Sequencing of the complete mitochondrial genomes of eight freshwater snail species exposes pervasive paraphyly within the Viviparidae family (Caenogastropoda)

Characterization of the Complete Mitochondrial Genome of Angulyagra polyzonata and Its Phylogenetic Status in Viviparidae

Angulyagra polyzonata is an economically important mollusk in China, but detailed insights into its mitochondrial genome remain scarce. In this study, we sequenced and comprehensively analyzed the structural features and selection pressures of the A. polyzonata mitochondrial genome. The maximum likelihood method and Bayesian phylogenetic inference method were used to construct a phylogenetic tree of A. polyzonata with 21 other species, including gastropods and bivalves. The full-length mitochondrial genome of 17,379 bp was found to include 22 transfer RNA genes, 2 ribosomal RNA genes, and 13 protein-coding genes, exhibiting similarity to the composition and arrangement of mitochondrial genes in other gastropod species. Notably, the Ka/Ks ratios of mitochondrial protein-coding genes (nad5, cox3, nad3, nad2, cox1, cox2, atp8, atp6, nadl, nad6, cob, nad4l, and nad4) were <1, which indicates that the snail genes of the three genera of the family may have been subjected to strong natural selection pressure during the evolutionary process, so that the number of synonymous mutations (ks) in genes was much more than that of nonsynonymous mutations (ka). Comparative genomic analysis indicated that, apart from the absence of trnW and trnQ, the gene composition of A. polyzonata shares a high degree of homology with other members of the conical snail family. Phylogenetic analysis demonstrated that the selected species could be classified into two primary clades in which A. polyzonata clustered with the Viviparidae family. This study bridges the knowledge gap regarding the mitochondrial genome of A. polyzonata and offers valuable insights into the systematic relationships within the Viviparidae family.

Comparative Genomic and Mitochondrial Phylogenetic Relationships of Ovulidae (Mollusca: Gastropoda) Along the Chinese Coast

The family Ovulidae, closely related to Cypraeidae (cowries), comprises approximately 260-280 species predominantly inhabiting tropical and subtropical shallow marine environments. Unlike cowries, ovulids have a more specialized diet, with most species feeding on soft corals, leather corals, or black corals. Given their proximity in distribution and close phylogenetic relationship, dietary specialization may have played a crucial role in the evolutionary divergence of cowries and ovulids. However, unlike cowries, the traditional morphological classification of Ovulidae has proven challenging due to substantial variability influenced by their host organisms, leading to ongoing debates regarding species delimitation and taxonomy. In this study, we collected 15 Ovulidae species from China's offshore waters, including the first regional record of Habuprionovolva aenigma (M. Azuma & C. N. Cate, 1971). We successfully obtained mitochondrial genomes for 14 of these species and found that, with the exception of H. aenigma, they exhibit the typical mitochondrial genome structure of Caenogastropoda. Our phylogenetic analyses based on mitochondrial genome data, along with the discovery of a unique mitochondrial tRNA gene order in the subfamily Prionovolvinae, support recent studies suggesting that the genera Naviculavolva and Contrasimnia should be reclassified from the Simniinae to the Prionovolvinae. Additionally, our results do not support the monophyly of the genus Cuspivolva. Furthermore, our findings indicate that mitochondrial gene rearrangements occurred after the divergence of the subfamilies Prionovolvinae and Ovulinae. Additionally, we found that Ovulidae species display significantly higher Ka/Ks ratios compared to Cypraeidae, indicating different selective pressures, possibly linked to their unique feeding habits. This research enhances the understanding of Ovulidae phylogeny and provides genomic resources for future studies.

A comprehensive study on the mitochondrial genome of Volva habei and exploring phylogenetic relationships in Littorinimorpha

