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Article

Phylomitogenomic Analyses Provided Further Evidence for the Resurrection of the Family Pseudoacanthocephalidae (Acanthocephala: Echinorhynchida)

1
Hebei Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology, Hebei Collaborative Innovation Center for Eco-Environment, College of Life Sciences, Hebei Normal University, Shijiazhuang 050024, China
2
Ministry of Education Key Laboratory of Molecular and Cellular Biology, Hebei Research Center of the Basic Discipline Cell Biology, Shijiazhuang 050024, China
3
Department of Zoology, University of Cambridge, Cambridge CB2 3EJ, UK
*
Author to whom correspondence should be addressed.
These authors contributed equally to this work.
Animals 2023, 13(7), 1256; https://doi.org/10.3390/ani13071256
Submission received: 13 February 2023 / Revised: 20 March 2023 / Accepted: 29 March 2023 / Published: 5 April 2023
(This article belongs to the Section Animal Genetics and Genomics)

Abstract

:

Simple Summary

Acanthocephalans, commonly known as spiny-headed or thorny-headed worms, are a small group of endoparasites with veterinary, medical and economic importance due to their ability to cause disease in domestic animals, wildlife, and humans. In recent decades, great progress has been made using mitochondrial genome data to clarify the phylogenetic relationships of acanthocephalans. However, the current mitochondrial genome database for acanthocephalans remains very limited. Herein, the characterization of the mitochondrial genome of Pseudoacanthocephalus bufonis (Shipley, 1903), the first representative of the family Pseudoacanthocephalidae, is reported. Phylogenetic analyses using the amino acid sequences of 12 protein-coding genes supported the validity of the family Pseudoacanthocephalidae and suggested a close affinity between Pseudoacanthocephalidae and Cavisomatidae. Our phylogenetic results also showed that the families Polymorphidae and Centrorhynchidae have a closer relationship than Plagiorhynchidae in the Polymorphida. These findings contribute to revealing the patterns of mitogenomic evolution in this group and represent a substantial step towards reconstructing the classification of the phylum Acanthocephala.

Abstract

The phylum Acanthocephala is an important monophyletic group of parasites, with adults parasitic in the digestive tracts of all major vertebrate groups. Acanthocephalans are of veterinary, medical, and economic importance due to their ability to cause disease in domestic animals, wildlife, and humans. However, the current genetic data for acanthocephalans are sparse, both in terms of the proportion of taxa surveyed and the number of genes sequenced. Consequently, the basic molecular phylogenetic framework for the phylum is still incomplete. In the present study, we reported the first complete mitochondrial genome from a representative of the family Pseudoacanthocephalidae Petrochenko, 1956. The mitogenome of Pseudoacanthocephalus bufonis (Shipley, 1903) is 14,056 bp in length, contains 36 genes (12 protein-coding genes (PCGs) (lacking atp8), 22 tRNA genes, and 2 rRNA genes (rrnL and rrnS)) and two non-coding regions (NCR1 and NCR2), and displayed the highest GC-skew in the order Echinorhynchida. Phylogenetic results of maximum likelihood (ML) and Bayesian inference (BI) using the amino acid sequences of 12 protein-coding genes in different models provided further evidence for the resurrection of the family Pseudoacanthocephalidae and also supported that the order Echinorhynchida is paraphyletic. A monophyletic clade comprising P. bufonis and Cavisoma magnum suggests a close affinity between Pseudoacanthocephalidae and Cavisomatidae. Our phylogenetic analyses also showed that Polymorphidae has a closer relationship with Centrorhynchidae than Plagiorhynchidae in the monophyletic order Polymorphida.

Graphical Abstract

1. Introduction

Acanthocephala is an important group of obligate endoparasites, with more than 1300 species parasitizing the digestive tracts of all major lineages of vertebrates and their larvae developing in arthropods [1,2,3,4]. According to the current classifications based on a combination of morphological and ecological traits, the phylum is divided into three classes, Archiacanthocephala, Eoacanthocephala, and Palaeacanthocephala, which include 10 orders, 26 families, and over 160 genera [1,5,6,7].
Some previous studies have made efforts to establish a basic molecular phylogenetic framework for Acanthocephala using various nuclear sequence data and mitochondrial genes [8,9,10,11,12,13,14,15,16,17]. Recently, mitochondrial genomic data were used to infer the phylogenetic relationships of the higher taxa in Acanthocephala [15,18,19,20,21,22,23,24,25]. However, to date, mitochondrial genome data are available for only 23 species of acanthocephalans, representing 13 families belonging to 6 orders. Several acanthocephalan families and orders were not represented in the above-mentioned phylogenetic studies, due to the paucity and inaccessibility of suitable material or genetic data for these groups.
Echinorhynchida is the largest order in the phylum Acanthocephala, containing more than 470 nominal species, which mainly parasitize teleost fishes but also occur in amphibians and reptiles [1,5,26,27]. Amin (2013) listed 11 families in the Echinorhynchida, including Arhythmacanthidae, Cavisomatidae, Echinorhynchidae, Fessisentidae, Heteracanthocephalidae, llliosentidae, Isthmosacanthidae, Pomphorhynchidae, Rhadinorhynchidae, Transvenidae, and Sauracanthorhynchidae. Later, two new families, namely Gymnorhadinorhynchidae and Spinulacorpidae, were erected [6,28]. Additionally, two families, Paracanthocephalidae and Pseudoacanthocephalidae, were resurrected [16]. However, the phylogenetic relationships of these families are still uncertain. Additionally, the non-monophyly of Echinorhynchida was also revealed by some previous phylogenetic studies [8,9,10,11,12,13,14,17,18,29,30].
In order to further test the monophyly of the orders Echinorhynchida and Polymorphida, assess the validity of the recently resurrected family Pseudoacanthocephalidae, and clarify the evolutionary relationships of the Pseudoacanthocephalidae and the other families in Palaeacanthocephala using mitogenome data, the complete mitochondrial genome of Pseudoacanthocephalus bufonis, the first mitogenome from the Pseudoacanthocephalidae, was sequenced and annotated for the first time. Moreover, phylogenetic analyses of the protein-coding genes of all available acanthocephalan mitogenomes were performed using maximum likelihood (ML) and Bayesian inference (BI) in different models.

2. Materials and Methods

2.1. Parasite Collection and Species Identification

A total of 14 spot-legged tree frogs, Polypedates megacephalus Hallowell (Anura: Rhacophoridae), were caught by hand at night in the Diaoluo Mountains, Hainan Island, China, and euthanized by injection of an overdose of pentobarbitone sodium solution. The acanthocephalan specimens were collected from the intestine of the host. For light microscopical studies, acanthocephalans were cleared in glycerine. Photomicrographs were recorded using a Nikon® digital camera coupled to a Nikon® optical microscopy (Nikon ECLIPSE Ni-U, Nikon Corporation, Tokyo, Japan). The specimens were identified as P. bufonis based on morphological features reported in previous studies [31,32,33,34,35,36]. The terminology is according to the previous study [37]. Voucher specimens were deposited in the College of Life Sciences, Hebei Normal University, Hebei Province, Shijiazhuang, China (HBNU-A-2022A001L).

2.2. Molecular Procedures

For molecular analysis, the genomic DNA was extracted using a modified CTAB (pH 8.0)-based DNA extraction protocol as described in Zhao et al. [38]. The genomic DNA library was constructed, and a total of 20 GB of clean data were generated using the pair-end 150 sequencing method on the Illumina NovaSeq 6000 platform by Novogene (Tianjin, China).
The complete mitochondrial genome was assembled using GetOrganelle v1.7.2a [39]. Protein coding genes (PCGs), rRNAs, and tRNAs were annotated using the MitoS web server (http://mitos2.bioinf.uni-leipzig.de/index.py, accessed on 20 January 2022) and MitoZ v2.4 [40]. The open reading frame (ORF) of each PCG was confirmed manually by the web version of ORF finder (https://www.ncbi.nlm.nih.gov/orffinder/, accessed on 10 March 2022). The “lost” tRNA genes ignored by both MitoS and MitoZ were identified using BLAST based on a database of the existing tRNA sequences of Acanthocephala. The secondary structures of tRNAs were predicted by the ViennaRNA module [41], building on MitoS2 [42] and RNAstructure v6.3 [43], followed by a manual correction. MitoZ v2.4 was used to visualize and depict gene element features [40]. The base composition, amino acid usage, and relative synonymous codon usage (RSCU) were calculated by a Python script, which refers to codon adaptation index (CAI) [44]. The total length of the base composition included ambiguous bases. The base skew analysis was used to describe the base composition of nucleotide sequences. The relative values were calculated using the formulas: A T s k e w = A T A + T and G C s k e w = G C G + C . The complete mitochondrial genome sequence of P. bufonis obtained herein was deposited in the GenBank database (http://www.ncbi.nlm.nih.gov, accessed on 5 October 2022).

