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

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

Introduction

The Mesozoa is an historic name given to two different groups of very small, vermiform and morphologically simple parasitic animals: the Dicyemida (=Rhombozoa), whose adults are made up of approximately 40 cells (Furuya and Tsuneki, 2003); and the Orthonectida, which posses just a few hundred cells. As there is uncertainty over whether Dicyemida and Orthonectida form a monophyletic group, the Mesozoa grouping is now generally used informally rather than as a formal taxonomic assignment as a phylum. Both dicyemids and orthonectids are parasites of various marine animals: the dicyemids live in the renal tissue of cephalopods, whilst orthonectids occupy the internal body spaces of a variety of marine invertebrates, including brittle stars, bivalve molluscs, nemerteans and polychaetes.

Adults of both dicyemids and orthonectids have just two cell layers. Although they are multicellular, they lack defined complex tissues and organs and there is no evidence for the presence of true ectoderm or endoderm (Margulis and Chapman, 2009). Adult mesozoans have an external layer of multiciliated cells, which facilitate movement, and at least one reproductive cell. Analysis of the orthonectid Intoshia linei found evidence for a simple nervous system, comprising just 10–12 nerve cells, and a simple muscular system, composed of four longitudinal and 9–11 circular muscle cells (Slyusarev and Starunov, 2016).

In the 19th century, their simple body organization led to the idea that members of the Mesozoa – as their name suggests – were an evolutionary intermediate between the protozoans and the metazoans. More recent reassessment of mesozoan species indicates that they are in fact bilaterian metazoans that have undergone extreme simplification from a more complex ancestor (Dodson, 1956). In situ hybridizations for 16 diverse genes in different life stages of Dicyema japonicum suggested the presence of multiple different cell types, providing further support for the idea of a complex ancestor of Dicyemida, followed by extreme simplification of body organization (Ogino et al., 2011).

Two significant contributions for understanding the evolutionary history of the Mesozoa are the recent publication of the nuclear genome of Intoshia linei (Mikhailov et al., 2016), which represents one of approximately 20 species of this genus; and a transcriptome of Dicyema japonicum (Lu et al., 2017). The genomic sequence of I. linei is 43 Mbp in length and encodes just ~9000 genes, including those essential for the development and activity of muscular and nervous systems. Neither a phylogenomic analysis based on 500 orthologous groups nor an analysis of transcriptomic data from D. japonicum and a dataset compiled from 29 taxa and >300 gene orthologues, could confidently place the Orthonectida or Dicyemida in a precise position within the Lophotrochozoa. However, analysis by Lu et al. (2017) found strong statistical support for a grouping of the Dicyemida with the Orthonectida in the phylum Mesozoa. A new and taxonomically broader phylogenomic analysis, however, found Intoshia to be nested within the annelids (Schiffer et al., 2018). While the position of Dicyema within the Lophotrochozoa could not be unambiguously resolved, it seems clear that Orthonectids and Dicyemida/Rhombozoa are not joined in a single taxon. Nevertheless, both of these groups can be regarded as examples of the extreme morphological and genomic simplification often found in parasites.

One resource that has not been extensively investigated to study the evolution and biology of the mesozoans is their mitochondrial genomes. Interestingly, the limited mitochondrial data analysed from Dicyemida to date suggest a highly unusual mitochondrial gene structure. The three mitochondrial genes that have been sequenced from D. misakiense (cox1, 2 and 3) appear to be on individual mini-circles of DNA, rather than being part of a typical circular mitochondrial genome (Watanabe et al., 1999; Awata et al., 2005; Catalano et al., 2015). Although the vast majority of metazoan mitochondrial genomes are found as a single circular molecule, a few multipartite circular genomes (that is, genomes where mitochondrial genes are found on more than one closed-circle molecule) have been reported across the Bilateria. The majority of these appear to come from parasitic species and multipartite mitochondrial genomes have been described, for example, from several species of lice (Shao et al., 2005; Cameron et al., 2011; Dong et al., 2014) and parasitic nematodes (Hunt et al., 2016; Phillips et al., 2016). The Dicyemida could, therefore, represent another example of a parasitic organism with a multipartite mitochondrial genome.

Cox1 genes have been deposited in GenBank for a number of Dicyemida species, (D icyema koinonum; D icyema acuticephalum; D icyema vincentense; D icyema multimegalum; D icyema coffinense), but these have not been used in a published molecular systematic study.

In order to provide new mitochondrial gene data from these species, we looked for mitochondrial sequences in publicly available short read sequence data from members of the genus Dicyema (D. japonicum and Dicyema sp.) and Orthonectida (Intoshia linei). We compared features of the mitochondrial genome of I. linei to other metazoan members to shed additional light on its possible rapid and extreme simplification and used mitochondrial protein-coding gene data from Dicyema sp. and D. japonicum to investigate the internal phylogeny of the dicyemids.