In order to enrich our taxonomic and systematic comprehension of Ovulidae within the evolutionary framework of Littorinimorpha. we present a comprehensive analysis of the mitochondrial genome (mitogenome) sequence of Volva habei using next-generation sequencing technology (GenBank accession number OR492307). The mitogenome spans a total length of 16,519 bp, encompassing a complete set of 37 genes, including 13 protein-coding genes (PCGs), 22 tRNAs and two rRNAs, demonstrating a distinct AT bias. Notably, trnS2 lacks a dihydrouracil (DHU) arm, thus preventing the formation of a typical secondary structure. In contrast, the remaining tRNAs exhibit a characteristic cloverleaf-like secondary structure. Comparative analysis with ancestral gastropods reveals substantial differences in three gene clusters (or genes), incorporating fifteen tRNAs and eight PCGs. Of particular significance are the observed inversions and translocations, representing the predominant types of rearrangements in V. habei. Phylogenetic analysis strongly supports the monophyletic grouping of all Littorinimorpha species, with V. habei forming a distinct Ovulidae clade. It is noteworthy that V. habei forms a sister group with Cypraeidae, collectively belonging to the Cypraeoidea. In summary, this study not only advances our comprehension of the entire mitochondrial dataset for Calyptraeoidea but also provides novel insights into the phylogenetic relationships within Littorinimorpha.

A High-Quality Chromosome-Level Genome Assembly of a Snail Cipangopaludina cathayensis (Gastropoda: Viviparidae)

Cipangopaludina cathayensis (Gastropoda: Prosobranchia; Mesogastropoda; Viviparidae) is widely distributed in the freshwater habitats of China. It is an economically important snail with high edible and medicinal value. However, the genomic resources and the reference genome of this snail are lacking. In this study, we assembled the first chromosome-level genome of C. cathayensis. The preliminary assembly genome was 1.48 Gb in size, with a contig N50 size of 93.49 Mb. The assembled sequences were anchored to nine pseudochromosomes using Hi-C data. The final genome after Hi-C correction was 1.48 Gb, with a contig N50 of 98.49 Mb and scaffold N50 of 195.21 Mb. The anchored rate of the chromosome was 99.99%. A total of 22,702 protein-coding genes were predicted. Phylogenetic analyses indicated that C. cathayensis diverged with Bellamya purificata approximately 158.10 million years ago. There were 268 expanded and 505 contracted gene families in C. cathayensis when compared with its most recent common ancestor. Five putative genes under positive selection in C. cathayensis were identified (false discovery rate <0.05). These genome data provide a valuable resource for evolutionary studies of the family Viviparidae, and for the genetic improvement of C. cathayensis.

Phylogenomic analyses reveal incongruences between divergence times and fossil records of freshwater snails in East Asia

Fossils provide important insight into our understanding of phylogenetic history by serving as calibration points for divergence time estimation. However, uncertainties in the fossil record due to parallel evolution and convergent evolution can critically affect estimates of node ages. Here, we compare and contrast estimates of phylogenetic divergence with geologic and fossil history for two freshwater snail genera of the family Viviparidae in East Asia (Cipangopaludina and Margarya). Cipangopaludina species are commonly widely distributed species in East Asia, but extant Margarya species are endemic to the ancient lakes in Yunnan, China. According to some previous studies, parallel evolution or convergent evolution of shell morphology has occurred in the family several times which may affect divergence time estimation using fossil records. In this study, we used SNP data derived from ddRAD-seq loci to investigate population demographic history of both genera. Our results show a common pattern of lake endemic lineages diversifying from widely distributed lineages in the Miocene, and multiple colonization to a single ancient lake occurred in the Pleistocene. Our results indicate substantial incongruence among estimated phylogenomic divergence times, some fossil records, and formation ages of ancient lakes. These findings suggest some fossil records may be misidentified in these groups and highlight the need to carefully evaluate geological evidence and fossil records when using these for divergence time estimation.

The complete mitochondrial genome of the freshwater snail Cipangopaludina ampullacea (Küster, 1852) (Gastropoda: Viviparidae)

Cipangopaludina ampullacea (Küster, 1852) is a freshwater snail endemic to China. In this study, the complete mitochondrial genome of C. ampullacea was sequenced using next-generation sequencing. The mitogenome is 16,892 bp long and comprises a total of 37 genes, including 13 protein-coding genes, two rRNA genes, and 22 tRNA genes. It is consistent with the basic characteristics of other known viviparid mitochondrial genomes. Phylogenetic analysis using related species mitogenomes showed that Cipangopaludina and Margarya are mutually non monophyletic. Our study provides valuable information to reconstruct the taxonomy and evolution of viviparid snails more comprehensively.