2.3. Phylogenetic Analyses

Phylogenetic analyses were performed based on concatenated amino acid sequences of 12 PCGs using maximum likelihood (ML) and Bayesian inference (BI). Gnathostomula armata and G. paradoxa (Gnathostomulida) were chosen as the out-group. The in-group included 7 species of rotifers and 24 species of acanthocephalans. Detailed information on representatives included in the present phylogeny was provided in Table 1. The phylogenetic trees were re-rooted on Gnathostomulida. Genes were aligned separately using MAFFT v7.313 under the iterative refinement method of E-INS-I [45]. Ambiguous sites and poorly aligned positions were pruned using BMGE v1.12 (m = BLOSUM90, h = 0.5) [46]. The aligned and pruned sequences were concatenated into a matrix by PhyloSuite v1.2.2 [47]. The pruned alignments were then concatenated into the “AA” matrix with the amino acid sequences of PCGs (2087 sites). Bayesian inference (BI) was implemented under the CAT + GTR + G4 model, using PhyloBayes-MPI 1.8 [45,48,49,50,51]. Two independent Markov Chain Monte Carlo (MCMC) runs of 8000 generations each were executed. A consensus tree was simultaneously built by pooling the remaining MCMC trees from both runs. Convergence was evaluated with the “bpcomp” and “tracecomp” procedures in the PhyloBayes package with a burn-in of the first 1000 generations. The maximum discrepancy in the convergence result is 0.017. The maximum likelihood (ML) inference was conducted in IQTREE v2.1.2 [52]. Substitution models were compared and selected according to the Bayesian Information Criterion (BIC) by using ModelFinder [53]. Additionally, a profile mixture model (C60) was used based on the best-fit substitution model of the NP datasets of amino acid datasets [54]. An edge-unlinked model was specified for both the full partition and the merged partition schemes. The best run is selected from the four independent runs based on log-likelihood. A total of 1000 Ultrafast bootstraps were used to evaluate the nodal support of the ML tree [55], and to estimate the consensus tree. For the “AA” matrix, three partition schemes were applied for ML (Table 2): (1) no partition (NP); (2) full partition (FP) that provides the best-fitting model for each individual gene; and (3) merged partition (MP) that implements a greedy strategy starting with the full partition model and subsequently merging pairs of genes until the model fit does not improve any further. The phylogenetic-terrace aware (PTA) data structure was used to facilitate the efficient analysis of the “AA” matrix under each partition model [56]. We selected the best final maximum likelihood and consensus trees according to the Akaike Information Criterion (AIC). Phylogenetic analyses ranked nodes with posterior probabilities (PP) and bootstrap support values (BS) = 1/100 as fully supported, 0.98–0.99/95–99 as strongly supported, 0.95–0.97/90–94 as generally supported, and <90/0.95 as weakly supported. The phylogenetic trees were visualized in iTOL v6.1.1 [57].

3. Results and Discussion

3.1. Morphology of Pseudoacanthocephalus bufonis (Figure 1, Table 3)

Trunks are medium-sized, smooth, and cylindrical. Females are much larger than males. Proboscis is nearly cylindrical, armed with 16–20 longitudinal rows of 3–5 rooted hooks each. Proboscis receptacle is double-walled with the cerebral ganglion at the posterior of the proboscis receptacle. The neck is short. Lemnisci are more or less equal, slightly longer or shorter than the proboscis receptacle. Morphometric data of the present specimens and morphometric comparisons of P. bufonis between our specimens and previous studies are shown in Table 3.
The morphology and measurements of the present material are more or less identical to the previous descriptions of P. bufonis [31,32,33,34,35,36], including the morphology and size of trunk and proboscis, the number of the longitudinal rows of proboscis hooks and the hooks per longitudinal row, the number and length of testes and cement-glands, and the morphology and size of eggs. However, the lengths of the proboscis receptacle and lemnisci are slightly ser than those of the previous studies. Additionally, we also sequenced the ITS region (OQ550505, OQ550506) of our specimens. Pairwise comparison of the ITS sequences of our specimens with the available ITS data (KC491878–KC491883) of P. bufonis reported in the previous study [70], displayed only 0.17% nucleotide divergence. Thus, we confirmed our specimens to be P. bufonis.

3.2. Gene Content and Organization of the Mitogenome

The complete mitogenome of P. bufonis is 14,056 bp in length and includes 36 genes, containing 12 PCGs (cox1–3, nad1–6, nad4l, cytb, and atp6), 22 tRNA genes, 2 rRNA genes (rrnS and rrnL), and two non-coding regions (NCR1 and NCR2) (Figure 2, Table 4). The lack of atp8 in the mitogenome of P. bufonis is typical for most of the available mitogenomes of acanthocephalans, except for Leptorhynchoides thecatus, which has two putative atp8 genes [55]. All genes in the mitogenome of P. bufonis are encoded on the same strand and in the same direction. Furthermore, the highest GC-skew (0.53) and the second lowest AT-skew (−0.28) of the mitogenome of P. bufonis in the order Echinorhynchida show its preference for G and T nucleotides (Figure 3), which was possibly a result of the propensity for low use of A-rich codons in their PCGs (Table 5). A similar situation also occurred in Polyacanthorhynchus caballeroi and some species of Polymorphida [19,21,25].

3.3. Protein-Coding Genes and Codon Usage

The length of 12 PCGs is 10,114 bp. 12 PCGs encode 3358 amino acids and include 3358 codons, excluding termination codons. The longest PCG is nad5 (1620 bp), while the shortest PCG is nad4l (243 bp) (Figure 2, Table 4).
The composition and usage of codons in the mitogenome of P. bufonis were shown in Figure 4 and Table 6. ATN (i.e., ATA, ATG, and ATT), GTG, and TTG are used as start codons for the 12 PCGs in the mitogenome of P. bufonis, whereas TAA, TAG, and incomplete codons of T or TA are used as termination codons, in accordance with those of other acanthocephalans [15,18,19,20,21,22,23,24,25,58,59,60,61,62,63,64]. GTG is the most common start codon, being used for six PCGs (cox1, cox3, nad2, nad4l, nad5, and nad6), followed by ATN for four PCGs (ATA: atp6; ATG: nad3 and nad4; ATT: nad1). Two genes (cytb and cox2) were inferred to use TTG as the start codon. Among the 12 PCGs, six genes (atp6, cytb, nad1, nad2, nad3, and nad4l) are terminated with complete stop codon TAA, while three genes (cox1, cox2, and nad5) were inferred to terminate with complete stop codon TAG. The incomplete stop codons T and TA are used for cox3 and nad4, and nad6, respectively.
In the PCGs of P. bufonis, the codon with the highest RSCU value is AGG (Ser), while the rarest codon is CTC (Leu). Val is the most frequently used amino acid (16.66%) in 12 PCGs of P. bufonis. Gln is the least commonly used amino acid (0.59%). The high frequency of Val (encoded by GTN) is associated with the high proportions of G and T in their protein-coding sequences (Figure 4 and Table 6).

3.4. Ribosomal and Transfer RNAs

A total of 22 tRNAs were identified, ranging in length from 42 bp (trnC) to 68 bp (trnI) (Table 4). The anticodons (Table 4) and secondary structures (Figure 5) of the 22 tRNAs were identified. Of the 22 tRNAs, four (trnA, trnN, trnL2, trnS1) have a short dihydrouridine (DHU) arm, six (trnA, trnE, trnG, trnI, trnL1, trnY) lack a TψC (T) arm, and two (trnD and trnC) have lost both arms (Figure 5). Moreover, the trnT has a short amino acid acceptor (AA) arm. The other nine tRNAs were predicted to be folded into typical cloverleaf secondary structures, as found in other acanthocephalans [19,23].
In the mitogenome of P. bufonis, two rRNAs, rrnL, located between trnY and trnL1, and rrnS, located between trnM and trnP, were identified. The rrnL is 908 bp in length, with 62.86% A + T content, whereas the rrnS is 572 bp in length with 64.37% A + T content (Figure 2 and Table 5).