Materials and methods

Genome and transcriptome assemblies

Genomic (I. linei: SRR4418796, SR4418797) and transcriptomic (Dicyema sp.: SRR827581; D. japonicum: DRR057371) data were downloaded from the NCBI short read archive. Adapter sequences and low-quality bases were removed from the sequencing reads using Trimmomatic (Bolger et al., 2014). The I. linei genome was re-assembled using the CLC assembly cell (v.5.0 https://www.qiagenbioinformatics.com/). The CLC assembly cell (v.5.0) and Trinity pipeline (Haas et al., 2013) (v.2.3.2) were used to assemble the Dicyema sp. and D. japonicum transcriptomes, with default settings.

Mitochondrial genome fragment identification and annotation

Mitochondrial protein-coding gene sequences from flatworms were used as tblastn queries to search for mitochondrial fragments in the I. linei genome assembly and Dicyema sp. and D. japonicum Trinity RNA-Seq assemblies, using NCBI translation table 5 ‘invertebrate mitochondrial’. Positively identified sequences were blasted against the NCBI nucleotide database in order to detect possible contaminant sequences from Dicyema host species. For each Dicyema sp. gene-bearing contig, a number of other contigs were found that had very high sequence similarity to Octopus or other cephalopods, indicating a degree of host species contamination in the RNA-Seq data. These sequences were discarded from the subsequent analysis.

A 14 176 bp mitochondrial contig was identified from initial blast queries against the reassembled I. linei genome. An additional mitochondrial contig was found that overlapped with this 14 176 bp contig to extend the mitochondrial sequence of I. linei to 14 247 bp long. This final contig was annotated using MITOS (Bernt et al., 2013). The locations of MITOS-predicted protein-coding genes were manually verified by aligning to orthologous protein-coding gene sequences taken from the published mitochondrial genomes of lophotrochozoan taxa. Where possible, the locations of protein-coding genes were inferred to start from the first in-frame start codon (ATN) and the C-terminal of the protein-coding genes inferred to be the first in-frame stop codon (TAA, TAG or TGA). Contigs from Dicyema sp. and D. japonicum identified as containing mitochondrial protein-coding genes were verified and annotated in the same way.

The secondary structure of tRNAs identified in the I. linei mitochondrial genome were inferred using the Mitfi program within MITOS. MITOS was also used to screen the Dicyema sp. and D. japonicum contigs which had been positively-identified as containing mitochondrial genes using blast. Using MITOS, we identified one reliable tRNA sequence for trnV on the same contig as cox3 from Dicyema sp. The secondary structure of this tRNA was also inferred using Mitfi in MITOS.

Dicyema internal phylogeny

cox1 nucleotide sequences from Dicyema sp. and D. japonicum were aligned to publicly available cox1 nucleotide sequences from other Dicyema species, and outgroup sequences from diverse lophotrochozoan taxa (see Supplementary Table S2). Sequences were aligned using Muscle v.3.8.31 (Edgar, 2004) visualized in Mesquite v.3.31 (http://mesquiteproject.org) and trimmed to remove uninformative residues with trimal v1.4.rev15. Maximum Likelihood inference was carried out for two trimmed alignments, one with all species, one with only the Dicyema species, using IQ-Tree (v.1.6.1) (Nguyen et al., 2015), letting the implemented model testing (ModelFinder (Kalyaanamoorthy et al., 2017)) pick the best-fitting phylogenetic model (TVM + I + G4 and TIM + F + I + G4, respectively), and performing 1000 bootstrap replicates (UFBoot (Hoang et al., 2018)). The trees were visualized using Seaview v.4.4.2 (Gouy et al., 2010) and annotated with Inkscape.

Data availability

All mitochondrial genome data presented in this study have been submitted to NCBI GenBank, under accession numbers: Intoshia linei mitochondrial genome sequence, MG839537; Dicyema sp. genes, MG839520-MG839528; D. japonicum genes, MG839529-MG839536.

Results

Intoshia linei mitochondrial genome composition

We assembled an I. linei mitochondrial genome sequence of 14 247 base pairs length but were unable to close the circular genome with paired-end reads. This could be attributed to the missing sequence being an AT-rich repetitive region, making it difficult to resolve. Furthermore, the I. linei mitochondrial genome we report is very AT-rich (83.40% AT).

Using MITOS and manual verification, we were able to predict the full reading frames of 12 protein-coding genes, 20 tRNAs and the small subunit rRNA (rrnS). No sequences resembling atp8, trnQ or trnR could be found in the final sequence. It is possible that rrnL is found between trnC and trnM based on a weak prediction using MITOS, but this could not be confirmed by aligning to known rrnL sequences. Genes in the I. linei mitochondrial genome are found in two blocks of opposing transcriptional polarity: those in the first 3104 base pairs are found on the reverse strand (trnK-trnV-trnT-trnY-nad4-trnS2-cox1-trnF); all other genes are found on the forward strand, where the forward strand is defined as that containing a greater portion of the protein-coding sequences (Fig. 1, Table 1). All protein-coding genes have standard initiation codons (ATA × 8; ATG × 1; and ATT × 3). Ten of the protein-coding genes have a standard termination codon (TAA). nad5 and nad6 appear to have a truncated stop codon (T--and TA-, respectively) (Table 1).

