Skip to main content

Basal position of two new complete mitochondrial genomes of parasitic Cymothoida (Crustacea: Isopoda) challenges the monophyly of the suborder and phylogeny of the entire order



Isopoda is a highly diverse order of crustaceans with more than 10,300 species, many of which are parasitic. Taxonomy and phylogeny within the order, especially those of the suborder Cymothoida Wägele, 1989, are still debated. Mitochondrial (mt) genomes are a useful tool for phylogenetic studies, but their availability for isopods is very limited. To explore these phylogenetic controversies on the mt genomic level and study the mt genome evolution in Isopoda, we sequenced mt genomes of two parasitic isopods, Tachaea chinensis Thielemann, 1910 and Ichthyoxenos japonensis Richardson, 1913, belonging to the suborder Cymothoida, and conducted comparative and phylogenetic mt genomic analyses across Isopoda.


The complete mt genomes of T. chinensis and I. japonensis were 14,616 bp and 15,440 bp in size, respectively, with the A+T content higher than in other isopods (72.7 and 72.8%, respectively). Both genomes code for 13 protein-coding genes, 21 transfer RNA genes (tRNAs), 2 ribosomal RNA genes (rRNAs), and possess a control region (CR). Both are missing a gene from the complete tRNA set: T. chinensis lacks trnS1 and I. japonensis lacks trnI. Both possess unique gene orders among isopods. Within the CR of I. japonensis (284 bp), we identified a repetitive region with four tandem repeats. Phylogenetic analysis based on concatenated nucleotide sequences of 13 protein-coding genes showed that the two parasitic cymothoids clustered together and formed a basal clade within Isopoda. However, another parasitic cymothoid, Gyge ovalis Shiino, 1939, formed a sister group with the suborder Limnoriidea Brandt & Poore in Poore, 2002, whereas two free-living cymothoid species were located in the derived part of the phylogram: Bathynomus sp. formed a sister group with the suborder Sphaeromatidea Wägele, 1989, and Eurydice pulchra Leach, 1815 with a clade including Bathynomus sp., Sphaeromatidea and Valvifera G. O. Sars, 1883.


Our results did not recover the suborders Cymothoida and Oniscidea Latreille, 1802 as monophyletic, with parasitic and free-living cymothoidans forming separate clades. Furthermore, two parasitic cymothoidans formed the sister-clade to all other isopods, separated from Epicaridea Latreille, 1825, which challenges currently prevalent isopod phylogeny. Additional mt genomes of parasitic and free-living isopods might confer a sufficient phylogenetic resolution to enable us to resolve their relationships, and ultimately allow us to better understand the evolutionary history of the entire isopod order.


Within Crustacea, the isopods form a diverse group (10,300 species) [1] comprising 11 recognized suborders [2]. They are common around the globe, with habitats ranging from deep seas to mountains, even including arid deserts [3, 4]. Species of the suborder Cymothoida Wägele, 1989 inhabits both freshwater and marine habitats (most diverse in the tropics), and includes mobile predators, scavengers and all isopods parasitizing on fishes and other crustaceans [5, 6]. Among other orders relevant for this study, members of the Valvifera G. O. Sars, 1883 and Sphaeromatidea Wägele, 1989 are benthic, and most species are detritivores [5]. Species of the Asellota Latreille, 1802, which occur both in freshwater and marine habitats, are the predominant deep-sea isopod taxon [7]. Species of the Limnoriidea Brandt & Poore in Poore, 2002 are herbivores, with the largest family, the Limnoriidae White, 1850, comprising predominately tropical borers feeding on wood [5, 7]. The Oniscidea Latreille, 1802 contains most of the terrestrial isopod species [8]. The classification of the Isopoda has been continuously studied and revised over the years; for example, the former suborder Flabellifera Sars, 1882 has been divided into two suborders, the Cymothoida and the Sphaeromatidea, but the Isopoda remains poorly resolved [4, 9]. A majority of morphology-based studies have agreed that the Phreatoicidea Stebbing, 1893, Asellota and Oniscidea are the basal isopod groups, whereas the Cymothoida is generally regarded as the most derived group [8, 10,11,12,13,14,15,16]. However, some analyses, based on nuclear (18S) and mitochondrial datasets [17, 18], resolved the Phreatoicidea as a derived clade, rather than a basal one, whereas parasitic Cymothoida comprised the basal branch. Monophyly of parasitic Cymothoida was also questioned by some morphological evidence [19]. In addition, the phylogenetic position of the infraorder Epicaridea Latreille, 1825 within the Cymothoida (and Isopoda) is controversial [5, 10, 16, 20]. Therefore, although the phylogenetic relationships within the Cymothoida have been revised [21] and discussed extensively, they remain far from resolved.

Parasitic isopods were traditionally assigned to three superfamilies, the Bopyroidea Rafinesque, 1815, the Cryptoniscoidea Kossmann, 1880 and the Cymothooidea Leach, 1814 [6]. The Cymothooidea includes ten families [2], which exhibit a progressive gradient from commensal predation and micropredation towards parasitism, culminating with the Cymothoidae Leach, 1818, with all species being obligatory parasites of fishes [3,4,5]. Due to problems in data collection and species identification, as well as the paucity of studies and specialists for this taxon, the large family Cymothoidae is still widely regarded as taxonomically the least understood and the most ‘troublesome’ isopod group [4, 22]. Studies of phylogenetic relationships within the Cymothoidae have been conducted using morphological [22, 23], zoogeographical [4, 22, 24], and ecological data, such as the host species [4, 6, 25] and site of attachment on the host [4, 22, 26]. However, relationships within the Cymothoidae are still not resolved, especially in relation to the question of the evolution of parasitic life-styles [4].

Incomplete or brief morphological descriptions available for some isopod species may result in synonymies; for example, a study of ten recognized species of Ichthyoxenos Herklots, 1870 in China concluded that they should all be synonymized with I. japonensis Richardson, 1913 [27]. Therefore, the taxonomy of this genus and its relationships to other similar genera (e.g. Elthusa Schioedte & Meinert, 1884 and Mothocya Costa, in Hope, 1851) remain poorly resolved [28, 29]. In conclusion, more molecular data and a comprehensive revision are urgently needed to resolve classification and identification of species belonging to Ichthyoxenos.

The use of complete mitochondrial (mt) genomes is becoming increasingly important for phylogenetic reconstruction [30,31,32,33]. Nucleotide and amino acid sequences, strand-specific nucleotide bias [30], tRNA secondary structures [34], as well as gene rearrangements [30] have been used for phylogenetic inference. In contrast to the 269 complete crustacean mt genomes currently (March 2018) available on GenBank, the number of complete isopod mt genomes appears strikingly small: Bathynomus sp. [35], Eophreatoicus sp. [36], Gyge ovalis Shiino, 1939 [37], Ligia oceanica Linnaeus, 1767 [38] and Limnoria quadripunctata Holthuis, 1949 [39]. Along with these five, ten incomplete (verified) mt genomes are also currently available (March 2018).