3.5. Gene Order

In the mitogenome of P. bufonis, gene arrangement of PCGs and rRNAs is in the following order: cox1, rrnL, nad6, atp6, nad3, nad4l, nad4, nad5, ctyb, nad1, rrnS, cox2, cox3, and nad1, a pattern which appears to be relatively conserved in acanthocephalans [22,23,24,25,64]. However, some tRNAs (i.e., trnS1, trnS2, trnM, trnV, trnK, trnR, and trnC) show more variability in translocation [21,65]. There are up to three translocations in tRNAs in the mitogenome of acanthocephalans reported so far (i.e., trnS1, trnS2, and trnK) [18,20,22,23,24,66] (Figure 6). There are two main gene arrangements of trnS2: type A (trnS2, atp6, nad3, trnW, trnV, trnK, trnE, and trnT) and type B (atp6, nad3, trnW, trnV, trnK, trnE, trnT, and trnS2). The trnK has two arrangements: type C (trnK and trnV) and type D (trnV and trnK). The gene arrangement of trnS1 has three order types: type E (trnS1, trnM, rrnS, trnF, cox2, trnC, cox3, trnA, trnR, and trnN), type F (trnM, rrnS, trnF, cox2, trnC, cox3, trnA, trnR, trnN, and trnS1), and type G (trnM, trnS1, rrnS, trnF, cox2, trnC, cox3, trnA, trnR, and trnN) [18,20,22,23,24,59,66,67]. In the mito-genome of P. bufonis, trnR is situated between trnA and trnN, while trnS2 lays between trnD and atp6 (Figure 6).
The gene order of trnS2 in the mitogenome of P. bufonis is type A (trnS2, atp6, nad3, trnW, trnV, trnK, trnE, trnT). The gene arrangement of trnK is of type D (trnK, trnV). The trnS1 of P. bufonis is of type F (trnM, rrnS, trnF, cox2, trnC, cox3, trnA, trnR, trnN, trnS1) (Figure 6).

3.6. Non-Coding Regions

In the mitogenome of P. bufonis, there are two non-coding regions (NCR1 and NCR2). NCR1 is located between trnI and trnM, is 610 bp in length. NCR2, located between trnW and trnV, is 503 bp. Their A + T contents are 61.97% and 56.86%, respectively (Table 5).

3.7. Molecular Phylogeny

Phylogenetic trees generated from BI and ML methods under different models have similar topologies and indicate that the Acanthocephala are monophyletic, which was widely accepted in previous studies. However, the evolutionary relationships of the Acanthocephala and the three subtaxa of Rotifera (Monogononta, Bdelloidea, and Seisonidea) have been under debate for a long time [19,71,72,73]. The present phylogenetic results showed that the Acanthocephala is sister to Bdelloidea (Rotaria rotatoria, Philodina citrina) and rejected the monophyly of Eurotatoria (Monogononta + Bdelloidea), which are identical to the previous phylogenetic results using EST libraries [72] and mitogenomic data [19], but conflicted with some other phylogenies based on 18S rDNA and transcriptomic data [71,73].
Our phylogeny also supported the division of the phylum Acanthocephala into three large clades (Clade I, Clade II, and Clade III) (Figure 7). Clade I, including Macracanthorhynchus hirudinaceus and Oncicola luehei (Oligacanthorhynchida: Oligacanthorhynchidae), represents Archiacanthocephala, a monophyletic group located at the base of the phylogenetic trees of Acanthocephala (Figure 7). The present results agree well with some previous phylogenetic studies [8,9,11,12,13,18,20,22,23,24,25,64,66]. The representative of Polyacanthocephala (Polyacanthorhynchus caballeroi) nested with species of Eoacanthocephala (Pallisentis celatus + Acanthogyrus bilaspurensis + Neoechinorhynchus violentum + Paratenuisentis ambiguus), forming Clade II. The present phylogenetic results challenged the validity of Polyacanthocephala, as have some previous molecular phylogenetic studies [19,22,23,25,64,66].
The representatives of Palaeacanthocephala formed Clade III. The monophyly of the order Polymorphida, including the representatives of Plagiorhynchus transversus, Polymorphus minutus, Southwellina hispida, Centrorhynchus clitorideus, C. milvus, C. aluconis, Sphaerirostris lanceoides, and S. picae, is strongly supported in our phylogenetic results. In Polymorphida, the Polymorphidae are more closely related to the Centrorhynchidae than the Plagiorhynchidae, in accordance with other recent mitogenomic phylogenies, but inconsistent with some previous phylogenetic studies based on nuclear and mitochondrial genetic markers [17,68,69,74]. Our phylogenetic results showed that the order Echinorhynchida is paraphyletic, which is consistent with previous molecular phylogenetic studies [12,14,28,30,69]. Furthermore, they supported the resurrection of Pseudoacanthocephalidae [16]. In the present mitogenomic phylogeny, P. bufonis clustered together with Cavisoma magnum, suggesting an affinity between Pseudoacanthocephalidae and Cavisomatidae. Our results agreed well with some recent phylogenetic studies based on nuclear gene sequences [16,75]. These indicated that the current classification of Echinorhynchida is based on unique combinations of characteristics, not shared derived features [13]. The systematics of Echinorhynchida needs to be revised so that its constituent families, subfamilies, and genera reflect the underlying lineages. This will require phylogenetic analysis of both nuclear and mitochondrial DNA datasets from representatives of a more diverse range of taxa than are currently available. It is essential to sequence mitogenomes from yet unrepresented taxa for constructing the molecular phylogenetic framework of Acanthocephala and further exploring the unusual patterns of mitogenomic evolution in this group. The complete mitogenome of P. bufonis obtained herein represents a valuable building block for future work.

4. Conclusions

In the present study, the complete mitochondrial genome of P. bufonis, the first representative of the family Pseudoacanthocephalidae, was characterized. Phylogenetic analyses based on the amino acid sequences of 12 protein-coding genes further confirmed the sister relationship of the Acanthocephala and Bdelloidea and rejected the monophyly of Eurotatoria (Monogononta + Bdelloidea) and Pararotatoria (Seisonidea + Acanthocephala). Our phylogeny also revealed that the order Echinorhynchida and the family Echinorhynchidae are both paraphyletic in the Acanthocephala. The current systematic status of Pseudoacanthocephalus in the Echinorhynchidae is challenged. The present phylogenetic results supported the recent resurrection of Pseudoacanthocephalidae and showed a close affinity between Pseudoacanthocephalidae and Cavisomatidae. Phylogenetic analyses also strongly supported the monophyly of the order Polymorphida and indicated that the Polymorphidae and Centrorhynchidae have a closer relationship than the Plagiorhynchidae. The present phylogenetic studies provided a new insight into the evolutionary relationships of higher taxa within Acanthocephala.

Author Contributions

Contributed to the study design and analyze genetic data, T.-Y.Z., R.-J.Y. and L.L. (Liang Li); collected and identified the acanthocephalan specimens, S.-S.R., H.-X.C., Y.-H.L. and L.L. (Liang Li); conducted the phylogenetic analyses, T.-Y.Z., R.-J.Y., L.L. (Liang Lü) and L.L. (Liang Li); wrote and revised the manuscript, T.-Y.Z., R.-J.Y., M.T.W. and L.L. (Liang Li). All authors have read and agreed to the published version of the manuscript.

Funding

This study was supported by the National Natural Science Foundation of China (Grant No. 31872197), the Strategic Priority Research Program of the Chinese Academy of Sciences (XDB26000000), and the Youth Top Talent Support Program of Hebei Province for Dr. Liang Li.

Institutional Review Board Statement

This study was conducted under the protocols of Hebei Normal University. All applicable national and international guidelines for the protection of animals were followed. All experimental procedures involving animals in this study, including the autopsy, were approved by the Animal Ethics Committee of Hebei Normal University, China (no. 2023LLSC001).

Informed Consent Statement

Not applicable.

Data Availability Statement

The mitogenome sequence of Pseudoacanthocephalus bufonis obtained in this study was deposited in the GenBank database. Voucher specimens of P. bufonis were deposited in the College of Life Sciences, Hebei Normal University, Hebei Province, under the accession number HBNU-A-2022A001L.

Conflicts of Interest

The authors declare no conflict of interest.