Fig. 1. Overview of the mitochondrial sequence resolved for Intoshia linei. Genes not drawn to scale. Numbers beneath the sequences show intergenic spaces (positive values) or intergenic overlap (negative values). Protein-coding genes are denoted by three letter abbreviations; ribosomal genes by four-letter abbreviations. tRNAs are shown by single uppercase letters (for recognized codons of L1, L2, S1 and S2 see Table 1). Genes found on the negative (reverse) strand are coloured green; genes found on the positive (forward) strand are coloured blue. The unreliable prediction for rrnS is shown in orange.

Table 1. Organization of the I. linei mitochondrial genome. Uncertain position of rrnL shown in brackets. Recognized codons for tRNAs L1, L2, S1 and S2 indicated in brackets

Protein-coding genes account for 70.9% of the 14 247 base pair long sequence (allowing for overlap between genes); tRNAs 8.13%; rRNAs (including the uncertain prediction for rrnL) 13.83%; and non-coding DNA 6.85%. Four regions of non-coding sequence greater than 100 base pairs are found in the I. linei genome: a 143 bp-long region between trnS2 and cox1; 230 bp between trnF and nad1 (where the two genes are found on opposite strands); 112 bp between trnW and nad3; and 112 bp following the nad5 at the end of the genomic sequence. There is very little overlap between coding sequences: rrnS and the best prediction for the trnM location overlap by 48 nucleotides, and there are eight incidences of overlap of coding sequences of fewer than 10 nucleotides across the sequence.

In total 20 out of 22 typical tRNAs were identified in the I. linei mitochondrial genome (see Supplementary Fig. S3). All predicted tRNAs have an amino-acyl acceptor stem composed of seven or eight base pairs and an anticodon stem composed of four or five base pairs, with the exception of trnA and trnV, which appear to have truncated acceptor stems. The structure of the DHU arm is, for the most part, consistent with standard tRNA secondary structure: 14 of the predicted tRNAs have a typical four or five base pair DHU stem; four tRNAs have a truncated or modified DHU arm (trnI, trnL1, trnL2 and trnP); and two tRNAs appear to have lost the DHU arm entirely (trnS1 and trnS2). More unusually, the TC arm in almost all of the predicted tRNAs is either truncated or replaced by a TV loop. The only tRNA found to have a ‘typical’ TC arm structure is trnS2.

Gene order

The protein-coding and rRNA gene order of I. linei was compared with a number of other metazoan taxa using CREx (Bernt et al., 2007). Our analysis included representatives from across the Lophotrochozoa, Ecdysozoa and Deuterostomia (see Supplementary Table S1). CREx analysis aims to identify common gene intervals between different mitochondrial genomes, and infer the reversals, transpositions and reverse transpositions required to obtain an observed gene order from the mitochondrial gene orders of other species.

Compared with the other taxa included for analysis, I. linei has a highly divergent mitochondrial gene order. The species with the most similar gene order was the carmine spider mite Tetranychus cinnabarinus (Arthropoda; Chelicerata) (Fig. 2). However, the similarity in gene order between these genomes is low, with the two sharing just four short gene ‘blocks’ and with a degree of variation in gene order even within these conserved regions. Of the lophotrochozoan species included for analysis, the species with the highest similarity to I. linei was found to be the nemertean Paranemertes peregrina (Fig. 2). Both species share the common arrangement of nad1-nad6-cob, and the adjacency of rrnL-rrnS-cox2-atp6 and nad4-nad5, but with variation in the order of these two blocks. Overall, conservation of gene order between I. linei and P. peregrina is very low given the number of possible shared gene boundaries. It is clear that the gene order of I. linei is novel and very divergent compared with other published metazoan mitochondrial genomes.

Fig. 2. Gene order comparison between the mitochondrial genomes of Intoshia linei, the chelicerate Teteranychus cinnabarinus and the nemertean Paranemertes peregrina, as analysed using CREx. Genes on the minus strand are denoted by a minus sign (-X). Conserved blocks of genes between I. linei and T. cinnabarinus are shown in orange (nad1), blue (nad6, cob), pink (nad3, rrnL), green (rrnS, cox2), yellow (nad4l, cox3) and red (nad2, nad5). Variation in gene order and translocation between strands is found within these blocks between the two species. Conserved blocks of genes between I. linei and P. peregrina are shown in grey (nad1, nad6, cob), purple (rrnL, rrnS, cox2, apt6) and light blue (nad4, nad5). As before, variation in gene order and translocation between strands is evident between these common intervals. For both comparisons, solid or dashed-line boxes show larger regions of the genomes that encompass the same genes, but with no conserved gene order.

Dicyema sp. and D. japonicum mitochondrial genes

Using BLAST and manual sequence verification of contigs assembled using Trinity (Haas et al., 2013) and the CLC assembly cell, we were able to identify nine reconstructed mitochondrial transcripts containing protein-coding genes from Dicyema sp. (cox1, 2, 3; cob; and nad1, 2, 3, 4 and 5). In D. japonicum we found contigs for eight mitochondrial transcripts of protein-coding genes (cox1, 2, 3; nad1, 3, 4 and 5; and cob). The identification of cob and nad3, nad4 and nad5 are novel for this taxon. All of the complete Dicyemida protein-coding genes identified have full initiation and termination codons, with the exception of D. japonicum nad1, which has a truncated TA stop codon.

