST analysis matched with DNA sequences of G. cichlidarum.

The mitochondrial genomes of three skippers: Insights into the evolution of the family Hesperiidae (Lepidoptera)

We sequenced the mitogenomes of Astictopterus jama, Isoteinon lamprospilus and Notocrypta curvifascia to obtain further insight into the mitogenomic architecture evolution and performed phylogenetic reconstruction using 29 Hesperiidae mitogenome sequences. The complete mitogenome sequences of A. jama, I. lamprospilus and N. curvifascia are 15,430, 15,430 and 15,546 bp in size, respectively. All contain 13 protein-coding genes, 2 ribosomal RNA genes, 22 transfer RNA genes, and an A + T-rich region. Nucleotide composition is A + T biased, and the majority of the protein-coding genes exhibit a negative AT-skew, which is reflected in the nucleotide composition, codon, and amino acid usage. The A + T-rich region is comprised of nonrepetitive sequences, including the motif ATAGA followed by a poly-T stretch, a microsatellite-like element next to the ATTTA motif, and a poly-A adjacent to tRNAs. Although most genes evolve under a strong purifying selection, the entire nad gene family (especially nad6) exhibits somewhat relaxed purifying selection, and atp8, evolving under a highly relaxed selection, is an outlier in the family Hesperiidae. Several different approaches relatively consistently indicated that nad6, atp8 and nad4 are comparatively fast-evolving genes in this family, which may have implications for future phylogenetic, population genetics and species diagnostics studies. For phylogenetic analyses of Hesperiidae, we tested a few datasets, and found that the one comprising all 37 genes produced the highest node support, indicating that the inclusion of RNAs improves the phylogenetic signal. Results indicate that subfamilies Euschemoninae, Heteropterinae, and Coeliadinae are monophyletic with strong nodal support, but Pyrginae and Eudaminae are paraphyletic. Finally, we confirm that A. jama and I. lamprospilus are close relatives.

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.

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.