References

  1. Amin, O.M. Classification of the Acanthocephala. Folia. Parasitol. 2013, 60, 273–305. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  2. Yamaguti, S. Acanthocephala. In Systema Helminthum; Interscience Publishers John Wiley and Sons: New York, NY, USA, 1963; Volume V, pp. 1–423. [Google Scholar]
  3. Kennedy, C.R. Ecology of the Acanthocephala; Cambridge University Press: Cambridge, UK, 2006; ISBN 978-0-521-85008-7. [Google Scholar]
  4. Schmidt, G.D. Development and life cycles. In Biology of Acanthocephala; Crompton, D.W.T., Nickol, B.B., Eds.; Cambridge University Press: Cambridge, UK, 1985; pp. 273–286. [Google Scholar]
  5. Amin, O.M. Key to the families and subfamilies of acanthocephala, with the Erection of a new class (Polyacanthocephala) and a new order (Polyacanthorhynchida). J. Parasitol. 1987, 73, 1216–1219. [Google Scholar] [CrossRef] [PubMed]
  6. Huston, D.C.; Smales, L.R. Proposal of Spinulacorpus biforme (Smales, 2014) n. g., n. comb. and the Spinulacorpidae n. fam. to resolve paraphyly of the acanthocephalan family Rhadinorhynchidae Lühe, 1912. Syst. Parasitol. 2020, 97, 477–490. [Google Scholar] [CrossRef] [PubMed]
  7. Zhang, Z.-Q. Animal biodiversity: An outline of higher-level classification and survey of taxonomic richness. Zootaxa 2011, 3148, 63–95. [Google Scholar] [CrossRef]
  8. Near, T.J.; Garey, J.R.; Nadler, S.A. Phylogenetic relationships of the Acanthocephala inferred from 18S ribosomal DNA Sequences. Mol. Phylogenet. Evol. 1998, 10, 287–298. [Google Scholar] [CrossRef]
  9. García-Varela, M.; Pérez-Ponce de León, G.; de la Torre, P.; Cummings, M.P.; Sarma, S.S.S.; Laclette, J.P. Phylogenetic relationships of Acanthocephala based on analysis of 18S ribosomal RNA gene sequences. J. Mol. Evol. 2000, 50, 532–540. [Google Scholar] [CrossRef]
  10. García-Varela, M.; Cummings, M.P.; Pérez-Ponce de León, G.; Gardner, S.L.; Laclette, J.P. Phylogenetic analysis based on 18S ribosomal RNA gene sequences supports the existence of class Polyacanthocephala (Acanthocephala). Mol. Phylogenet. Evol. 2002, 23, 288–292. [Google Scholar] [CrossRef] [Green Version]
  11. Near, T.J. Acanthocephalan phylogeny and the evolution of parasitism1. Integr. Comp. Biol. 2002, 42, 668–677. [Google Scholar] [CrossRef]
  12. Verweyen, L.; Klimpel, S.; Palm, H.W. Molecular phylogeny of the Acanthocephala (class Palaeacanthocephala) with a paraphyletic assemblage of the orders Polymorphida and Echinorhynchida. PLoS ONE 2011, 6, e28285. [Google Scholar] [CrossRef] [Green Version]
  13. García-Varela, M.; Nadler, S.A. Phylogenetic relationships of Palaeacanthocephala (Acanthocephala) inferred from SSU and LSU rDNA gene sequences. J. Parasitol. 2005, 91, 1401–1409. [Google Scholar] [CrossRef] [Green Version]
  14. García-Varela, M.; Nadler, S.A. Phylogenetic relationships among Syndermata inferred from nuclear and mitochondrial gene sequences. Mol. Phylogenet. Evol. 2006, 40, 61–72. [Google Scholar] [CrossRef]
  15. Gazi, M.; Sultana, T.; Min, G.-S.; Park, Y.C.; García-Varela, M.; Nadler, S.A.; Park, J.-K. The complete mitochondrial genome sequence of Oncicola luehei (Acanthocephala: Archiacanthocephala) and its phylogenetic position within Syndermata. Parasitol. Int. 2012, 61, 307–316. [Google Scholar] [CrossRef]
  16. García-Varela, M.; Andrade-Gómez, L. First steps to understand the systematics of Echinorhynchidae Cobbold, 1876 (Acanthocephala), inferred through nuclear gene sequences. Parasitol. Int. 2021, 81, 102264. [Google Scholar] [CrossRef]
  17. García-Varela, M.; Park, J.-K.; Hernández-Orts, J.S.; Pinacho-Pinacho, C.D. Morphological and molecular data on a new species of Plagiorhynchus Lühe, 1911 (Acanthocephala: Plagiorhynchidae) from the long-billed curlew (Numenius americanus) from northern Mexico. J. Helminthol. 2019, 94, e61. [Google Scholar] [CrossRef]
  18. Gazi, M.; Kim, J.; Park, J.-K. The complete mitochondrial genome sequence of Southwellina hispida supports monophyly of Palaeacanthocephala (Acanthocephala: Polymorphida). Parasitol. Int. 2015, 64, 64–68. [Google Scholar] [CrossRef]
  19. Gazi, M.; Kim, J.; García-Varela, M.; Park, C.; Littlewood, D.T.J.; Park, J.-K. Mitogenomic phylogeny of Acanthocephala reveals novel class relationships. Zool. Scr. 2016, 45, 437–454. [Google Scholar] [CrossRef]
  20. Weber, M.; Wey-Fabrizius, A.R.; Podsiadlowski, L.; Witek, A.; Schill, R.O.; Sugár, L.; Herlyn, H.; Hankeln, T. Phylogenetic analyses of endoparasitic Acanthocephala based on mitochondrial genomes suggest secondary loss of sensory organs. Mol. Phylogenet. Evol. 2013, 66, 182–189. [Google Scholar] [CrossRef]
  21. Song, F.; Li, H.; Liu, G.-H.; Wang, W.; James, P.; Colwell, D.D.; Tran, A.; Gong, S.; Cai, W.; Shao, R. Mitochondrial genome fragmentation unites the parasitic lice of eutherian mammals. Syst. Biol. 2019, 68, 430–440. [Google Scholar] [CrossRef] [Green Version]
  22. Muhammad, N.; Suleman; Ma, J.; Khan, M.S.; Wu, S.-S.; Zhu, X.-Q.; Li, L. Characterization of the complete mitochondrial genome of Centrorhynchus milvus (Acanthocephala: Polymorphida) and its phylogenetic implications. Infect. Genet. Evol. 2019, 75, 103946. [Google Scholar] [CrossRef]
  23. Muhammad, N.; Suleman; Ma, J.; Khan, M.S.; Li, L.; Zhao, Q.; Ahmad, M.S.; Zhu, X.-Q. Characterization of the complete mitochondrial genome of Sphaerirostris picae (Rudolphi, 1819) (Acanthocephala: Centrorhynchidae), representative of the genus Sphaerirostris. Parasitol. Res. 2019, 118, 2213–2221. [Google Scholar] [CrossRef]
  24. Muhammad, N.; Li, L.; Suleman; Zhao, Q.; Bannai, M.A.; Mohammad, E.T.; Khan, M.S.; Zhu, X.-Q.; Ma, J. Characterization of the complete mitochondrial genome of Cavisoma magnum (Acanthocephala: Palaeacanthocephala), first representative of the family Cavisomidae, and its phylogenetic implications. Infect. Genet. Evol. 2020, 80, 104173. [Google Scholar] [CrossRef] [PubMed]
  25. Muhammad, N.; Suleman; Ahmad, M.S.; Li, L.; Zhao, Q.; Ullah, H.; Zhu, X.-Q.; Ma, J. Mitochondrial DNA dataset suggest that the genus Sphaerirostris Golvan, 1956 is a synonym of the genus Centrorhynchus Lühe, 1911. Parasitology 2020, 147, 1149–1157. [Google Scholar] [CrossRef] [PubMed]
  26. Smales, L.R.; Allain, S.J.R.; Wilkinson, J.W.; Harris, E. A new species of Pseudoacanthocephalus (Acanthocephala: Echinorhynchidae) from the guttural toad, Sclerophrys gutturalis (Bufonidae), introduced into Mauritius, with comments on the implications of the introductions of toads and their parasites into the UK. J. Helminthol. 2020, 94, e119. [Google Scholar] [CrossRef] [PubMed]
  27. Pichelin, S.; Cribb, T.H. The status of the Diplosentidae (Acanthocephala: Palaeacanthocephala) and a new family of acanthocephalans from Australian wrasses (Pisces: Labridae). Folia Parasitol. Praha 2001, 48, 289–303. [Google Scholar] [CrossRef] [Green Version]