As parasitic isopods were not represented on GenBank when we began this study (the first mitogenome of a parasitic isopod, G. ovalis [37], was published as we were finishing writing the paper), the aim of our study was to sequence the complete mitogenomes of two parasitic isopods belonging to two different cymothoid families: Tachaea chinensis Thielmann, 1910 (Corallanidae), an ectoparasite that attaches to the ventral thoracic region of many freshwater shrimp species [40, 41], and Ichthyoxenos japonensis Richardson, 1913 (Cymothoidae) that parasitises the body cavity of freshwater fish [27, 42,43,44,45]. As the family Corallanidae Hansen, 1890 is generally regarded as a sister group to all remaining parasitic taxa within the suborder Cymothoida [5, 11, 25, 46, 47], the availability of these two mt genomes might help resolve questions of the identity of the basal isopod group and the monophyly of the suborder Cymothoida.


Sample collection and identification

Tachaea chinensis was collected from the body surface of a freshwater shrimp (Macrobrachium sp.) obtained from a fish market in Wuhan, China. Ichthyoxenos japonensis was collected from the body cavity of a goldfish (Carassius auratus) obtained in the Baihe River, Nanyang, China. Ichthyoxenos japonensis was morphologically identified according to the available literature [43, 48]; T. chinensis was identified according to the morphological traits [49], and its identity verified using the complete 16S rDNA sequence (Additional file 1: Figure S1). Total genomic DNA was extracted from a single specimen using SDS/Proteinase K using TIANamp Genomic DNA kit (Tiangen Biotech, Beijing, China) following the manufacturer’s protocol. Voucher specimens for both species (T. chinensis and I. japonensis) are permanently stored in absolute ethanol under accession numbers IHB20160505001 and IHB20150714001, respectively, in the Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China. Photographs of T. chinensis and I. japonensis are provided in Additional file 2: Figure S2 and Additional file 3: Figure S3, respectively.

Mt genome amplification and sequencing

We designed primers (Additional file 4: Table S1) according to conserved regions of mitochondrial genes in other available isopod mitogenomes, and then used these (amplified and sequenced) fragments to design specific primers for amplification of the complete mt genomes (Additional file 4: Table S1). PCR reactions were conducted in a 20 μl reaction mixture, containing 7.4 μl double-distilled water, 10 μl 2× PCR buffer (Mg2+, dNTP plus; Takara, Dalian, China), 0.6 μl of each primer, 0.4 μl rTaq polymerase (250 U, Takara) and 1 μl DNA template. Amplification was performed under the following conditions: initial denaturation at 98 °C for 2 min; followed by 40 cycles at 98 °C for 10 s, 48–60 °C for 15 s, 68 °C for 1 min/kb; and a final extension at 68 °C for 10 min. PCR products were sequenced (Sanger) bidirectionally at Sangon Company (Shanghai, China).

Mt genome assembly, annotation and analysis

The complete mt sequences were assembled manually and aligned against other published mt genome sequences of isopods using the program MAFFT 7.149 [50] to determine the gene boundaries. BLAST and ORF Finder NCBI tools were also used to identify and annotate the protein-coding genes (PCGs) and rRNAs. The boundaries of the two rRNAs were tentatively identified via sequence comparison with the published isopod mt rRNAs. Transfer RNA genes and their secondary structures were identified using tRNAscan-SE 1.21 [51] and ARWEN 1.2 [52]. Secondary structures of the rRNAs and the CR were predicted using Mfold software [53]. Tandem repetitive elements were detected with Tandem Repeats Finder software [54]. Nucleotide composition (%) of each gene, non-coding region and the complete mt genome were calculated using DNASTAR’s Lasergene sequence analysis software [55]. Nucleotide compositions of different regions, codon usage and relative synonymous codon usage (RSCU) values of PCGs were analyzed with MEGA v.6.0 software [56].

Phylogenetic analysis

Phylogenetic analysis was carried out using the two mitogenomes sequenced for this study, as well as 15 isopod mitogenomes (5 complete and 10 partial) available on GenBank (March 2018). To facilitate the comparison with previous phylogenetic analyses based on the mt genomes of isopods, following the methodology adopted by Shen et al. [35] and Yu et al. [37], we also used six decapod species as the outgroup: Alvinocaris longirostris Kikuchi & Ohta, 1995 (GenBank: AB821296) [57], Austinograea rodriguezensis Tsuchida & Hashimoto, 2002 (GenBank: JQ035658) [58], Geothelphusa dehaani White, 1847 (GenBank: AB187570) [59], Halocaridina rubra Holthuis, 1963 (GenBank: KF437508) [60], Panulirus japonicus Von Siebold, 1824 (GenBank: NC_004251) [61] and Shinkaia crosnieri Baba & Williams, 1998 (GenBank: NC_011013) [62]. Nucleotide sequence alignments were individually built for all 13 PCGs using MAFFT 7.149 [50], and then concatenated (10,494 nt in total) using an in-house program, MitoTool [63]. Poorly aligned positions were removed by Gblocks v.0.91b [64]. We used jModelTest 2 [65] to determine the optimal nucleotide model for phylogenetic analysis (evaluated according to the Akaike information criterion) [66]. GTR+I+G was the best-fit model, used for both maximum likelihood (ML) and Bayesian inference (BI). Bayesian inference analysis, conducted using MrBayes 3.2 [67], was used for phylogenetic reconstruction: 2,000,000 generations, four MC chains, and the trees were sampled every 1000 generations. The confidence values for the BI tree were expressed as the Bayesian posterior probabilities. The ML tree was constructed using RAxML [68], and the robustness of the phylogenetic results was tested through bootstrap analysis with 1000 replicates. Being aware of the debate regarding the usage of terms ‘basal’ and ‘derived’ [69], we use them specifically to refer to common ancestors, and not extant species when interpreting phylogenetic relationships.


Mt genome organisation and base composition

The mt genomes of T. chinensis (GenBank: MF419232) and I. japonensis (GenBank: MF419233) are circular, double-stranded DNA molecules. The sizes of these two mt genomes are 14,616 bp and 15,440 bp, respectively. Both contain 36 genes, including 13 PCGs, 2 rRNAs, and 21 tRNA genes (Fig. 1). Tachaea chinensis lacks the trnS1 gene and I. japonensis lacks the trnI gene. In I. japonensis, the heavy strand (H) encodes 23 genes and the light strand (L) encodes 13 genes (Table 1), whereas in T. chinensis the H and L strands encode 21 and 15 genes, respectively (Table 2). The A+T content of the two mitogenomes are 72.7% (T. chinensis) and 72.8% (I. japonensis).