All mitochondrial protein-coding genes found for Dicyema sp. and D. japonicum were located on individual contigs. In no instance were two or more protein-coding genes found on the same reconstructed transcript. However, each reconstructed mitochondrial transcript did contain non-coding sequence in addition to protein-coding gene sequence (Fig. 3). The length and location (5′ and/or 3′) of non-coding sequence in the reconstructed transcripts was variable between the two species and between genes (Fig. 3). For each protein-coding gene, we compared contigs assembled using both the CLC-assembler and Trinity in order to identify reconstructed mitochondrial transcripts with the longest stretch of protein-coding sequence. Of the 17 dicyemid genes we report, seven were derived from CLC-assembled contigs (cox1, 2, 3, nad3, 5 from D. japonicum and nad2, nad5 from Dicyema sp.) and ten from Trinity-assembled contigs (cob, nad1, 4 from D. japonicum and cox1, 2, 3, cob, nad1, 3, 4 from Dicyema sp.). The best reconstructed mitochondrial contig we identified for nad1 (Dicyema sp.) was found to contain duplicated stretches of the identical protein-coding gene sequence. We attribute this to an assembly artefact rather than speculating about this providing potential evidence for mitochondrial gene mini-circles. We also identified and corrected a frameshift in the coding sequence for nad2 from Dicyema sp. in the longest reconstructed mitochondrial contig from this species (Fig. 3).

Fig. 3. Overview of the reconstructed mitochondrial transcripts of protein-coding genes found in Dicyema japonicum and Dicyema sp. Transcripts are not to scale. Regions coloured blue indicate protein-coding sequence; regions coloured white indicate non-coding sequence. Numbers under each transcript correspond to the length of each respective coding or non-coding region, in base pairs. For cox3 in Dicyema sp. the location of the putative trnV sequence is shown in green (nucleotides 1130–1200). For nad2 in Dicyema sp., the location of a frameshift at position 463 in the longest coding sequence assembly is denoted by an asterisk (*).

By screening the Dicyema sp. gene-containing contigs with MITOS standalone software, we were able to predict one reliable tRNA sequence for trnV adjacent to cox3 (Fig. 3). Dicyema sp. trnV has an eight base pair acceptor stem; a five base pair anti-codon stem; and a four base pair DHU stem (Supplementary Information S3). As was found in I. linei, the TC arm appears to be modified from a standard ‘cloverleaf’ structure. In no other cases did we find any sequence from more than one gene on a single contig.

Dicyemida internal phylogeny using cox1

Cox1 is commonly used as a species ‘barcoding’ gene and can be used in phylogenetic inference to discriminate between closely related species (Hebert et al., 2003). Given that a number of cox1 genes have been sequenced from different Dicyemida species, we used publicly available cox1 sequences along with the two new cox1 sequences found in this study for phylogenetic inference to determine the relationship of Dicyema sp. and D. japonicum to other dicyemids. After aligning the cox1 nucleotide sequences from dicyemids to other metazoans, we found that all Dicyemida cox1 sequences had several conserved deletions, not present in other metazoan cox1 sequences included in our alignment (Fig. 4). These comprise in-frame deletions of two, five, four and two amino acids moving from the N-terminus to the C-terminus of the protein. These deletions appear to be unique to members of the Dicyemida and were present in all Dicyemida species included in the alignment.

Fig. 4. Conserved deletions in the amino acid sequence of cox1 taken from publicly available dicyemid sequences (D. vincentense, D. multimegalum, D. coffinense, D. furuyi, D. misakiense, D. koinonum, D. papuceum) and the Dicyema species presented in this analysis (D. japonicum and Dicyema sp.), in alignment with other lophotrochozoan cox1 sequences. The location of the deletions (two amino acids; five amino acids; four amino acids and two amino acids) moving from the N-terminus to the C-terminus of the protein, are shown by red stars. Colours in the alignment correspond to amino acid colours as used by Mesquite v.3.31.

Maximum likelihood phylogenetic analysis was carried out using cox1 sequences from publicly available Dicyema species; the D. japonicum and Dicyema sp. cox1 sequences assembled in this study; and cox1 sequences from a diverse representation of lophotrochozoans as outgroup taxa (Supplementary Table S2). As anticipated, the dicyemids included in analysis form their own branch on the tree. The topology of the subtree containing the Dicyemida species and the unrooted tree inferred from Dicyemida sequences alone is identical (Fig. 5). The analyses found a close affinity between D. japonicum with D. misakiense, with 97% bootstrap support at this node. At the nucleotide level, sequences from D. japonicum and D. misakiense are ~98% identical. The remaining Dicyema species branch into four groups, with the Dicyema sp. sequence from our analysis being an outgroup to the other six species. As found for D. japonicum and D. misakiense, the cox1 sequences from D. multimegalum and D. coffinense are ~98% identical at the nucleotide level (Fig. 5).