Neogastropod (Mollusca, Gastropoda) phylogeny: A step forward with mitogenomes

The Neogastropoda (Mollusca, Gastropoda) encompass more than 15,000 described species of marine predators, including several model organisms in toxinology, embryology and physiology. However, their phylogenetic relationships remain mostly unresolved and their classification unstable. We took advantage of the many mitogenomes published in GenBank to produce a new molecular phylogeny of the neogastropods. We completed the taxon sampling by using an in-house bioinformatic pipeline to retrieve mitochondrial genes from 13 transcriptomes, corresponding to five families not represented in GenBank, for a final dataset of 113 taxa. Because mitogenomic data are prone to reconstruction artefacts, eight different evolutionary models were applied to reconstruct phylogenetic trees with IQTREE, RAxML and MrBayes. If the over-parametrization of some models produced trees with aberrant internal long branches, the global topology of the trees remained stable over models and softwares, and several relationships were revealed or found supported here for the first time. However, even if our dataset encompasses 60% of the valid families of neogastropods, some key taxa are missing and should be added in the future before proposing a revision of the classification of the neogastropods. Our study also demonstrates that even complex models struggle to satisfactorily handle the evolutionary history of mitogenomes, still leading to long-branch attractions in phylogenetic trees. Other approaches, such as reduced-genome strategies, must be envisaged to fully resolve the neogastropod phylogeny.

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

BACKGROUND

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

METHODS

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

RESULTS

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

CONCLUSIONS

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

Complete mitochondrial genome of the freshwater snail Tarebia granifera (Lamarck, 1816) (Gastropoda: Cerithioidea: Thiaridae)

The freshwater gastropod Tarebia granifera (Lamarck, 1816) is found in Taiwan, Hainan, and Guangdong provinces in China, and is one of the main intermediate hosts of trematodes that infect humans. The taxonomic positions of some cerithioidean families are still unclear, and whole mitochondrial genome studies are scarce in the Thiaridae. In this study, we describe the complete mitogenome of Tarebia granifera (Lamarck, 1816). The mitogenome is 15,555 bp in length, with a total of 37 genes, including 13 protein-coding genes, 2 rRNA genes, and 22 tRNA genes. It is consistent with the essential features of previously studied mitochondrial genomes of species belonging to the superfamily Cerithioidea. Our study demonstrates the usefulness of mitogenomic data for resolving phylogenetic relationships of families within Cerithioidea and may also contribute to the prevention and control of the parasitic diseases caused by trematodes, which use T. granifera as an intermediate host.

Mitochondrial genomes of two Polydora (Spionidae) species provide further evidence that mitochondrial architecture in the Sedentaria (Annelida) is not conserved

Contrary to the early evidence, which indicated that the mitochondrial architecture in one of the two major annelida clades, Sedentaria, is relatively conserved, a handful of relatively recent studies found evidence that some species exhibit elevated rates of mitochondrial architecture evolution. We sequenced complete mitogenomes belonging to two congeneric shell-boring Spionidae species that cause considerable economic losses in the commercial marine mollusk aquaculture: Polydora brevipalpa and Polydora websteri. The two mitogenomes exhibited very similar architecture. In comparison to other sedentarians, they exhibited some standard features, including all genes encoded on the same strand, uncommon but not unique duplicated trnM gene, as well as a number of unique features. Their comparatively large size (17,673 bp) can be attributed to four non-coding regions larger than 500 bp. We identified an unusually large (putative) overlap of 14 bases between nad2 and cox1 genes in both species. Importantly, the two species exhibited completely rearranged gene orders in comparison to all other available mitogenomes. Along with Serpulidae and Sabellidae, Polydora is the third identified sedentarian lineage that exhibits disproportionally elevated rates of mitogenomic architecture rearrangements. Selection analyses indicate that these three lineages also exhibited relaxed purifying selection pressures.