Fig. 1

Maps of the mitochondrial genomes of Tachaea chinensis and Ichthyoxenos japonensis. The 13 protein-coding genes (blue), 21 tRNA genes (yellow) and two rRNA genes (green), as well as the control regions (grey), are depicted

Table 1 Gene content of the complete mitochondrial genome of Ichthyoxenos japonensis
Table 2 Gene content of the complete mitochondrial genome of Tachaea chinensis

Protein-coding genes and codon usage

The total length of the concatenated 13 PCGs of T. chinensis and I. japonensis was 10,956 bp and 10,950 bp, respectively (minus the stop codons). All PCGs of T. chinensis and I. japonensis start with the typical ATN start codons: ATA, ATC, ATG and ATT. The PCGs use TAA and TAG as termination codons, with the exception of the nad4 gene of both species, cob and nad3 genes of I. japonensis, and cox2 of T. chinensis, which use an incomplete termination codon (T-- or TA-). The incomplete termination codons, commonly found in metazoan mt genomes, are believed to be completed by mRNA polyadenylation [70]. Codon usage, relative synonymous codon usage (RSCU) and codon family proportion (corresponding to the amino acid usage) of the two parasitic isopods are presented in Additional file 5: Figure S4. The most frequent amino acids in the PCGs of T. chinensis are Ile (10.34%), Leu2 (9.69%), Phe (8.92%) and Ser2 (7.86%), and in I. japonensis: Leu2 (10.96%), Ile (10%), Phe (8.41%) and Met (7.97%). In T. chinensis, the most frequent codons were ATT (isoleucine, 7.89%), TTA (leucine, 7.86%) and TTT (phenylalanine, 7.15%), whereas the GCG codon for alanine only appeared once. For I. japonensis, the most frequent codons were TTA (leucine, 8.71%), ATT (isoleucine, 7.42%) and ATA (methionine, 6.71%), whereas the CTG codon for leucine and CGG for arginine were the least frequent codons, both appearing only twice. Relative synonymous codon usage values in the mt genomes of T. chinensis and I. japonensis reflected a significant bias towards A and T nucleotides (Additional file 5: Figure S4).

Transfer RNA genes

We could only identify 21 tRNAs in the mt genome of T. chinensis (trnS1 appears to be missing), ranging in size from 52 bp (trnC) to 69 bp (trnQ). In the mt genome of I. japonensis, we also only identified 21 tRNA genes (trnI missing), ranging in size from 51 bp (trnE) to 66 bp (trnS1). Concatenated lengths of all tRNA genes in the two mt genomes were 1292 and 1251 bp, with A+T contents of 76.4% and 75.4%, respectively. Eleven tRNAs in T. chinensis and 13 in I. japonensis are encoded on the H-strand, while the remaining tRNAs are encoded on the L-strand.

Ribosomal RNA genes

The lengths of rRNA genes are relatively similar in T. chinensis and I. japonensis: the large ribosomal subunit (rrnL) is 1113 and 1076 bp, respectively, whereas the small ribosomal subunit (rrnS) is 790 bp and 800 bp, respectively. Among the published isopod mt genes, the rrnL sequences ranged from 600 bp (Armadillidium vulgare) to 1367 bp (L. quadripunctata), while the rrnS sequences ranged from 687 bp (A. vulgare) to 850 bp (L. oceanica). The rrnL gene of T. chinensis and I. japonensis is found between the trnS2 and trnQ genes. The rrnS gene, however, is found in different locations: between trnN and trnI in T. chinensis, but between trnN and the control region in I. japonensis. This might be merely an annotation artefact caused by our failure to identify the trnI gene in the latter species. Predicted secondary structures of rrnS and rrnL genes of T. chinensis (used as a representative for Isopoda) are shown in Figs. 2 and 3, respectively. The structures of the two rRNA genes in T. chinensis generally resemble orthologs in other crustaceans. Secondary structures of rrnS and rrnL genes contain three and five domains, respectively. The domain III of rrnL is absent (this gene normally possesses six domains), which was also reported in other arthropod rrnL genes [71, 72]. Multiple alignment of of rrnS sequences of three species of the Cymothooidea (T. chinensis, I. japonensis and E. pulchra) comprised 857 positions, 341 of which were conserved (39.8%), with domain III being the most conserved region (42.2%).

Fig. 2

Predicted secondary structure of the Tachaea chinensis mitochondrial rrnS gene. Positions conserved between T. chinensis and Ichthyoxenos japonensis are colored in red. Positions conserved among the three species of the Cymothooidea, T. chinensis, I. japonensis and Eurydice pulchra, are circled in red. Different domains are labelled with Roman numerals

Fig. 3

Predicted secondary structure of the Tachaea chinensis mitochondrial rrnL gene. Positions conserved between T. chinensis and Ichthyoxenos japonensis are colored in red. Positions conserved among the three species of the Cymothooidea, T. chinensis, I. japonensis and Eurydice pulchra, are circled in red. Different domains are labelled with Roman numerals

Multiple alignment of the rrnL gene of the three species of the Cymothooidea comprised 1189 positions, 501 of which were conserved (42.1%). Domains I, II and VI were highly variable, with only 25.8–39.3% conserved positions, while domains IV and V were more conserved, with 49.4 and 52.4% conserved positions (Fig. 3). We also found that rRNA genes were more conserved between T. chinensis and I. japonensis (rrnS, 61.4%; rrnL, 66.8%) than between T. chinensis and E. pulchra (42.4 and 49.2%, respectively).

Non-coding regions

We identified eleven short intergenic regions (1–60 bp) interspersed within the mt genome of T. chinensis, adding up to a total of 178 bp (Table 2). The control region (CR) is 322 bp in size and located between trnI and trnE. In addition, we could not identify any repetitive sequences in the CR of T. chinensis. In the mt genome of I. japonensis, we identified nine short intergenic regions (1–56 bp; Table 1), adding up to 97 bp. The CR (1319 bp) was identified between rrnS and nad1. Within the CR there is a highly repetitive region (HRR): a 284 bp sequence tandemly repeated four times, with a partial fifth repeat (Fig. 4). Repeat units 2 and 4 are identical in nucleotide composition (both 284 bp). In comparison to these two repeat units, units 1 and 3 differ in one nucleotide. Repeat unit 5 shared the same SNP as unit 1, but it was considerably truncated (79 bp), with approximately 205 bp missing at the 3′-end. Stem-loop secondary structure of the consensus repeat unit is presented in Fig. 4. The adjacent downstream sequence (not containing repeats) can also be folded into two stem-loop structures (Fig. 4).