  28. Braicovich, P.E.; Lanfranchi, A.L.; Farber, M.D.; Marvaldi, A.E.; Luque, J.L.; Timi, J.T. Genetic and morphological evidence reveals the existence of a new family, genus and species of Echinorhynchida (Acanthocephala). Folia Parasitol. Praha 2014, 61, 377–384. [Google Scholar] [CrossRef] [Green Version]
  29. Monks, S. Phylogeny of the Acanthocephala based on morphological characters. Syst. Parasitol. 2001, 48, 81–115. [Google Scholar] [CrossRef]
  30. García-Varela, M.; Pérez-Ponce de León, G. Validating the systematic position of Profilicollis Meyer, 1931 and Hexaglandula Petrochenko, 1950 (Acanthocephala: Polymorphidae) using cytochrome c oxidase (Cox 1). J. Parasitol. 2008, 94, 212–217. [Google Scholar] [CrossRef]
  31. Petrochenko, V.I. Thorny-headed worms (Acanthocephala) of U. S. S. R. amphibians. In Contributions on Helminthology in Commemoration of the Birthday of K. I. Skrjabin; Petrov, A.M., Ed.; Izdatel’stvo Akademii Nauk SSSR: Moscow, Russia, 1953; pp. 507–517. [Google Scholar]
  32. Kennedy, C.R.; Murray, J. A redescription of Acanthocephalus bufonis (Shipley, 1903) Southwell and Macfie, 1925 (Acanthocephala: Echinorhynchidae) from the black-spotted toad, Bufo melanostictus, from Bogor, Indonesia. Can. J. Zool. 1982, 60, 356–360. [Google Scholar] [CrossRef]
  33. Wang, Y.-Y. Studies on the life history of Pseudoacanthpcephalus bufonis (Shipley, 1903) Petrotschenko, 1958. J. Fujian Norm. Univ. Nat. Sci. Ed. 1989, 5, 88–93. [Google Scholar]
  34. Bush, S.E.; Duszynski, D.W.; Nickol, B.B. Acanthocephala from Amphibians in China with the description of a new species of Pseudoacanthocephalus (Echinorhynchida). J. Parasitol. 2009, 95, 1440–1445. [Google Scholar] [CrossRef] [Green Version]
  35. Shipley, A.E. On the ento-parasites collected by the “Skeat-Expedition” to Lower Siam and the Malay Peninsula in the years 1899–1900. Proc. Zool. Soc. Lond. 1903, 2, 145–156. [Google Scholar]
  36. Yuen, P.H.; Fernando, C.H. On Acanthocephalus bufonis (Shipley) a Common Parasite of Malayan amphibians. Bull. natn. Mus. Singap. 1967, 33, 91–93. [Google Scholar]
  37. Herlyn, H.; Röhrig, H. Ultrastructure and overall organization of ligament sac, uterine bell, uterus and vagina in Paratenuisentis ambiguus (Acanthocephala, Eoacanthocephala)—The character evolution within the Acanthocephala. Acta Zool. Stockholm 2003, 84, 239–247. [Google Scholar] [CrossRef]
  38. Zhao, T.-Y.; Zhang, C.-J.; Lv, L. Comparative description of the mitochondrial genome of Scaphidium formosanum Pic, 1915 (Coleoptera: Staphylinidae: Scaphidiinae). Zootaxa 2021, 4941, 487–510. [Google Scholar] [CrossRef]
  39. Jin, J.-J.; Yu, W.-B.; Yang, J.-B.; Song, Y.; de Pamphilis, C.W.; Yi, T.-S.; Li, D.-Z. GetOrganelle: A fast and versatile toolkit for accurate de novo assembly of organelle genomes. Genome Biol. 2020, 21, 241. [Google Scholar] [CrossRef]
  40. Meng, G.; Li, Y.; Yang, C.; Liu, S. MitoZ: A toolkit for animal mitochondrial genome assembly, annotation and visualization. Nucleic Acids Res. 2019, 47, e63. [Google Scholar] [CrossRef] [Green Version]
  41. Gruber, A.R.; Bernhart, S.H.; Lorenz, R. The ViennaRNA Web Services. In RNA Bioinformatics; Picardi, E., Ed.; Methods in Molecular Biology; Springer: New York, NY, USA, 2015; Volume 1269, pp. 307–326. ISBN 978-1-4939-2291-8. [Google Scholar]
  42. Bernt, M.; Merkle, D.; Ramsch, K.; Fritzsch, G.; Perseke, M.; Bernhard, D.; Schlegel, M.; Stadler, P.F.; Middendorf, M. CREx: Inferring genomic rearrangements based on common intervals. Bioinformatics 2007, 23, 2957–2958. [Google Scholar] [CrossRef] [Green Version]
  43. Reuter, J.S.; Mathews, D.H. RNAstructure: Software for RNA secondary structure prediction and analysis. BMC Bioinform. 2010, 11, 129. [Google Scholar] [CrossRef] [Green Version]
  44. Lee, B.D. Python implementation of codon adaptation index. J. Open Source Softw. 2018, 3, 905. [Google Scholar] [CrossRef] [Green Version]
  45. Katoh, K.; Standley, D.M. MAFFT multiple sequence alignment software version 7: Improvements in performance and usability. Mol. Biol. Evol. 2013, 30, 772–780. [Google Scholar] [CrossRef] [Green Version]
  46. Criscuolo, A.; Gribaldo, S. BMGE (Block Mapping and Gathering with Entropy): A new software for selection of phylogenetic informative regions from multiple sequence alignments. BMC Evol. Biol. 2010, 10, 210. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  47. Zhang, D.; Gao, F.; Jakovlić, I.; Zou, H.; Zhang, J.; Li, W.X.; Wang, G.T. PhyloSuite: An integrated and scalable desktop platform for streamlined molecular sequence data management and evolutionary phylogenetics studies. Mol. Ecol. Resour. 2020, 20, 348–355. [Google Scholar] [CrossRef] [PubMed]
  48. Lartillot, N.; Rodrigue, N.; Stubbs, D.; Richer, J. PhyloBayes MPI: Phylogenetic reconstruction with infinite mixtures of profiles in a parallel environment. Syst. Biol. 2013, 62, 611–615. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  49. Lartillot, N.; Philippe, H. A bayesian mixture model for across-site heterogeneities in the amino-acid replacement process. Mol. Biol. Evol. 2004, 21, 1095–1109. [Google Scholar] [CrossRef]
  50. Lartillot, N.; Philippe, H. Computing bayes factors using thermodynamic integration. Syst. Biol. 2006, 55, 195–207. [Google Scholar] [CrossRef] [Green Version]
  51. Lartillot, N.; Brinkmann, H.; Philippe, H. Suppression of long-branch attraction artefacts in the animal phylogeny using a site-heterogeneous model. BMC Evol. Biol. 2007, 7, S4. [Google Scholar] [CrossRef] [Green Version]
  52. Minh, B.Q.; Schmidt, H.A.; Chernomor, O.; Schrempf, D.; Woodhams, M.D.; von Haeseler, A.; Lanfear, R. IQ-TREE 2: New models and efficient methods for phylogenetic inference in the genomic era. Mol. Biol. Evol. 2020, 37, 1530–1534. [Google Scholar] [CrossRef] [Green Version]
  53. Kalyaanamoorthy, S.; Minh, B.Q.; Wong, T.K.F.; von Haeseler, A.; Jermiin, L.S. ModelFinder: Fast model selection for accurate phylogenetic estimates. Nat. Methods 2017, 14, 587–589. [Google Scholar] [CrossRef] [Green Version]
  54. Le, S.-Q.; Gascuel, O.; Lartillot, N. Empirical profile mixture models for phylogenetic reconstruction. Bioinformatics 2008, 24, 2317–2323. [Google Scholar] [CrossRef] [Green Version]
  55. Golombek, A.; Tobergte, S.; Struck, T.H. Elucidating the phylogenetic position of Gnathostomulida and first mitochondrial genomes of Gnathostomulida, Gastrotricha and Polycladida (Platyhelminthes). Mol. Phylogenet. Evol. 2015, 86, 49–63. [Google Scholar] [CrossRef]
  56. Chernomor, O.; von Haeseler, A.; Minh, B.Q. Terrace aware data structure for phylogenomic inference from supermatrices. Syst. Biol. 2016, 65, 997–1008. [Google Scholar] [CrossRef] [Green Version]