Fig. 5. Phylogenetic analysis of cox1 genes from dicyemids using Maximum Likelihood (IQ-Tree), including the two Dicyema species presented in this analysis (Dicyema sp. and D. japonicum). Cox1 sequences from diverse lophotrochozoan taxa included as outgroups (see Supplementary Fig. S4 for a tree based on the Dicyema species alone). Bootstrap support is shown at relevant nodes. Phylogenetic inference shows a split of dicyemid species into two groups, one containing D. japonicum and D. misakiense (green box) and the other containing all other dicyemid species included in analysis (pink box). Within the second group, Dicyema sp. is found on a separate branch from the rest of the included dicyemids. Very short branch lengths between both D. coffinense and D. multimegalum and D. japonicum and D. misakiense, indicate that they are very closely related or could be identical species (dashed-line boxes).

Discussion

Although the mitochondrial genome we found from I. linei is not a closed circular molecule, this represents the first mitochondrial genome from an orthonectid species and includes 12 protein-coding genes, 20 tRNAs and (possibly) both ribosomal RNAs. Atp8 was not found, but this gene has been lost from the mitochondrial genomes of taxa in many different metazoan lineages (Boore, 1999) and so its absence from our assembly may be real rather than representing missing data. Compared with the drastically reduced I. linei nuclear genome, its mitochondrial genome has a gene complement that is fairly standard across the Metazoa (Mikhailov et al., 2016). Genes in the I. linei mitochondrial genome are clustered into two blocks of opposite transcriptional polarity. The block comprising trnK-trnV-trnT-trnY-nad4-trnS2-cox1-trnF at the ‘start’ of the sequence is found on the negative strand, whilst all other genes are transcribed from the positive strand, suggesting an inversion event (Fig. 1).

The ~84% A + T content found in the I. linei mitochondrial genome is high compared with other invertebrate mitochondrial genomes – for example, the chelicerate Limulus polyphemus (A + T content = 67.6%) (Lavrov et al., 2000) and the annelid Lumbricus terrestris (A + T content = 61.6%) (Boore and Brown, 1995). The very high A + T content of the mitochondrial genome is even higher than the high A + T content of the I. linei nuclear genome (73%), and provides evidence for the very fast rate of mitochondrial evolution in this species.

The small proportion of non-coding mtDNA we found for I. linei is typical of mitochondrial genomes. Although there is very little gene overlap in the sequence found for I. linei, the sequence for trnM is predicted with significant overlap with rrnS. Whilst it is possible that this is a mis-prediction, large gene overlaps have been reported in other mitochondrial genomes and this overlap could result from selection to minimize mitochondrial genome size (Robertson et al., 2017).

Mitochondrial gene order can be a useful tool for inferring phylogenetic relationships. Gene order in the mitochondrial genomes of different lineages are largely stable, with the rearrangement of protein-coding genes occurring relatively infrequently. Where rearrangement events do occur, they are thought to be a result of tandem duplications and multiple random deletions. In this model, a portion of the mitochondrial genome is erroneously duplicated, and the subsequent random loss of one copy of a gene (by deletion or the accumulation of mutations) results in a novel gene order (Boore, 2000). Comparing mitochondrial gene order between different taxa has been informative not only for the study of larger-scale evolutionary lineages (Boore et al., 1998) but also for understanding the phylogeny of, for example, parasitic flatworms (Le et al., 2000; Liu et al., 2013).

Our analysis demonstrated that I. linei has a highly divergent mitochondrial gene order in comparison with other published metazoan mitochondrial genomes. Of the species included – chosen as a broad representation of different metazoan lineages (see Supplementary Table S1) – the closest similarity was found to be to the chelicerate T. cinnabarinus (Fig. 2). However, of the highest possible conserved gene order score of 204 (that is, when two mitochondrial genomes have identical gene orders for the 12 protein-coding genes included for analysis (atp8 is not present in I. linei) and two rRNAs included in the CREx matrix calculation), similarity of gene order between I. linei and T. cinnabarinus was still poor, with a score of just 32. In light of the proposed affinity of I. linei to the Lophotrochozoa, the highest-scoring similarity to the lophotrochozoan species included in the analysis was with the nemertean P. peregrina. Again, these two species share comparatively little gene order conservation: just three common gene blocks were identified, one of which (rrnL-rrnS-cox2-atp6) has further rearrangement therein (Fig. 2). Of the common intervals identified, the block of nad1-nad6-cob is conserved between I. linei and P. peregrina and it is possible that this arrangement is plesiomorphic within the Lophotrochozoa.

Interestingly, previous analysis of five mitochondrial genomes from early branching annelids found that gene order was highly variable between these species (Weigert et al., 2016). Other studies of various lophotrochozoan mitochondrial genomes – including Brachiopoda (Lingula anatina) (Luo et al., 2015); various Schistosoma species (Webster and Littlewood, 2012); and nemerteans (Podsiadlowski et al., 2009) – also indicate that extensive gene order rearrangements have occurred in different lophotrochozoan lineages. It is possible that the divergent gene order in I. linei can be associated with the parasitic lifestyle and rapid rate of evolution seen for this species: studies in a number of other parasitic taxa indicate that an accelerated rate of gene rearrangement in mitochondrial genomes could be associated with this lifestyle. For example, various Schistosoma species have mitochondrial genomes with a unique gene order (Le et al., 2000) and this has also been observed in the ectoparasitic louse Heterodoxus macropus (Shao et al., 2001), various species of mosquito (Beard et al., 1993) and parasitic hymenopterans (Dowton and Austin, 1999), amongst others.