Fig. 4

Organization and secondary structure of the major non-coding region of Ichthyoxenos japonensis. a Organization of the major non-coding region of I. japonensis. Turquoise ovals indicate tandem repeats in the repetitive region, and the blue box indicates the non-repetitive region. b Secondary structure of the consensus repeat unit (repeat 1) of the repetitive region. c Secondary structure of the non-repetitive region

Gene translocations

Both newly-sequenced species (T. chinensis and I. japonensis) possess unique gene order (compared to other isopods) (Additional file 6: Figure S5), exhibiting rearrangements (relative to the pancrustacean ground pattern) in rrnS, nad1, cob, nad5 and nine tRNA genes (Fig. 5). Among the latter, trnR, trnV, trnE, trnL1, trnW, trnL2, trnT and trnF were rearranged in both species, whereas trnI rearrangement was unique to T. chinensis, and trnS1 to I. japonensis. Gene order was conserved between these two species except for the location of nad1 and five tRNAs: trnL1, trnS1 (not found in T. chinensis), trnI (not found in I. japonensis), trnW and trnH. nad1 was located between trnV and trnN in T. chinensis (and a few other isopods), but in I. japonensis it was found between the CR and trnL1.

Fig. 5

Comparison of mitochondrial gene arrangements of six complete isopod mt genomes and the putative pancrustacean ground pattern. Colored genes mark translocated genes in comparison to the ground pattern

Phylogenetic analyses

Both phylogenetic trees (BI and ML; based on nucleotide sequences of 13 PCGs) had identical topologies (Fig. 6). Tachaea chinensis and I. japonensis formed a sister-clade to all other isopods included in the analysis, with a maximum nodal support (BP = 100, BPP = 1). The other parasitic species of the Cymothoida, G. ovalis, formed a clade with the single species of the Limnoriidea, L. quadripunctata, and then clustered together with L. oceanica a species of the Oniscidea. The two free-living species of the Cymothoida were found in the derived portion of the phylogram; Bathynomus sp. formed a sister clade with the single species of the Sphaeromatidea (S. serratum), and then grouped with a monophyletic Valvifera (G. cf. antarcticus and I. baltica). Eurydice pulchra formed a sister-clade with this entire clade (Bathynomus sp. + Sphaeromatidea + Valvifera). Apart from the Cymothoida and Oniscidea, the remaining major isopod suborders were monophyletic.

Fig. 6

Phylogenetic tree for isopod mt genomes and six outgroup species inferred using BI and ML analyses based on concatenated nucleotide sequences of 13 protein-coding genes. Numbers next to nodes indicate bootstrap percentages of the RAxML analysis (left) and Bayesian posterior probabilities (right), where “-” indicates that bootstrap value was below 50%. Species names are colored by suborder (shown to the right). The scale-bar indicates evolutionary distance (substitutions per site)


Mt genome organization and base composition

Both mt genome sequences studied here had high A+T content (T. chinensis: 72.7%; I. japonensis: 72.8%). This is higher than in the remaining five complete isopod mt genomes: 58.7% in Bathynomus sp.; 59.6% in G. ovalis; 60.9% in L. oceanica; 66.3% in L. quadripunctata; and 69.6% in Eophreatoicus sp. (Additional file 7: Table S2). The A+T content varied profoundly between RNAs (77.6% in rRNAs, 76.4% in tRNAs in T. chinensis; 75.5% in rRNAs, 75.4% in tRNAs in I. japonensis) and PCGs (71.2% in T. chinensis and 71.7% in I. japonensis). This trend is shared by the remaining sequenced isopod mt genomes.

Protein-coding genes and codon usage

Similar frequencies of the most frequent amino acids in T. chinensis and I. japonensis were also observed in other isopod species. For example, Leu2 is the most frequent amino acid in the PCGs of the other eight isopods, followed by Phe in four species. However, in Eurydice pulchra and Bathynomus sp., the other two sequenced cymothooidean free-living isopods, the most frequent amino acids are notably different from the two studied sequences: Gly, Val, Leu1, and Leu2. In G. ovalis, the other sequenced cymothooidean parasitic isopod, the most frequent amino acids are Leu1, Val, Gly and Phe. In addition, Cys is the least used codon in all published isopods, with the utilization rate less than 1% in 14 of 17 species. Almost all of the most frequently used codons ended with A/T, which is reflected in the high A+T bias in isopod mt genomes.

Transfer RNA genes

Most identified tRNAs could be folded into the standard cloverleaf structure, with the exception of five tRNAs that lacked the TψC arm (trnA, trnE, trnQ and trnV in I. japonensis, and trnI in T. chinensis) and trnC, which lacked the DHU arm in both species (Fig. 7). All tRNAs had the standard anti-codons for Arthropoda, except trnI in T. chinensis, which used the AAT anticodon.

Fig. 7

tRNAs of Tachaea chinensis and Ichthyoxenos japonensis exhibiting a non-standard secondary structure

Ribosomal RNA genes

Comparative analyses of the secondary structure of rrnS among three species of the Cymothooidea (T. chinensis, I. japonensis and E. pulchra) showed uneven distribution of conserved nucleotides, with domain III being the most conserved region. Multiple alignment of the rrnL gene of the three species showed that domains IV and V were more conserved, which is similar to the conservation pattern reported in amphipod rrnL genes [72]. We also found that rRNA genes were more conserved between T. chinensis and I. japonensis than between T. chinensis and E. pulchra, which indicates a closer relationship between T. chinensis and I. japonensis.

Non-coding regions

The location of the control region (CR) in T. chinensis is similar to that of the CR of L. oceanica and Eophreatoicus sp. Compared to the CRs of other published isopod species, which range from 410 bp (Eophreatoicus sp.) [36] to 1525 bp (L. quadripunctata) [39], it is relatively short. We did not identify any repetitive sequences in the CR of T. chinensis, as opposed to the CR of another isopod, L. oceanica, which contains repetitive sequences with high variability in length and number of repetitions [38]. Stem-loop secondary structure of the consensus repeat unit and the adjacent downstream sequence were found within the CR of the mt genome of I. japonensis. Similar stem-loop structures were found in other crustacean species, such as the mantis shrimp Squilla mantis, the spiny lobster Panulirus japonicus, the common sea slater, L. oceanica [38], and the holoparasitic isopod G. ovalis [37], so we suspect that this structure may be associated with the origin of replication [73].