  57. Letunic, I.; Bork, P. Interactive tree of life (iTOL) v5: An online tool for phylogenetic tree display and annotation. Nucleic Acids Res. 2021, 49, W293–W296. [Google Scholar] [CrossRef]
  58. Steinauer, M.L.; Nickol, B.B.; Broughton, R.; Ortí, G. First sequenced mitochondrial genome from the phylum Acanthocephala (Leptorhynchoides thecatus) and its phylogenetic position within Metazoa. J. Mol. Evol. 2005, 60, 706–715. [Google Scholar] [CrossRef]
  59. Pan, T.S.; Nie, P. The complete mitochondrial genome of Pallisentis celatus (Acanthocephala) with phylogenetic analysis of Acanthocephalans and Rotifers. Folia Parasitol. 2013, 60, 181–191. [Google Scholar] [CrossRef] [Green Version]
  60. Song, R.; Zhang, D.; Deng, S.; Ding, D.; Liao, F.; Liu, L. The complete mitochondrial genome of Acanthosentis cheni (Acanthocephala: Quadrigyridae). Mitochondrial DNA Part B 2016, 1, 797–798. [Google Scholar] [CrossRef] [Green Version]
  61. Pan, T.; Jiang, H. The complete mitochondrial genome of Hebesoma Violentum (Acanthocephala). Mitochondrial DNA Part B 2018, 3, 582–583. [Google Scholar] [CrossRef] [Green Version]
  62. Lei, M.-T.; Cai, J.-Z.; Li, C.-H.; Fu, Y.; Sun, J.; Ma, D.-D.; Li, Y.-P.; Zhang, Y.-M. Prevalence and genetic diversity of Echinorhynchus gymnocyprii (Acanthocephala: Echinorhynchidae) in schizothoracine fishes (Cyprinidae: Schizothoracinae) in Qinghai-Tibetan Plateau, China. Parasite. Vector 2020, 13, 357. [Google Scholar] [CrossRef]
  63. Mauer, K.; Hellmann, S.L.; Groth, M.; Fröbius, A.C.; Zischler, H.; Hankeln, T.; Herlyn, H. The genome, transcriptome, and proteome of the fish parasite Pomphorhynchus laevis (Acanthocephala). PLoS ONE 2020, 15, e0232973. [Google Scholar] [CrossRef]
  64. Muhammad, N.; Suleman; Khan, M.S.; Li, L.; Zhao, Q.; Ullah, H.; Zhu, X.-Q.; Ma, J. Characterization of the complete mitogenome of Centrorhynchus clitorideus (Meyer, 1931) (Palaeacanthocephala: Centrorhynchidae), the largest mitochondrial genome in Acanthocephala, and its phylogenetic implications. Mol. Biochem. Parasitol. 2020, 237, 111274. [Google Scholar] [CrossRef]
  65. Kilpert, F.; Podsiadlowski, L. The complete mitochondrial genome of the common sea slater, Ligia oceanica (Crustacea, Isopoda) bears a novel gene order and unusual control region features. BMC Genomics 2006, 7, 241. [Google Scholar] [CrossRef] [Green Version]
  66. Song, R.; Zhang, D.; Gao, J.-W.; Cheng, X.-F.; Xie, M.; Li, H.; Wu, Y.-A. Characterization of the complete mitochondrial genome of Brentisentisyangtzensis Yu & Wu, 1989 (Acanthocephala, Illiosentidae). ZooKeys 2019, 861, 1–14. [Google Scholar] [CrossRef] [PubMed]
  67. Sarwar, H.; Zhao, W.-T.; Kibet, C.J.; Sitko, J.; Nie, P. Morphological and complete mitogenomic characterisation of the Acanthocephalan Polymorphus minutus infecting the duck anas platyrhynchos. Folia Parasitol. 2021, 68, e015. [Google Scholar] [CrossRef] [PubMed]
  68. García-Varela, M.; González-Oliver, A. The systematic position of Leptorhynchoides (Kostylew, 1924) and Pseudoleptorhynchoides (SalgadoMaldonado, 1976), inferred from nuclear and mitochondrial DNA gene sequences. J. Parasitol. 2008, 94, 959–962. [Google Scholar] [CrossRef] [PubMed]
  69. García-Varela, M.; Pérez-Ponce de León, G.; Aznar, F.J.; Nadler, S.A. Phylogenetic relationship among genera of Polymorphidae (Acanthocephala), inferred from nuclear and mitochondrial gene sequences. Mol. Phylogenet. Evol. 2013, 68, 176–184. [Google Scholar] [CrossRef] [PubMed]
  70. Tkach, V.V.; Lisitsyna, O.I.; Crossley, J.L.; Binh, T.T.; Bush, S.E. Morphological and molecular differentiation of two new species of Pseudoacanthocephalus Petrochenko, 1958 (Acanthocephala: Echinorhynchidae) from amphibians and reptiles in the Philippines, with identification key for the genus. Syst. Parasitol. 2013, 85, 11–26. [Google Scholar] [CrossRef]
  71. Herlyn, H.; Piskurek, O.; Schmitz, J.; Ehlers, U.; Zischler, H. The syndermatan phylogeny and the evolution of acanthocephalan endoparasitism as inferred from 18S rDNA sequences. Mol. Phylogenet. Evol. 2003, 26, 155–164. [Google Scholar] [CrossRef]
  72. Witek, A.; Herlyn, H.; Meyer, A.; Boell, L.; Bucher, G.; Hankeln, T. EST based phylogenomics of Syndermata questions monophyly of Eurotatoria. BMC Evol. Biol. 2008, 8, 345. [Google Scholar] [CrossRef] [Green Version]
  73. Wey-Fabrizius, A.R.; Herlyn, H.; Rieger, B.; Rosenkranz, D.; Witek, A.; Welch, D.B.M.; Ebersberger, I.; Hankeln, T. Transcriptome data reveal syndermatan relationships and suggest the evolution of endoparasitism in Acanthocephala via an epizoic stage. PLoS ONE 2014, 9, e88618. [Google Scholar] [CrossRef] [Green Version]
  74. Abdel-Ghaffar, F.; Morsy, K.; Abdel-Gaber, R.; Mehlhorn, H.; Al Quraishy, S.; Mohammed, S. Prevalence, morphology, and molecular analysis of Serrasentis sagittifer (Acanthocephala: Palaeacanthocephala: Rhadinorhynchidae), a parasite of the gilthead sea bream Sparus aurata (Sparidae). Parasitol. Res. 2014, 113, 2445–2454. [Google Scholar] [CrossRef]
  75. Costa Fernandes, V.S.; Amin, O.; Borges, J.N.; Santos, C.P. A new species of the Acanthocephalan genus Filisoma (Cavisomidae) from perciform fishes in Rio de Janeiro, Brasil. Acta Parasit. 2019, 64, 176–186. [Google Scholar] [CrossRef] [Green Version]
Figure 1. Photomicrographs of Pseudoacanthocephalus bufonis. (A) Proboscis; (B) Presoma of female; (C) Metasoma of male; (D) Metasoma of female; (E) egg. Abbreviations: ac, acanthor; bu, copulatory bursa; cg, cement glands; ep, epidermis; h, hooks; le, lemniscs; me, membrane; p, proboscis; pr, proboscis receptacle; sh, shell of egg, te, testis; ub, uterine bell; va, vagina.
Figure 1. Photomicrographs of Pseudoacanthocephalus bufonis. (A) Proboscis; (B) Presoma of female; (C) Metasoma of male; (D) Metasoma of female; (E) egg. Abbreviations: ac, acanthor; bu, copulatory bursa; cg, cement glands; ep, epidermis; h, hooks; le, lemniscs; me, membrane; p, proboscis; pr, proboscis receptacle; sh, shell of egg, te, testis; ub, uterine bell; va, vagina.
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Figure 2. Gene map of the mitochondrial genome of Pseudoacanthocephalus bufonis. The outermost circle shows the gene features, sandy brown for rRNAs, salmon for tRNAs, and light sea green for PCGs. The innermost circle shows the GC content calculated in every 50-site window.
Figure 2. Gene map of the mitochondrial genome of Pseudoacanthocephalus bufonis. The outermost circle shows the gene features, sandy brown for rRNAs, salmon for tRNAs, and light sea green for PCGs. The innermost circle shows the GC content calculated in every 50-site window.
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Figure 3. Comparison of genome-wide nucleotide skews among Acanthocephala, Gnathostomulida, and Rotifera. Species of Acanthocephala are coloured according to their taxonomic placement at the Order level.