The queen conch mitogenome: intra- and interspecific mitogenomic variability in Strombidae and phylogenetic considerations within the Hypsogastropoda

Aliger gigas is an economically important and vulnerable marine species. We present a new mitogenome of A. gigas from the Mexican Caribbean and use the eight publicly available Strombidae mitogenomes to analyze intra- and interspecific variation. We present the most complete phylogenomic understanding of Hypsogastropoda to date (17 superfamilies, 39 families, 85 genera, 109 species) to revisit the phylogenetic position of the Stromboidea and evaluate divergence times throughout the phylogeny. The A. gigas mitogenome comprises 15,460 bp including 13 PCGs, 22 tRNAs, and two rRNAs. Nucleotide diversity suggested divergence between the Mexican and Colombian lineages of A. gigas. Interspecific divergence showed high differentiation among Strombidae species and demonstrated a close relationship between A. gigas and Strombus pugilis, between Lambis lambis and Harpago chiragra, and among Tridentarius dentatus/Laevistrombus canarium/Ministrombus variabilis. At the intraspecific level, the gene showing the highest differentiation is ATP8 and the lowest is NAD4L, whereas at the interspecific level the NAD genes show the highest variation and the COX genes the lowest. Phylogenomic analyses confirm that Stromboidea belongs in the non-Latrogastropoda clade and includes Xenophoridea. The phylogenomic position of other superfamilies, including those of previously uncertain affiliation, is also discussed. Finally, our data indicated that Stromboidea diverged into two principal clades in the early Cretaceous while Strombidae diversified in the Paleocene, and lineage diversification within A. gigas took place in the Pleistocene.

Bivalve molluscs as model systems for studying mitochondrial biology

The class Bivalvia is a highly successful and ancient taxon including ∼25,000 living species. During their long evolutionary history bivalves adapted to a wide range of physicochemical conditions, habitats, biological interactions, and feeding habits. Bivalves can have strikingly different size, and despite their apparently simple body plan, they evolved very different shell shapes, and complex anatomic structures. One of the most striking features of this class of animals is their peculiar mitochondrial biology: some bivalves have facultatively anaerobic mitochondria that allow them to survive prolonged periods of anoxia/hypoxia. Moreover, more than 100 species have now been reported showing the only known evolutionarily stable exception to the strictly maternal inheritance of mitochondria in animals, named doubly uniparental inheritance. Mitochondrial activity is fundamental to eukaryotic life, and thanks to their diversity and uncommon features, bivalves represent a great model system to expand our knowledge about mitochondrial biology, so far limited to a few species. We highlight recent works studying mitochondrial biology in bivalves at either genomic or physiological level. A link between these two approaches is still missing, and we believe that an integrated approach and collaborative relationships are the only possible ways to be successful in such endeavour.

Characterization of the complete mitochondrial genome of Cavisoma magnum () (Acanthocephala: Palaeacanthocephala), first representative of the family Cavisomidae, and its phylogenetic implications

The phylum Acanthocephala is a small group of endoparasites occurring in the alimentary canal of all major lineages of vertebrates worldwide. In the present study, the complete mitochondrial (mt) genome of Cavisoma magnum (Southwell, 1927) (Palaeacanthocephala: Echinorhynchida) was determined and annotated, the representative of the family Cavisomidae with the characterization of the complete mt genome firstly decoded. The mt genome of this acanthocephalan is 13,594 bp in length, containing 36 genes plus two non-coding regions. The positions of trnV and SNCR (short non-coding region) in the mt genome of C. magnum are different comparing to those of the other acanthocephalan species available in GenBank. Phylogenetic analysis based on amino acid sequences of 12 protein-coding genes using Bayesian inference (BI) supported the class Palaeacanthocephala and its included order Polymorphida to be monophyletic, but rejected monophyly of the order Echinorhynchida. Our phylogenetic results also challenged the validity of the genus Sphaerirostris (Polymorphida: Centrorhynchidae). The novel mt genomic data of C. magnum are very useful for understanding the evolutionary history of this group of parasites and establishing a natural classification of Acanthocephala.

The first complete mitochondrial genome of a cyclophorid land snail, with implications for architaenioglossan relationships (Mollusca, Caenogastropoda, Cyclophoroidea)