Gene translocations

Among the 15 studied isopod mt genomes, each possessed a unique arrangement, but differences were mostly limited to the position of tRNA genes or a few PCGs (Additional file 6: Figure S5). The gene order of isopod mt genomes generally differs from the pancrustacean ground pattern [36, 38, 39, 74], and the two studied mt genomes are no exception in this aspect. When compared with the pancrustacean ground pattern, major translocations in isopods can mostly be localized to a highly variable “rearrangement hotspot” region around the CR [30], between trnV and nad4 (Fig. 5). Except for this region, gene orders of I. japonensis and T. chinensis are identical, and highly conserved in relation to the majority of published isopod mt genomes.

Phylogenetic analyses

Under the currently prevalent classification of isopods, the Phreatoicidea is considered to be the basal group, whereas the Cymothoida is the most derived [11, 15, 75]. However, our results indicate that two parasitic species of the Cymothoida, T. chinensis and I. japonensis, form the basal isopod group. This topology is inconsistent with phylogenetic relationships inferred from morphological data [10, 15, 16] but is supported by some other molecular phylogenetic analyses relying on 18S and combined nuclear and mitochondrial sequences [15, 17, 18]. Brusca & Wilson [10] suggested that the Phreatoicidea is the basal group, and the Cirolanidae, Corallanidae and Cymothoidae are highly derived within the isopods. Wilson [15] evaluated the relationships of isopods, relying on combined 18S and morphological datasets; 18S data suggested the basal position for the Asellota, whereas the two included species of the Phreatoicidea were among the derived isopod species. However, the combined analysis resolved the parasitic isopod groups Bopyroidea, Gnathiidae and Cymothoidae as basal isopod groups. Finally, a very recent phylogenetic analysis based on nuclear (18S and 28S) and mitochondrial (cox1) genes also found that three parasitic species of the Cymothoida and a single species of the Sphaeromatidea formed the basal clade of isopods [18].

Phylogenetic analyses of nine and twelve nearly complete isopod mt genomes indicated that Phreatoicidea (and Asellota) clades form a sister clade to all other isopods [30, 35]. However, a recent analysis of a mt genome dataset included sequences from 17 isopod species and found that the Limnoriidae is the basal clade, followed by Asellota, while Phreatoicidea was placed centrally in the isopods [18]. The most recent analysis of mt genome sequences of 12 isopod species [37] resolved Asellota as the basal clade, followed by the Phreatoicidea, with the holoparasitic G. ovalis placed centrally in the cladogram and not clustering with other cymothoid taxa.

Brandt & Poore [5] conducted a cladistic analysis with morphological characters to explore relationships within the Flabellifera (now accepted as Cymothoida and Sphaeromatidea), and suggested that the Cymothoida comprised two monophyletic clades. They also suggested that the Cirolanidae should be elevated to a superfamily rank, the Anthuridea be treated as a superfamily, and the Epicaridea as two superfamilies.

Our results question the monophyly of the Cymothoida, with a deep evolutionary split between the two free-living species (E. pulchra and Bathynomus sp.) + one parasitic species (G. ovalis) and the two newly-sequenced parasitic Cymothoida species (disregarding the L. quadripunctata issue discussed above). Wilson [15] suggested that monophyly of the Cymothoida is supported by morphological data (202 characters, 52 isopods and 23 other malacostracans), but rejected by molecular data (18S); indeed, monophyly of the Cymothoida has been rejected by several phylogenetic analyses based on molecular data [15, 18, 35, 37]. For example, 18S data produced a topology where several parasitic cymothoids formed a clade external to the main isopod clade [15]; in a combined nuclear (18S and 28S) and mitochondrial (cox1) dataset, three parasitic cymothoids and a single species of the Sphaeromatidea formed the basal isopod clade, followed by a clade including 11 species of the Cymothoida, whereas free-living species of the Cymothoida clustered with five species of the Oniscidea [18]. Mitochondrial phylogenomic analysis of 12 isopod species [37] revealed that the holoparasitic G. ovalis did not cluster with the other two free-living cymothoid species. Furthermore, even a combined morpho-molecular dataset produced a deep split between the free-living and parasitic cymothoidans [15].

In addition, although both E. pulchra and Bathynomus sp. belong to the Cirolanidae, they did not form a monophyletic clade. A paraphyletic Cirolanidae was also produced by two other studies based on mitogenomic data [18, 35] and a study based on combined mito-nuclear molecular markers [18].

Except for the separation of parasitic and free-living groups in the Cymothoida, another noteworthy finding is the phylogenetic position of the holoparasitic epicaridean G. ovalis. Both nuclear (18S) [75] and morphological [5] data usually produce closely related positions of the Epicaridea and Cymothoidae. However, different phylogenetic position of the Epicaridea within Isopoda were proposed. Dreyer & Wagele [11] suggested that epicarideans evolved from species that parasitized fishes (Cymothoidae) and should be considered a family-level taxon within the superfamily Cymothooidea. Brandt & Poore [5] proposed that Epicaridea should be recognized as two superfamilies, Bopyroidea and Cryptoniscoidea, within the suborder Cymothoida. Boyko et al. [21] found that 18S data supported retaining Epicaridea as a taxon within the Cymothoida, but distinct from the Cymothooidea. A dataset comprised of mt genome sequences of 12 isopod species, supported the Epicaridea (represented by G. ovalis) as a suborder [37]. However, our study suggests that G. ovalis is placed centrally in the cladogram, where it clusters with the Limnoriidea, and not with either the basal parasitic clade (families Cymothoidae and Corallanidae) or the other free-living cymothoid taxa (family Cirolanidae). However, as both species (G. ovalis and L. quadripuncata) exhibit rather long branches, a possibility of a long-branch attraction artifact should not be excluded here.

Therefore, this study indicates that the evolution and monophyly of the Cymothoida are not resolved. The relationships of parasitic and free-living groups require deeper attention, with more data and further analyses on a broader scale. Availability of a larger number of molecular data (mt genomes and nuclear genes) of parasitic and free-living isopods might confer a sufficiently high phylogenetic resolution to enable us to resolve their relationships, and ultimately allow us to better understand the evolutionary history of the entire Isopoda.

In addition, it should be noted that we did not recover the Oniscidea as monophyletic. Several phylogenetic analyses relying on whole mt genome data also found that L. oceanica is more closely related to non-oniscid taxa [18, 30, 35, 37]. Moreover, recent nuclear 18S [46] and mito-nuclear analyses [18] also presented evidence that the Oniscidea is not a monophyletic group.