Figure 3. Comparison of genome-wide nucleotide skews among Acanthocephala, Gnathostomulida, and Rotifera. Species of Acanthocephala are coloured according to their taxonomic placement at the Order level.
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Figure 4. Relative synonymous codon usage (RSCU) of Pseudoacanthocephalus bufonis. Codon families (in alphabetical order) are provided below the horizontal axis.
Figure 4. Relative synonymous codon usage (RSCU) of Pseudoacanthocephalus bufonis. Codon families (in alphabetical order) are provided below the horizontal axis.
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Figure 5. Predicted secondary structures of 22 tRNAs in the mitogenome of Pseudoacanthocephalus bufonis (Watson-Crick bonds indicated by lines, GU bonds indicated by dots, red bases representing anticodons).
Figure 5. Predicted secondary structures of 22 tRNAs in the mitogenome of Pseudoacanthocephalus bufonis (Watson-Crick bonds indicated by lines, GU bonds indicated by dots, red bases representing anticodons).
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Figure 6. Comparison of the linearized mitochondrial genome arrangement for 24 acanthocephalans species. All genes are transcribed in the same direction, from left to right. The tRNAs are labelled by a single-letter code for the corresponding amino acid. A–B: the position of trnS2; C–D: the position of trnK; E–G: the position of trnS1. Translocations of individual tRNAs are marked with red boxes. The shadowed regions highlighted bin pink represent Pomphorhynchidae (Pseudoacanthocephalus bufonis indicated by asterisk).
Figure 6. Comparison of the linearized mitochondrial genome arrangement for 24 acanthocephalans species. All genes are transcribed in the same direction, from left to right. The tRNAs are labelled by a single-letter code for the corresponding amino acid. A–B: the position of trnS2; C–D: the position of trnK; E–G: the position of trnS1. Translocations of individual tRNAs are marked with red boxes. The shadowed regions highlighted bin pink represent Pomphorhynchidae (Pseudoacanthocephalus bufonis indicated by asterisk).
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Figure 7. Phylogenetic relationships of Acanthocephala are presented based on the topology of Bayesian inference results. The branch length scale is marked according to the tree of Bayesian inference. The species followed by an asterisk (*) are sequenced in this study. Coloured circles indicate posterior probabilities/bootstrap support. Nodes of the cladogram with 0.95–0.97/90–94 are labelled orange; 0.98–0.99/95–99 by blue; 1/100 by green. Nodes divided into five parts indicate the different supports of five methods: (1) Bootstrap support of ML methods with no partition (NP) scheme under the mtZOA + F + R5 model; (2) with full partition (FP) scheme; (3) with merged partition (MP) scheme; (4): Bootstrap support of ML methods under the mtZOA + F + R5 + C60 model; and (5) Posterior probabilities of Bayesian inference.
Figure 7. Phylogenetic relationships of Acanthocephala are presented based on the topology of Bayesian inference results. The branch length scale is marked according to the tree of Bayesian inference. The species followed by an asterisk (*) are sequenced in this study. Coloured circles indicate posterior probabilities/bootstrap support. Nodes of the cladogram with 0.95–0.97/90–94 are labelled orange; 0.98–0.99/95–99 by blue; 1/100 by green. Nodes divided into five parts indicate the different supports of five methods: (1) Bootstrap support of ML methods with no partition (NP) scheme under the mtZOA + F + R5 model; (2) with full partition (FP) scheme; (3) with merged partition (MP) scheme; (4): Bootstrap support of ML methods under the mtZOA + F + R5 + C60 model; and (5) Posterior probabilities of Bayesian inference.
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Table 1. Detailed information on representatives included in the present phylogeny.
Table 1. Detailed information on representatives included in the present phylogeny.
Phylum/ClassOrderFamilySpeciesAccessionLengthAT%References
Outgroup
GnathostomulidaBursovaginoideaGnathostomulidaeGnathostomula armataNC_02698314,03080.2[55]
Gnathostomula paradoxaNC_02698414,19771.8[55]
Ingroup
RotiferaBdelloideaPhilodinidaeRotaria rotatoriaNC_01356815,31973.2[58]
Philodina citrinaFR85688414,00377.7[20]
MonogonontaBrachionidaeBrachionus calyciflorusKX82278127,68368.7[59]
Brachionus plicatilisNC_01048412,67262.9[60]
Brachionus rubensMN25653213,79567.2[61]
ProalidaeProales similisMN97021616,81967.2[62]
SeisonideaSeisonidaeSeison sp.KP74296415,12070.0[63]
Acanthocephala
ArchiacanthocephalaOligacanthorhynchidaOligacanthorhynchidaeMacracanthorhynchus hirudinaceusNC_01980814,28265.2[20]
Oncicola lueheiNC_01675414,28160.2[15]
EoacanthocephalaGyracanthocephalaQuadrigyridaePallisentis celatusNC_02292113,85561.5[64]
Acanthogyrus bilaspurensisMT47658913,36059.3unpublished
NeoechinorhynchidaNeoechinorhynchidaeNeoechinorhynchus violentumKC41500413,39359.4[65]
TenuisentidaeParatenuisentis ambiguusNC_01980713,57466.9[20]
PalaeacanthocephalaEchinorhynchidaCavisomidaeCavisoma magnumMN56258613,59463.0[24]
EchinorhynchidaeEchinorhynchus truttaeNC_01980513,65963.1[20]
PseudoacanthocephalidaePseudoacanthocephalus bufonisMZ95823614,05658.4present study
IlliosentidaeBrentisentis yangtzensisMK65125813,86468.3[66]
PomphorhynchidaePomphorhynchus bulbocolliJQ82437113,91559.9unpublished
Pomphorhynchus laevisJQ80944613,88957.1unpublished
Pomphorhynchus rocciJQ82437313,84560.7unpublished
Pomphorhynchus tereticollisJQ80945113,96556.9unpublished
RhadinorhynchidaeLeptorhynchoides thecatusNC_00689213,88871.4[67]
PolymorphidaCentrorhynchidaeCentrorhynchus clitorideusMT11335515,88455.5[68]
Centrorhynchus milvusMK92234414,31454.5[22]
Centrorhynchus aluconisKT5923571514454.5[19]
Sphaerirostris lanceoidesMT47658813,47858.0[25]
Sphaerirostris picaeMK47135515,17058.1[23]
PolymorphidaePolymorphus minutusMN64617514,14964.4[69]
Southwellina hispidaNC_02651614,74263.9[18]
PlagiorhynchidaePlagiorhynchus transversusNC_02976715,47761.1[19]
PolyacanthocephalaPolyacanthorhynchidaPolyacanthorhynchidaePolyacanthorhynchus caballeroiNC_02976613,95656.3[19]
Table 2. Models, partitioning schemes, and model comparisons of the maximum-likelihood analyses. t: number of partitions; k: number of free parameters; ln (Lik): log-likelihood; AIC: Akaike information criterion; ΔAIC: difference from the minimum AIC; BIC: Bayesian information criterion NP: unpartitioned model; FP: edge-unlinked full partition model; MP: merged and edge-unlinked partition model.
Table 2. Models, partitioning schemes, and model comparisons of the maximum-likelihood analyses. t: number of partitions; k: number of free parameters; ln (Lik): log-likelihood; AIC: Akaike information criterion; ΔAIC: difference from the minimum AIC; BIC: Bayesian information criterion NP: unpartitioned model; FP: edge-unlinked full partition model; MP: merged and edge-unlinked partition model.