Herein, we described the complete mitochondrial genome ('mitogenome') of the Chinese land snail Cyclophorus martensianus, which is the first published mitogenome for the caenogastropod family Cyclophoridae. This mitogenome is 15,308 bp long consisting of 37 genes: 13 protein-coding genes (PCGs), 22 tRNA genes and two rRNA genes. The A + T content (69.6%) is distinctly higher than the GC content (30.4%). Most PCGs start with ATN as initiation codons, and all PCGs have the conventional stop codons TAA and TAG. Overall, the biochemical properties and gene order of the cyclophorid mitogenome are very similar to those of other documented caenogastropod mitogenomes. We corroborate the findings of earlier studies that mitochondrial gene order is rather conserved among caenogastropods. Caenogastropoda are the taxonomically, morpho-anatomically and ecologically most diverse group of living gastropods comprising lineages inhabiting marine, freshwater, and terrestrial environments. Traditionally, the three most speciose groups of non-marine caenogastropods have all been placed in a single group, the Architaenioglossa. This group contains two freshwater lineages, the Viviparoidea and Ampullaroidea, and the terrestrial Cyclophoroidea. However, architaenioglossan relationships have remained controversial with several morphology-based on molecular phylogenetic analyses supporting contradicting phylogenetic hypotheses. In order to more robustly resolve the relationships among the Architaenioglossa, we have performed phylogenetic analyses of caenogastropod mitogenomes including the new mitogenome of Cyclophorus martensianus. Our phylogenetic reconstructions are based on the amino acid sequences of all protein-coding genes and consistently recovered Architaenioglossa as non-monophyletic.

Characterization of the complete mitochondrial genome of Brentisentisyangtzensis Yu & Wu, 1989 (Acanthocephala, Illiosentidae)

The mitogenome of Brentisentisyangtzensis is 13,864 bp in length and has the circular structure typical of metazoans. It contains 36 genes: 22 transfer RNA genes (tRNAs), two ribosomal RNA genes (rRNAs) and 12 protein-encoding genes (PCGs). All genes are transcribed from the same strand. Thirteen overlapping regions were found in the mitochondrial genome. The overall A+T content of B.yangtzensis is 68.3% versus 31.7% of G+C content (A = 27.8%, T = 40.5%, C = 9.0%, G = 22.7%). B.yangtzenensis (Illiosentidae) and Leptorhynchoidesthecatus (Rhadinorhynchidae) form a sister clade, showing the relatively close relationship between the Illiosentidae and the Rhadinorhynchidae. The mitochondrial gene arrangements of acanthocephalan species are relatively conserved, with only a few translocations of tRNAs (trnS1, trnS2, trnV, and trnK) detected. An identical gene order was found both in a sister clade (Centrorhynchusaluconis and Plagiorhynchustransversus) and across different classes (B.yangtzensis (Palaeacanthocephala), Acanthosentischeni (Eoacanthocephala) and Macracanthorhynchushirudinaceus (Archiacanthocephala), Oncicolaluehei and L.thecatus (Palaeacanthocephala)). More studies and more sequences of acanthocephalan species are needed to gain a clear understanding of the phylogenetic relationships.

Enigmatic incongruence between mtDNA and nDNA revealed by multi-locus phylogenomic analyses in freshwater snails

Phylogenetic incongruence has frequently been encountered among different molecular markers. Recent progress in molecular phylogenomics has provided detailed and important information for evolutionary biology and taxonomy. Here we focused on the freshwater viviparid snails (Cipangopaludina chinensis chinensis and C. c. laeta) of East Asia. We conducted phylogenetic analyses and divergence time estimation using two mitochondrial markers. We also performed population genetic analyses using genome-wide SNPs. We investigated how and which phylogenetic patterns reflect shell morphology. The results showed these two species could be separated into four major mitochondrial clades, whereas the nuclear clusters supported two groups. The phylogenetic patterns of both mtDNA and nDNA largely reflected the geographical distribution. Shell morphology reflected the phylogenetic clusters based on nDNA. The findings also showed these two species diversified in the Pliocene to early Pleistocene era, and occurred introgressive hybridisation. The results also raise the taxonomic issue of the two species.

The Complete Mitochondrial Genome Sequences of the Philomycus bilineatus (Stylommatophora: Philomycidae) and Phylogenetic Analysis