Another aspect of isopod evolution that scientists are paying attention to is the expansion of the Cymothoidae into freshwater habitats. When discussing the habitat expansion, the acquisition and shifts of attachment modes must be considered as well, because it is considered that parasitic isopods always expand into new habitats by changing their attachment modes and hosts [25]. Smit et al. [4] suggested that Cymothoidae may have originated in the Jurassic era, on the basis of the existence of fossils of bopyrid isopods dated to that period, as this family (Bopyridae) is closely related to the Cymothoidae [21]. Recently, two fossil records of early cymothoid isopods dated to the Jurassic also supported this viewpoint [23, 47]. Hata et al. [25] suggested that cymothoids may have originated in deep seas, subsequently expanded to shallow seas, and then to brackish and/or freshwater, by shifting host species. Invasion of freshwater habitats may have occurred independently several times [22, 25]. The freshwater habitat and the burrowing habit may be correlated within the Cymothoidae [22]. However, the availability of molecular data for freshwater and burrowing cymothoid species is limited to two freshwater species, a burrowing parasite (Artystone sp.) and a buccal parasite (Ichthyoxenos tanganyikae). Therefore, more molecular data are needed to define the timing and frequency of evolution of freshwater and abdominal cavity-burrowing parasites [25].


In this study we sequenced the mt genomes of two parasitic cymothoid isopods, T. chinensis and I. japonensis, and conducted a comparative analysis using the available isopod mt genomes. Among the 17 compared isopod mt genomes (including the two studied species), each has a unique gene arrangement, which signifies high variability of gene order in the Isopoda. The two parasitic cymothoids examined here clustered together at the base of the isopod phylogram, forming a sister group to all remaining (available) isopods, which challenges the traditional phylogeny of this order. Moreover, parasitic and free-living Cymothoida formed evolutionary distant clades, and G. ovalis did not cluster with the two parasitic species of the Cymothoidae. The mt genome sequences of T. chinensis and I. japonensis, as representatives of micropredators and burrowing parasites in freshwater habitats, present a useful resource for further evolutionary and taxonomic studies of the Cymothoida, especially the phylogenetic position of epicarideans, the evolution of different life-styles, the evolution of parasitic strategies, invasion of freshwater habitats and the classification and identification of the genus Ichthyoxenos. Due to the current shortage of molecular data carrying a sufficient amount of phylogenetic information, the relationships of the Epicaridea, Cymothooidea, Limnoriidea, Valvifera and Spharomatidea, as well as the monophyly of the Cymothoida and Oniscidea, remain unresolved. In order to resolve these phylogenetic questions, future studies should aim to sequence a much larger number of isopod mt genomes and nuclear genes across a broad range of isopod taxa.



Bayesian inference


control region


maximum likelihood




protein-coding genes


ribosomal RNA genes

rrnL :

large ribosomal subunit

rrnS :

small ribosomal subunit


relative synonymous codon usage


transfer RNA genes


  1. 1.

    Wilson GD. Global diversity of isopod crustaceans (Crustacea; Isopoda) in freshwater. Hydrobiologia. 2008;595:231–40.

    Article  Google Scholar 

  2. 2.

    WoRMS: World Register of Marine Species. 2018. Accessed 15 Aug 2018.

  3. 3.

    Poore GC, Bruce NL. Global diversity of marine isopods (except Asellota and crustacean symbionts). PLoS One. 2012;7:e43529.

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  4. 4.

    Smit NJ, Bruce NL, Hadfield KA. Global diversity of fish parasitic isopod crustaceans of the family Cymothoidae. Int J Parasitol Parasit Wildl. 2014;3:188–97.

    Article  Google Scholar 

  5. 5.

    Brandt A, Poore GC. Higher classification of the flabelliferan and related Isopoda based on a reappraisal of relationships. Invertebr Syst. 2003;17:893–923.

    Article  Google Scholar 

  6. 6.

    Williams JD, Boyko CB. The global diversity of parasitic isopods associated with crustacean hosts (Isopoda: Bopyroidea and Cryptoniscoidea). PLoS One. 2012;7:e35350.

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  7. 7.

    Wetzer R. Collecting and preserving marine and freshwater Isopoda (Crustacea: Peracarida). Biodivers Data J. 2015;3:e4912.

    Article  Google Scholar 

  8. 8.

    Schmidt H. Phylogeny of the terrestrial Isopoda (Oniscidea): a review. Arth Syst Phyl. 2008;66:191–226.

    Google Scholar 

  9. 9.

    Boyko CB, Bruce NL, Hadfield KA, Merrin KL, Ota Y, Poore GCB, et al. World Marine, Freshwater and Terrestrial Isopod Crustaceans Database. Flabellifera. 2008. Accessed 27 Apr 2018.

  10. 10.

    Brusca RC, Wilson GDF. A phylogenetic analysis of the Isopoda with some classificatory recommendations. Mem Queensl Mus. 1991;31:143–204.

    Google Scholar 

  11. 11.

    Dreyer H, Wagele JW. Parasites of crustaceans (Isopoda: Bopyridae) evolved from fish parasites: molecular and morphological evidence. Zoology (Jena). 2001;103:157–78.

    CAS  Google Scholar 

  12. 12.

    Gouws G, Stewart BA, Matthee CA. Lack of taxonomic differentiation in an apparently widespread freshwater isopod morphotype (Phreatoicidea: Mesamphisopidae: Mesamphisopus) from South Africa. Mol Phylogen Evol. 2005;37:289–305.

    CAS  Article  Google Scholar 

  13. 13.

    Schmalfuss H. Phylogenetics in Oniscidea. Monit Zool Ital Monogr. 1989;4:3–27.

    Google Scholar 

  14. 14.

    Wilson GD, Keable SJ. Systematics of the Phreatoicidea. Crust Issues. 2001;13:175–94.

    Google Scholar 

  15. 15.

    Wilson GDF. The phylogenetic position of the Isopoda in the Peracarida (Crustacea: Malacostraca). Arth Syst Phyl. 2009;67:159–98.

    Google Scholar 

  16. 16.

    Wägele JW. Evolution und phylogenetisches System der Isopoda. Zoologica (Stuttgart). 1989;140:1–262.

    Google Scholar 

  17. 17.

    Lins LS, Ho SY, Wilson GD, Lo N. Evidence for Permo-Triassic colonization of the deep sea by isopods. Biol Lett. 2012;8:979–82.

    Article  PubMed  PubMed Central  Google Scholar 

  18. 18.

    Lins LS, Ho SY, Lo N. An evolutionary timescale for terrestrial isopods and a lack of molecular support for the monophyly of Oniscidea (Crustacea: Isopoda). Org Divers Evol. 2017;17:813–20.

    Article  Google Scholar 

  19. 19.

    Wilson GD, Sims CA, Grutter AS. Toward a taxonomy of the Gnathiidae (Isopoda) using juveniles: the external anatomy of Gnathia aureamaculosa zuphea stages using scanning electron microscopy. J Crust Biol. 2011;31:509–22.

    Article  Google Scholar 

  20. 20.