All of the tRNAs predicted from I. linei and the one tRNA found in Dicyema sp. have deviations from the ‘standard’ secondary structure of the TC arm (Supplementary Information S3). Although it is unusual amongst typical metazoan mitochondrial genomes to have such consistent modifications to one element of the tRNA cloverleaf structure, a great deal of variation can be found in tRNA structures across the Metazoa. Mitochondrial genomes with almost all tRNAs lacking either the TC arm or DHU arm – termed ‘minimal functional tRNAs’ – have been reported in a number of different lineages. In nematodes, analysis of tRNAs with TV loops in place of a TC arm suggests that an ‘L-shaped’ tRNA, analogous to a typical cloverleaf-structure tRNA – can maintain normal tertiary interactions and remain functional. Furthermore, it is likely that the tRNAs reported in this analysis are functional, as the acceptor stems and anti-codon stems are, for the most part, complete, and it is highly likely that they would have accumulated mutations should they have lost functionality. Instead, the reduction we observe in tRNA secondary structure could be a result of selective pressure to reduce the TC arm and provide another example of minimally functional tRNAs, in addition to those already found across the Metazoa.

Previous analyses had suggested that mitochondrial genes (cox1, cox2 and cox3) in dicyemids are found on individual mini-circles in somatic cells, as opposed to being located on a larger circular mitochondrial genome (Watanabe et al., 1999; Catalano et al., 2015). Mitochondrial mini-circles – although rare across the Metazoa – do appear to be most prevalent in parasitic species. A number of studies have reported the presence of mini-circle mitochondrial genomes, fragmented to various degrees, in a number of lice and nematode species (Shao et al., 2009; Cameron et al., 2011; Dong et al., 2014; Hunt et al., 2016; Phillips et al., 2016).

We identified a mitochondrial contig for nad1 in Dicyema sp. that contained repeated nad1 protein-coding sequence. This could be an assembly artefact resulting from sequencing a circular nad1 molecule, but the question of the presence of mini-circles remains unresolved in our analysis. Further investigating the validity of mitochondrial mini-circles was outside of the scope of the present study, but future approaches involving long-range polymerase chain reaction or long-read sequencing should be conducted to resolve this question.

All dicyemid cox1 sequences were found to have a series of four in-frame deletions within a region of the gene that was well-aligned with cox1 sequences taken from other invertebrate species (Fig. 4). Insertions and deletions (indels) in genes are rare genomic changes that can be used to infer common evolutionary history (Belinky et al., 2010), but this set of conserved deletions are so far known only from the Dicyema genus. No such deletions are found in the I. linei cox1 gene, or in the same protein-coding sequence taken from across the Lophotrochozoa.

The internal phylogeny of dicyemids was inferred using Maximum Likelihood reconstruction based on cox1 gene sequences. Based on our analysis it is possible that D. coffinense and D. multimegalum are the same species, with both dicyemids isolated from Australian Sepia species (Catalano, 2013) and with a greater than 98% sequence similarity at the nucleotide sequence level. Our analysis also found a very close affinity for D. japonicum with D. misakiense, with 97% bootstrap support. As found for D. coffinense and D. multimegalum these cox1 sequences are >98% identical at the nucleotide level and it is thus likely that they are very closely related or the same species, both found in octopus living in the North West Pacific off the coast of Honshu Island, Japan. The Dicyema sp., despite being isolated from Sepia living off the coast of Florida, is a close sister to D. coffinense and D. multimegalum based on the similarities of the cox 1 assembled in this analysis, hinting at long-range dispersal with the host species. Further investigation into dicyemid members isolated from hosts in other geographical locations could help to inform whether the phylogenetic structure of the parasitic dicyemids is reflective of dispersal of the host octopus (Tobias et al., 2017).

Supplementary material

The supplementary material for this article can be found at https://doi.org/10.1017/pao.2018.12.

Acknowledgements

We thank members of the Telford and Oliveri labs at UCL for helpful comments on the analyses and manuscript.

Financial support

The research was funded by a European Research Council grant (ERC-2012-AdG 322790) to MJT.

Conflicts of interest

None.

Ethical standards

Not applicable.