Partition Scheme (t)ModelParameters (k)ln (Lik)AICΔAICBIC
NP (1)mtZOA + F + R5 + C60150−64,770.62129,841.23 130,683.08
MP (2)-112−64,937.53130,099.06257.83130,727.65
NP (1)mtZOA + F + R590−65,020.09130,220.18378.94130,725.29
FP (12)-287−64,983.58130,541.16699.92132,151.90
Table 3. Comparative morphometric data for Pseudoacanthocephalus bufonis (all measurements are in millimetres).
Table 3. Comparative morphometric data for Pseudoacanthocephalus bufonis (all measurements are in millimetres).
HostPolypedates megacephalusBufo melanostictus, Rana cancrivora, Takydromus sexlineatusBufo melanostictusPolypedates megacephalus, P. mutus, Fejervarya limnocharis, Limnonectes kuhlii, Philautus odontotarsus, Odorrana versabilis, Rana livida, Amolops sp.
LocalityChina Indonesia ChinaChina
SourcePresent studyKennedy (1982) [32]Wang (1989) [33]Bush (2009) [34]
CharacteristicsMaleFemaleMaleFemaleMaleFemaleMaleFemale
Trunk length5.43–8.9810.0–18.05.29–9.3811.2–16.1 6.80–8.0015.0–20.05.70–11.815.3–28.0
Trunk width1.00–1.500.98–1.450.98–1.511.13–2.100.88–1.521.40–1.601.00–2.201.10–2.30
Proboscis length0.31–0.500.38–0.530.31–0.44 0.33–0.540.48–0.520.56–0.640.41–0.54 0.41–0.54
Proboscis width0.28–0.310.30–0.410.17–0.310.22–0.330.32–0.450.32–0.460.28–0.360.28–0.36
Lemnisci length0.48–0.95 0.59–1.230.74–1.321.16–1.700.96–1.440.72–1.440.80–1.420.80–1.42
Proboscis receptacle length 0.41–0.710.58–0.910.65–0.90 0.88–1.100.96–1.120.88–1.120.69–0.95 0.69–0.95
Proboscis receptacle width0.25–0.300.25–0.450.19–0.350.31–0.530.21–0.320.24–0.320.27–0.350.27–0.35
Size of the anterior testis0.45–0.80 N/A0.47–0.79N/A0.56–0.68 N/A0.51–0.95N/A
× 0.40–0.62× 0.31–0.53 × 0.40–0.48× 0.29–0.58
Size of the posterior testis0.45–0.74 N/A0.54–0.72N/A0.52–0.72 N/A0.51–0.95N/A
× 0.37–0.65× 0.28–0.50× 0.48–0.51× 0.29–0.58
Cement-gland length0.76–1.46 N/AN/AN/A0.77–1.51N/A
Size of the copulatory bursa0.40–0.46 N/AN/AN/AN/A
× 0.46–0.84
Uterine bell lengthN/A0.34–0.62N/AN/A0.80–0.85N/A0.45–0.68
Uterus lengthN/A0.26–0.47N/AN/AN/A0.29–0.38
Size of the eggN/A0.06–0.09N/A0.08–0.09N/A0.06–0.09 N/A0.06–0.07
× 0.02–0.03× 0.02–0.03× 0.02–0.03× 0.02
Table 4. Annotations and gene organization of Pseudoacanthocephalus bufonis. The positive number in the “Gap or overlap” column indicates the length of intergenic sequence, and the negative number indicates the length (absolute number) that adjacent genes overlap (negative sign).
Table 4. Annotations and gene organization of Pseudoacanthocephalus bufonis. The positive number in the “Gap or overlap” column indicates the length of intergenic sequence, and the negative number indicates the length (absolute number) that adjacent genes overlap (negative sign).
GeneTypeStartEndLengthStart CodonStop CodonAnticodonGap or Overlap
cox1CDS115391539GTGTAG −2
trnGtRNA1538158952 UCC−11
trnQtRNA1579164163 UUG−13
trnYtRNA1629167951 GUA1
rrnLrRNA16812588908 0
trnL1tRNA2589263850 UAG0
nad6CDS26393063425GTGTA 4
trnDtRNA3068311144 GUC85
trnS2tRNA3197325357 UGA−22
atp3CDS32323771540ATATAA −1
nad3CDS37714118348ATGTAA 1
trnWtRNA4120417960 UCA0
NCR2Non-coding region41804682503 0
trnVtRNA4683474260 UAC−14
trnKtRNA4729479365 UUU−11
trnEtRNA4783483351 UUC5
trnTtRNA4839489456 UGU35
nad4lCDS49305172243GTGTAA 0
nad4CDS517363971225ATGT 1
trnHtRNA6399645355 GUG−6
nad5CDS644880671620GTGTAG 4
trnL2tRNA8072813362 UAA−23
trnPtRNA8111817363 UGG0
cytbCDS817492981125TTGTAA 1
nad1CDS930010,190891ATTTAA 47
trnItRNA10,23810,30568 GAU0
NCR1Non-coding region10,30610,915610 0
trnMtRNA10,91610,96954 CAU0
rrnSrRNA10,97011,541572 0
trnFtRNA11,54211,60564 GAA8
cox2CDS11,61412,216603TTGTAG −2
trnCtRNA12,21512,25642 GCA19
cox3CDS12,27612,978703GTGT 0
trnAtRNA12,97913,03254 UGC5
trnRtRNA13,03813,08952 UCG−20
trnNtRNA13,07013,12758 GUU−10
trnS1tRNA13,11813,17457 ACU−1
nad2CDS13,17514,055882GTGTAA 1
Table 5. Base composition and skewness of Pseudoacanthocephalus bufonis.
Table 5. Base composition and skewness of Pseudoacanthocephalus bufonis.
LocationA%T%C%G%AT%AT-SkewGC-SkewTotal
Whole mitochondrial genome34.3537.319.8731.7158.42−0.280.5314,056
Protein coding genes (PCGs)18.8838.079.2733.7856.95−0.452.6510,144
1st codon21.5830.129.5838.7251.70−0.183.043383
2nd codon13.0747.9710.6828.2861.05−0.901.653381
3rd codon21.9836.127.5434.3558.11−0.343.563380
tRNAs25.2037.4810.5026.8262.68−0.200.441238
rRNAs28.1835.5410.6125.6863.72−0.120.4263.72
rrnS27.9737.068.7426.2265.03−0.140.5065.03
rrnL28.3034.5811.7825.3362.89−0.100.3762.89
Non-coding region 128.3633.6119.3418.6961.97−0.08−0.02610
Non-coding region 226.6430.225.5737.5756.86−0.060.74503
Table 6. Relative synonymous codon usage (RSCU) of Pseudoacanthocephalus bufonis (The asterisk represents termination codon).
Table 6. Relative synonymous codon usage (RSCU) of Pseudoacanthocephalus bufonis (The asterisk represents termination codon).
CodonaaNo.%CodonaaNo.%
TAA*60.18TTALeu1835.44
TAG*30.09TTGLeu1885.58
GCAAla481.43AAALys341.01
GCCAla160.48AAGLys120.36
GCGAla200.59ATAMet862.55
GCTAla501.49ATGMet902.67
CGAArg100.30TTCPhe280.83
CGCArg30.09TTTPhe1865.52
CGGArg90.27CCAPro270.80
CGTArg180.53CCCPro140.42
AACAsn90.27CCGPro80.24
AATAsn491.46CCTPro230.68
GACAsp100.30AGASer361.07
GATAsp431.28AGCSer200.59
TGCCys160.48AGGSer1083.21
TGTCys601.78AGTSer551.63
CAAGln90.27TCASer200.59
CAGGln110.33TCCSer40.12
GAAGlu230.68TCGSer50.15
GAGGlu531.57TCTSer451.34
GGAGly361.07ACAThr180.53
GGCGly280.83ACCThr120.36
GGGGly3049.03ACGThr120.36
GGTGly1143.39ACTThr391.16
CACHis100.30TGATrp290.86
CATHis381.13TGGTrp1063.15
ATCIle190.56TACTyr230.68
ATTIle1293.83TATTyr1083.21
CTALeu351.04GTAVal1394.13
CTCLeu20.06GTCVal411.22
CTGLeu511.51GTGVal1765.23
CTTLeu551.63GTTVal2056.09
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Zhao, T.-Y.; Yang, R.-J.; Lü, L.; Ru, S.-S.; Wayland, M.T.; Chen, H.-X.; Li, Y.-H.; Li, L. Phylomitogenomic Analyses Provided Further Evidence for the Resurrection of the Family Pseudoacanthocephalidae (Acanthocephala: Echinorhynchida). Animals 2023, 13, 1256. https://doi.org/10.3390/ani13071256

AMA Style

Zhao T-Y, Yang R-J, Lü L, Ru S-S, Wayland MT, Chen H-X, Li Y-H, Li L. Phylomitogenomic Analyses Provided Further Evidence for the Resurrection of the Family Pseudoacanthocephalidae (Acanthocephala: Echinorhynchida). Animals. 2023; 13(7):1256. https://doi.org/10.3390/ani13071256

Chicago/Turabian Style

Zhao, Tian-You, Rui-Jia Yang, Liang Lü, Si-Si Ru, Matthew Thomas Wayland, Hui-Xia Chen, Yuan-Hao Li, and Liang Li. 2023. "Phylomitogenomic Analyses Provided Further Evidence for the Resurrection of the Family Pseudoacanthocephalidae (Acanthocephala: Echinorhynchida)" Animals 13, no. 7: 1256. https://doi.org/10.3390/ani13071256

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