    Strömberg J. Isopod phylogeny. Aspects based on embryological, morphological and palaeontological evidence. Contrib Zool Inst Univ Lund. 1972;1972:1–112.

    Google Scholar 

  21. 21.

    Boyko CB, Moss J, Williams JD, Shields JD. A molecular phylogeny of Bopyroidea and Cryptoniscoidea (Crustacea: Isopoda). Syst Biodivers. 2013;11:495–506.

    Article  Google Scholar 

  22. 22.

    Brusca RC. A monograph on the Isopoda Cymothoidae (Crustacea) of the eastern Pacific. Zool J Linn Soc. 1981;73:117–99.

    Article  Google Scholar 

  23. 23.

    Nagler C, Haug C, Resch U, Kriwet J, Haug JT. 150 million years old isopods on fishes: a possible case of palaeo-parasitism. Bull Geosci. 2016;91:1–12.

    Article  Google Scholar 

  24. 24.

    Martin MB. Taxonomy and phylogeny of the buccal-attaching Cymothoidae (Crustacea: Isopoda) of Australia. PhD Thesis, University of Tasmania; Launceston, Australia; 2016.

  25. 25.

    Hata H, Sogabe A, Tada S, Nishimoto R, Nakano R, Kohya N, et al. Molecular phylogeny of obligate fish parasites of the family Cymothoidae (Isopoda, Crustacea): evolution of the attachment mode to host fish and the habitat shift from saline water to freshwater. Mar Biol. 2017;164:105.

    Article  Google Scholar 

  26. 26.

    Hadfield KA. The biodiversity and systematics of marine fish parasitic isopods of the family Cymothoidae from Southern Africa. PhD Thesis, University of Johannesburg, Johannesburg, South Africa; 2012.

  27. 27.

    Kuang PR, Qian JH. Economic fauna of China: parasitic Crustacea of freshwater fishes. Beijing, China: Science Press; 1991. p.177–180 (In Chinese).

  28. 28.

    Bruce NL. The genera Catoessa, Elthusa, Ichthyoxenus, Idusa, Livoneca and Norileca, n. gen. (Isopoda, Cymothoidae), crustacean parasites of marine fishes, with descriptions of eastern Australian species. Rec Aust Mus. 1990;42:247–300.

    Article  Google Scholar 

  29. 29.

    Martin MB, Bruce NL, Nowak BF. Redescription of Ichthyoxenus puhi (Bowman, 1962) (Isopoda, Cymothoidae), parasite of the moray eel Gymnothorax griseus (Lacepede, 1803) from Mauritius. Crustaceana. 2014;87:654–65.

    Article  Google Scholar 

  30. 30.

    Kilpert F, Held C, Podsiadlowski L. Multiple rearrangements in mitochondrial genomes of Isopoda and phylogenetic implications. Mol Phylogen Evol. 2012;64:106–17.

    CAS  Article  Google Scholar 

  31. 31.

    Aunins AW, Nelms DL, Hobson CS, King TL. Comparative mitogenomic analyses of three North American stygobiont amphipods of the genus Stygobromus (Crustacea: Amphipoda). Mito DNA B. 2016;1:560–3.

    Article  Google Scholar 

  32. 32.

    Harrison RG. Animal mitochondrial DNA as a genetic marker in population and evolutionary biology. Trends Ecol Evol. 1989;4:6–11.

    CAS  Article  PubMed  Google Scholar 

  33. 33.

    Gissi C, Iannelli F, Pesole G. Evolution of the mitochondrial genome of Metazoa as exemplified by comparison of congeneric species. Heredity. 2008;101:301–20.

    CAS  Article  PubMed  Google Scholar 

  34. 34.

    Macey JR, Schulte JA, Larson A. Evolution and phylogenetic information content of mitochondrial genomic structural features illustrated with acrodont lizards. Syst Biol. 2000;49:257–77.

    CAS  Article  PubMed  Google Scholar 

  35. 35.

    Shen Y, Kou Q, Zhong Z, Li X, He L, He S, et al. The first complete mitogenome of the South China deep-sea giant isopod Bathynomus sp. (Crustacea: Isopoda: Cirolanidae) allows insights into the early mitogenomic evolution of isopods. Ecol Evol. 2017;7:1869–81.

    Article  PubMed  PubMed Central  Google Scholar 

  36. 36.

    Kilpert F, Podsiadlowski L. The Australian fresh water isopod (Phreatoicidea: Isopoda) allows insights into the early mitogenomic evolution of isopods. Comp Biochem Phys D Genom Pro. 2010;5:36–44.

    Google Scholar 

  37. 37.

    Yu J, An J, Li Y, Boyko CB. The first complete mitochondrial genome of a parasitic isopod supports Epicaridea Latreille, 1825 as a suborder and reveals the less conservative genome of isopods. Syst Parasitol. 2018;95:465–78.

    Article  PubMed  Google Scholar 

  38. 38.

    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.

    Article  PubMed  PubMed Central  Google Scholar 

  39. 39.

    Lloyd RE, Streeter SD, Foster PG, Littlewood DTJ, Huntley J, Beckham GT, et al. The complete mitochondrial genome of Limnoria quadripunctata Holthuis (Isopoda: Limnoriidae). Mit DNA. 2015;26:825–6.

    CAS  Article  Google Scholar 

  40. 40.

    Yu HY, Li XZ. Introduction and prospect of the systematic study of Isopoda in China. Mar Sci. 1998;22:28–9 (In Chinese).

    Google Scholar 

  41. 41.

    Cheng RY, Niu Y, Guo YM. A new record of freshwater isopod crustacean from Henan (Crustacea: Isopoda: Corallanidae). J Hen Nor Univ. 2011;39:133–5 (In Chinese with English abstract).

    Google Scholar 

  42. 42.

    Ding RH. A preliminary study on some propagation characteristics and distribution of Ichthyoxenus japonensis in Sichuan. Acta Ecol Sin. 1986;6:275–82 (In Chinese).

    Google Scholar 

  43. 43.

    Kuang P, Qian JY. Parasitic Crustacea of freshwater fishes. Beijing, China: Science Press; 1991. p. 178–180.

  44. 44.

    Hua CJ, Zhang D, Zou H, Wu SG, Wang GT, Braicovich PE, et al. Effects of the parasitic isopod Ichthyoxenus japonensis Richardson, 1913 (Isopoda, Cymothoidae) on the growth and gonad development of the goldfish Carassius auratus Linnaeus, 1758. J Crust Biol. 2017;37:356–8.

    Article  Google Scholar 

  45. 45.

    Huang QY, Qian JY. A study on the Ichthyoxenus japonensis of Carassius auratus. Shuichan Xuebao. 1980;4:71–80 (In Chinese).