References

Awata, H, Noto, T and Endoh, H (2005) Differentiation of somatic mitochondria and the structural changes in mtDNA during development of the dicyemid Dicyema japonicum (Mesozoa). Molecular Genetics and Genomics 273, 441449.
Beard, CB, Hamm, DM and Collins, FH (1993) The mitochondrial genome of the mosquito Anopheles gambiae: DNA sequence, genome organization, and comparisons with mitochondrial sequences of other insects. Insect Molecular Biology 2, 103124.
Belinky, F, Cohen, O and Huchon, D (2010) Large-scale parsimony analysis of metazoan indels in protein-coding genes. Molecular Biology and Evolution 27, 441451.
Bernt, M, Merkle, D, Ramsch, K, Fritzsch, G, Perseke, M, Bernhard, D, Schlegel, M, Stadler, PF and Middendorf, M (2007) CREx: inferring genomic rearrangements based on common intervals. Bioinformatics (Oxford, England) 23, 29572958.
Bernt, M, Donath, A, Jühling, F, Externbrink, F, Florentz, C, Fritzsch, G, Pütz, J, Middendorf, M and Stadler, PF (2013) MITOS: improved de novo metazoan mitochondrial genome annotation. Molecular Phylogenetics and Evolution 69, 313319.
Bolger, AM, Lohse, M and Usadel, B (2014) Trimmomatic: a flexible trimmer for illumina sequence data. Bioinformatics (Oxford, England) 30, 21142120.
Boore, JL (1999) Animal mitochondrial genomes. Nucleic Acids Research 27, 17671780.
Boore, JL (2000) The duplication/random loss model for gene rearrangement exemplified by mitochondrial genomes of deuterostome animals. In Sankoff, D and Nadeau, JH (eds), Comparative Genomics: Empirical and Analytical Approaches to Gene Order Dynamics, Map Alignment and the Evolution of Gene Families, Netherlands, Dordrecht: Springer, pp. 133147.
Boore, JL and Brown, WM (1995) Complete sequence of the mitochondrial DNA of the annelid worm Lumbricus terrestris. Genetic 141, 305319.
Boore, JL, Lavrov, DV and Brown, WM (1998) Gene translocation links insects and crustaceans. Nature 392, 667668.
Cameron, SL, Yoshizawa, K, Mizukoshi, A, Whiting, MF and Johnson, KP (2011) Mitochondrial genome deletions and minicircles are common in lice (Insecta: Phthiraptera). BMC Genomics 12, 394394.
Catalano, SR (2013) Five new species of dicyemid mesozoans (Dicyemida: Dicyemidae) from two Australian cuttlefish species, with comments on dicyemid fauna composition. Systematic Parasitology 86, 125151.
Catalano, SR, Whittington, ID, Donnellan, SC, Bertozzi, T and Gillanders, BM (2015) First comparative insight into the architecture of COI mitochondrial minicircle molecules of dicyemids reveals marked inter-species variation. Parasitology 142, 10661079.
Dodson, EO (1956) A note on the systematic position of the Mesozoa. Systematic Zoology 5, 3740.
Dong, W-G, Song, S, Guo, X-G, Jin, D-C, Yang, Q, Barker, SC and Shao, R (2014) Fragmented mitochondrial genomes are present in both major clades of the blood-sucking lice (suborder Anoplura): evidence from two Hoplopleura rodent lice (family Hoplopleuridae). BMC Genomics 15, 751.
Dowton, M and Austin, AD (1999) Evolutionary dynamics of a mitochondrial rearrangement ‘hotspot’ in the Hymenoptera. Molecular Biology and Evolution 16, 298309.
Edgar, RC (2004) MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Research 32, 17921797.
Furuya, H and Tsuneki, K (2003) Biology of dicyemid mesozoans. Zoological Science 20, 519532.
Gouy, M, Guindon, S and Gascuel, O (2010) Seaview version 4: a multiplatform graphical user interface for sequence alignment and phylogenetic tree building. Molecular Biology and Evolution 27, 221224.
Haas, BJ, Papanicolaou, A, Yassour, M, Grabherr, M, Blood, PD and Bowden, J (2013) De novo transcript sequence reconstruction from RNA-seq using the trinity platform for reference generation and analysis. Nature Protocols 8, 14941512.
Hebert, PDN, Ratnasingham, S and deWaard, JR (2003) Barcoding animal life: cytochrome c oxidase subunit 1 divergences among closely related species. Proceedings of the Royal Society B: Biological Sciences 270, S96S99.
Hoang, DT, Chernomor, O, von Haeseler, A, Minh, BQ and Vinh, LS (2018) UFBoot2: improving the ultrafast bootstrap approximation. Molecular Biology and Evolution 35, 518522.
Hunt, VL, Tsai, IJ, Coghlan, A, Reid, AJ, Holroyd, N, Foth, BJ, Tracey, A, Cotton, JA, Stanley, EJ, Beasley, H, Bennett, HM, Brooks, K, Harsha, B, Kajitani, R, Kulkarni, A, Harbecke, D, Nagayasu, E, Nichol, S, Ogura, Y, Quail, MA, Randle, N, Xia, D, Brattig, NW, Soblik, H, Ribeiro, DM, Sanchez-Flores, A, Hayashi, T, Itoh, T, Denver, DR, Grant, W, Stoltzfus, JD, Lok, JB, Murayama, H, Wastling, J, Streit, A, Kikuchi, T, Viney, M and Berriman, M (2016) The genomic basis of parasitism in the Strongyloides clade of nematodes. Nature Genetics 48, 299307.