The mitochondrial genome (mitogenome) can provide information for phylogenetic analyses and evolutionary biology. We first sequenced, annotated, and characterized the mitogenome of Philomycus bilineatus in this study. The complete mitogenome was 14,347 bp in length, containing 13 protein-coding genes (PCGs), 23 transfer RNA genes, two ribosomal RNA genes, and two non-coding regions (A + T-rich region). There were 15 overlap locations and 18 intergenic spacer regions found throughout the mitogenome of P. bilineatus. The A + T content in the mitogenome was 72.11%. All PCGs used a standard ATN as a start codon, with the exception of cytochrome c oxidase 1 (cox1) and ATP synthase F0 subunit 8 (atp8) with TTG and GTG. Additionally, TAA or TAG was identified as the typical stop codon. All transfer RNA (tRNA) genes had a typical clover-leaf structure, except for trnS1 (AGC), trnS2 (TCA), and trnK (TTT). A phylogenetic analysis with another 37 species of gastropods was performed using Bayesian inference, based on the amino acid sequences of 13 mitochondrial PCGs. The results indicated that P. bilineatus shares a close ancestry with Meghimatium bilineatum. It seems more appropriate to reclassify it as Arionoidea rather than Limacoidea, as previously thought. Our research may provide a new meaningful insight into the evolution of P. bilineatus.

Relation between mitochondrial DNA hyperdiversity, mutation rate and mitochondrial genome evolution in Melarhaphe neritoides (Gastropoda: Littorinidae) and other Caenogastropoda

Mitochondrial DNA hyperdiversity is primarily caused by high mutation rates (µ) and has potential implications for mitogenome architecture and evolution. In the hyperdiverse mtDNA of Melarhaphe neritoides (Gastropoda: Littorinidae), high mutational pressure generates unusually large amounts of synonymous variation, which is expected to (1) promote changes in synonymous codon usage, (2) reflect selection at synonymous sites, (3) increase mtDNA recombination and gene rearrangement, and (4) be correlated with high mtDNA substitution rates. The mitogenome of M. neritoides was sequenced, compared to closely related littorinids and put in the phylogenetic context of Caenogastropoda, to assess the influence of mtDNA hyperdiversity and high µ on gene content and gene order. Most mitogenome features are in line with the trend in Mollusca, except for the atypical secondary structure of the methionine transfer RNA lacking the TΨC-loop. Therefore, mtDNA hyperdiversity and high µ in M. neritoides do not seem to affect its mitogenome architecture. Synonymous sites are under positive selection, which adds to the growing evidence of non-neutral evolution at synonymous sites. Under such non-neutrality, substitution rate involves neutral and non-neutral substitutions, and high µ is not necessarily associated with high substitution rate, thus explaining that, unlike high µ, a high substitution rate is associated with gene order rearrangement.

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

BACKGROUND

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

RESULTS

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

CONCLUSIONS

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

Comparative Characterization of the Complete Mitochondrial Genomes of the Three Apple Snails (Gastropoda: Ampullariidae) and the Phylogenetic Analyses

The apple snails Pomacea canaliculata, Pomacea diffusa and Pomacea maculate (Gastropoda: Caenogastropoda: Ampullariidae) are invasive pests causing massive economic losses and ecological damage. We sequenced and characterized the complete mitochondrial genomes of these snails to conduct phylogenetic analyses based on comparisons with the mitochondrial protein coding sequences of 47 Caenogastropoda species. The gene arrangements, distribution and content were canonically identical and consistent with typical Mollusca except for the tRNA-Gln absent in P. diffusa. An identifiable control region (d-loop) was absent. Bayesian phylogenetic analysis indicated that all the Ampullariidae species clustered on the same branch. The genus Pomacea clustered together and then with the genus Marisa. The orders Architaenioglossa and Sorbeoconcha clustered together and then with the order Hypsogastropoda. Furthermore, the intergenic and interspecific taxonomic positions were defined. Unexpectedly, Ceraesignum maximum, Dendropoma gregarium, Eualetes tulipa and Thylacodes squamigerus, traditionally classified in order Hypsogastropoda, were isolated from the order Hypsogastropoda in the most external branch of the Bayesian inference tree. The divergence times of the Caenogastropoda indicated that their evolutionary process covered four geological epochs that included the Quaternary, Neogene, Paleogene and Cretaceous periods. This study will facilitate further investigation of species identification to aid in the implementation of effective management and control strategies of these invasive species.