Kalyaanamoorthy, S, Minh, BQ, Wong, TKF, von Haeseler, A and Jermiin, LS (2017) Modelfinder: fast model selection for accurate phylogenetic estimates. Nature Methods 14, 587.
Lavrov, DV, Boore, JL and Brown, WM (2000) The complete mitochondrial DNA sequence of the horseshoe crab Limulus polyphemus. Molecular Biology and Evolution 17, 813824.
Le, TH, Blair, D, Agatsuma, T, Humair, P-F, Campbell, NJH, Iwagami, M, Littlewood, DTJ, Peacock, B, Johnston, DA, Bartley, J, Rollinson, D, Herniou, EA, Zarlenga, DS and McManus, DP (2000) Phylogenies inferred from mitochondrial gene orders—A cautionary tale from the parasitic flatworms. Molecular Biology and Evolution 17, 11231125.
Liu, G-H, Shao, R, Li, D-H, Li, H and Zhu, X-Q (2013) The complete mitochondrial genomes of three parasitic nematodes of birds: a unique gene order and insights into nematode phylogeny. BMC Genomics 14, 414.
Lu, T-M, Kanda, M, Satoh, N and Furuya, H (2017) The phylogenetic position of dicyemid mesozoans offers insights into spiralian evolution. Zoological Letters 3, 6.
Luo, Y-J, Satoh, N and Endo, K (2015) Mitochondrial gene order variation in the brachiopod Lingula anatina and its implications for mitochondrial evolution in lophotrochozoans. Marine Genomics 24, Part 1, 3140.
Margulis, L and Chapman, MJ (2009) Chapter three – Animalia. In Kingdoms and Domains. London: Academic Press, pp. 231377.
Mikhailov, KV, Slyusarev, GS, Nikitin, MA, Logacheva, MD, Penin, AA and Aleoshin, VV (2016) The genome of Intoshia linei affirms orthonectids as highly simplified spiralians. Current Biology 26, 17681774.
Nguyen, L-T, Schmidt, HA, von Haeseler, A and Minh, BQ (2015) IQ-TREE: a fast and effective stochastic algorithm for estimating Maximum-likelihood phylogenies. Molecular Biology and Evolution 32, 268274.
Ogino, K, Tsuneki, K and Furuya, H (2011) Distinction of cell types in Dicyema japonicum (phylum Dicyemida) by expression patterns of 16 genes. Journal of Parasitology 97, 596601.
Phillips, WS, Brown, AMV, Howe, DK, Peetz, AB, Blok, VC, Denver, DR and Zasada, IA (2016) The mitochondrial genome of Globodera ellingtonae is composed of two circles with segregated gene content and differential copy numbers. BMC Genomics 17, 706.
Podsiadlowski, L, Braband, A, Struck, TH, von Döhren, J and Bartolomaeus, T (2009) Phylogeny and mitochondrial gene order variation in Lophotrochozoa in the light of new mitogenomic data from Nemertea. BMC Genomics 10, 364.
Robertson, HE, Lapraz, F, Egger, B, Telford, MJ and Schiffer, PH (2017) The mitochondrial genomes of the acoelomorph worms Paratomella rubra, Isodiametra pulchra and Archaphanostoma ylvae. Scientific Reports 7, 1847.
Schiffer, P, Robertson, H and Telford, MJ (2018) Orthonectids are highly degenerate annelid worms. Current Biology 28, 19701974.
Shao, R, Campbell, NJH and Barker, SC (2001) Numerous gene rearrangements in the mitochondrial genome of the Wallaby Louse, Heterodoxus macropus (Phthiraptera). Molecular Biology and Evolution 18, 858865.
Shao, R, Barker, SC, Mitani, H, Aoki, Y and Fukunaga, M (2005) Evolution of duplicate control regions in the mitochondrial genomes of Metazoa: a case study with Australian Ixodes ticks. Molecular Biology and Evolution 22, 620629.
Shao, R, Kirkness, EF and Barker, SC (2009) The single mitochondrial chromosome typical of animals has evolved into 18 minichromosomes in the human body louse, Pediculus humanus. Genome Research 19, 904912.
Slyusarev, GS and Starunov, VV (2016) The structure of the muscular and nervous systems of the female Intoshia linei (Orthonectida). Organisms Diversity & Evolution 16, 6571.
Tobias, ZJC, Yadav, AK, Schmidt-Rhaesa, A and Poulin, R (2017) Intra- and interspecific genetic diversity of New Zealand hairworms (Nematomorpha). Parasitology 144, 10261040.
Watanabe, KI, Bessho, Y, Kawasaki, M and Hori, H (1999) Mitochondrial genes are found on minicircle DNA molecules in the mesozoan animal Dicyema. Journal of Molecular Biology 286, 645650.
Webster, BL and Littlewood, DTJ (2012) Mitochondrial gene order change in Schistosoma (Platyhelminthes: Digenea: Schistosomatidae). International Journal for Parasitology 42, 313321.
Weigert, A, Golombek, A, Gerth, M, Schwarz, F, Struck, TH and Bleidorn, C (2016) Evolution of mitochondrial gene order in Annelida. Molecular Phylogenetics and Evolution 94, 196206.