Sequencing of complete mitochondrial genomes confirms synonymization of Hyalomma asiaticum asiaticum and kozlovi, and advances phylogenetic hypotheses for the Ixodidae

Phylogeny of hard ticks (Ixodidae) remains unresolved. Mitochondrial genomes (mitogenomes) are increasingly used to resolve phylogenetic controversies, but remain unavailable for the entire large Hyalomma genus. Hyalomma asiaticum is a parasitic tick distributed throughout the Asia. As a result of great morphological variability, two subspecies have been recognised historically; until a morphological data-based synonymization was proposed. However, this hypothesis was never tested using molecular data. Therefore, objectives of this study were to: 1. sequence the first Hyalomma mitogenome; 2. scrutinise the proposed synonymization using molecular data, i.e. complete mitogenomes of both subspecies: H. a. asiaticum and kozlovi; 3. conduct phylogenomic and comparative analyses of all available Ixodidae mitogenomes. Results corroborate the proposed synonymization: the two mitogenomes are almost identical (99.6%). Genomic features of both mitogenomes are standard for Metastriata; which includes the presence of two control regions and all three "Tick-Box" motifs. Gene order and strand distribution are perfectly conserved for the entire Metastriata group. Suspecting compositional biases, we conducted phylogenetic analyses (29 almost complete mitogenomes) using homogeneous and heterogeneous (CAT) models of substitution. The results were congruent, apart from the deep-level topology of prostriate ticks (Ixodes): the homogeneous model produced a monophyletic Ixodes, but the CAT model produced a paraphyletic Ixodes (and thereby Prostriata), divided into Australasian and non-Australasian clades. This topology implies that all metastriate ticks have evolved from the ancestor of the non-Australian branch of prostriate ticks. Metastriata was divided into three clades: 1. Amblyomminae and Rhipicephalinae (Rhipicephalus, Hyalomma, Dermacentor); 2. Haemaphysalinae and Bothriocrotoninae, plus Amblyomma sphenodonti; 3. Amblyomma elaphense, basal to all Metastriata. We conclude that mitogenomes have the potential to resolve the long-standing debate about the evolutionary history of ticks, but heterogeneous evolutionary models should be used to alleviate the effects of compositional heterogeneity on deep-level relationships.

The complete mitochondrial genome of parasitic nematode Camallanus cotti: extreme discontinuity in the rate of mitogenomic architecture evolution within the Chromadorea class

BACKGROUND

Complete mitochondrial genomes are much better suited for the taxonomic identification and phylogenetic studies of nematodes than morphology or traditionally-used molecular markers, but they remain unavailable for the entire Camallanidae family (Chromadorea). As the only published mitogenome in the Camallanina suborder (Dracunculoidea superfamily) exhibited a unique gene order, the other objective of this research was to study the evolution of mitochondrial architecture in the Spirurida order. Thus, we sequenced the complete mitogenome of the Camallanus cotti fish parasite and conducted structural and phylogenomic comparative analyses with all available Spirurida mitogenomes.

RESULTS

The mitogenome is exceptionally large (17,901 bp) among the Chromadorea and, with 46 (pseudo-) genes, exhibits a unique architecture among nematodes. Six protein-coding genes (PCGs) and six tRNAs are duplicated. An additional (seventh) tRNA (Trp) was probably duplicated by the remolding of tRNA-Ser2 (missing). Two pairs of these duplicated PCGs might be functional; three were incomplete and one contained stop codons. Apart from Ala and Asp, all other duplicated tRNAs are conserved and probably functional. Only 19 unique tRNAs were found. Phylogenomic analysis included Gnathostomatidae (Spirurina) in the Camallanina suborder.

CONCLUSIONS

Within the Nematoda, comparable PCG duplications were observed only in the enoplean Mermithidae family, but those result from mitochondrial recombination, whereas characteristics of the studied mitogenome suggest that likely rearrangement mechanisms are either a series of duplications, transpositions and random loss events, or duplication, fragmentation and subsequent reassembly of the mitogenome. We put forward a hypothesis that the evolution of mitogenomic architecture is extremely discontinuous, and that once a long period of stasis in gene order and content has been punctuated by a rearrangement event, such a destabilised mitogenome is much more likely to undergo subsequent rearrangement events, resulting in an exponentially accelerated evolutionary rate of mitogenomic rearrangements. Implications of this model are particularly important for the application of gene order similarity as an additive source of phylogenetic information. Chromadorean nematodes, and particularly Camallanina clade (with C. cotti as an example of extremely accelerated rate of rearrangements), might be a good model to further study this discontinuity in the dynamics of mitogenomic evolution.

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.