    Google Scholar 

  46. 46.

    Wetzer R, Perez-Losada M, Bruce NL. Phylogenetic relationships of the family Sphaeromatidae Latreille, 1825 (Crustacea: Peracarida: Isopoda) within Sphaeromatidea based on 18S-rDNA molecular data. Zootaxa. 2013;3599:161–77.

    Article  PubMed  Google Scholar 

  47. 47.

    Nagler C, Hyžný M, Haug JT. 168 million years old “marine lice” and the evolution of parasitism within isopods. BMC Evol Biol. 2017;17:76.

    Article  PubMed  PubMed Central  Google Scholar 

  48. 48.

    Richardson H. The isopod genus Ichthyoxenus Herklots, with description of a new species from Japan. Proc USNM. 1913;45:559–62.

    Google Scholar 

  49. 49.

    Wei CD, Chen YS. Fauna of Zhejiang: Crustacea. Hangzhou: Zhejiang Science and Technology Publishing House; 1991. p. 114–5 (In Chinese)

  50. 50.

    Katoh K, Standley DM. MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol Biol Evol. 2013;30:772–80.

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  51. 51.

    Lowe TM, Eddy SR. tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res. 1997;25:955–64.

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  52. 52.

    Laslett D, Canback B. ARWEN: a program to detect tRNA genes in metazoan mitochondrial nucleotide sequences. Bioinformatics. 2008;24:172–5.

    CAS  Article  PubMed  Google Scholar 

  53. 53.

    Zuker M. Mfold Web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res. 2003;31:3406–15.

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  54. 54.

    Benson G. Tandem repeats finder: a program to analyze DNA sequences. Nucleic Acids Res. 1999;27:573–80.

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  55. 55.

    Burland TG. DNASTAR’s Lasergene sequence analysis software. Bioinf Meth Prot. 1999;3:71–91.

    Article  Google Scholar 

  56. 56.

    Tamura K, Stecher G, Peterson D, Filipski A, Kumar S. MEGA6: Molecular Evolutionary Genetics Analysis Version 6.0. Mol Biol Evol. 2013;30:2725–9.

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  57. 57.

    Hui M, Wang M, Sha Z. The complete mitochondrial genome of the alvinocaridid shrimp Shinkaicaris leurokolos (Decapoda, Caridea): insight into the mitochondrial genetic basis of deep-sea hydrothermal vent adaptation in the shrimp. Comp Biochem Phys D Genom Pro. 2018;25:42–52.

    Google Scholar 

  58. 58.

    Yang J-S, Lu B, Chen DF, Yu YQ, Yang F, Nagasawa H, et al. When did decapods invade hydrothermal vents? Clues from the Western Pacific and Indian Oceans. Mol Biol Evol. 2012;30:305–9.

    Article  PubMed  Google Scholar 

  59. 59.

    Segawa RD, Aotsuka T. The mitochondrial genome of the Japanese freshwater crab, Geothelphusa dehaani (Crustacea: Brachyura): evidence for its evolution via gene duplication. Gene. 2005;355:28–39.

    CAS  Article  PubMed  Google Scholar 

  60. 60.

    Ivey JL, Santos SR. The complete mitochondrial genome of the Hawaiian anchialine shrimp Halocaridina rubra Holthuis, 1963 (Crustacea: Decapoda: Atyidae). Gene. 2007;394:35–44.

    CAS  Article  PubMed  Google Scholar 

  61. 61.

    Yamauchi MM, Miya MU, Nishida M. Complete mitochondrial DNA sequence of the Japanese spiny lobster, Panulirus japonicus (Crustacea: Decapoda). Gene. 2002;295:89–96.

    CAS  Article  PubMed  Google Scholar 

  62. 62.

    Yang JS, Yang WJ. The complete mitochondrial genome sequence of the hydrothermal vent galatheid crab Shinkaia crosnieri (Crustacea: Decapoda: Anomura): a novel arrangement and incomplete tRNA suite. BMC Genomics. 2008;9:257.

    Article  PubMed  PubMed Central  Google Scholar 

  63. 63.

    Zhang D. MitoTool software. 2016. Accessed 12 Oct 2017.

  64. 64.

    Talavera G, Castresana J. Improvement of phylogenies after removing divergent and ambiguously aligned blocks from protein sequence alignments. Syst Biol. 2007;56:564–77.

    CAS  Article  PubMed  Google Scholar 

  65. 65.

    Darriba D, Taboada GL, Doallo R, Posada D. jModelTest 2: more models, new heuristics and parallel computing. Nat Methods. 2012;9:772.

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  66. 66.

    Abascal F, Zardoya R, Posada D. ProtTest: selection of best-fit models of protein evolution. Bioinformatics. 2005;21:2104–5.

    CAS  Article  PubMed  Google Scholar 

  67. 67.

    Ronquist F, Teslenko M, Mark PVD, Ayres DL, Darling A, Höhna S, et al. MrBayes 3.2: efficient Bayesian phylogenetic inference and model choice across a large model space. Syst Biol. 2012;61:539–42.

    Article  PubMed  PubMed Central  Google Scholar 

  68. 68.

    Stamatakis A. RAxML Version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics. 2014;30:1312–3.

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  69. 69.

    Krell FT, Cranston PS. Which side of the tree is more basal? Syst Entomol. 2004;29:279–81.

    Article  Google Scholar 

  70. 70.

    Anderson S, Bankier AT, Barrell BG, de Bruijn MH, Coulson AR, Drouin J, et al. Sequence and organization of the human mitochondrial genome. Nature. 1981;290:457–65.

    CAS  Article  PubMed  Google Scholar 

  71. 71.

    Cannone JJ, Subramanian S, Schnare MN, Collett JR, D’Souza LM, Du Y, et al. The comparative RNA web (CRW) site: an online database of comparative sequence and structure information for ribosomal, intron, and other RNAs. BMC Bioinformatics. 2002;3:2. 

  72. 72.

    Pons J, Bauzà-Ribot MM, Jaume D, Juan C. Next-generation sequencing, phylogenetic signal and comparative mitogenomic analyses in Metacrangonyctidae (Amphipoda: Crustacea). BMC Genomics. 2014;15:566.

    Article  PubMed  PubMed Central  Google Scholar 

  73. 73.

    Zhang DX, Szymura JM, Hewitt GM. Evolution and structural conservation of the control region of insect mitochondrial DNA. J Mol Evol. 1995;40:382–91.

    CAS  Article  PubMed  Google Scholar 

  74. 74.

    Boore JL, Lavrov DV, Brown WM. Gene translocation links insects and crustaceans. Nature. 1998;392:667–8.

    CAS  Article  PubMed  Google Scholar 

  75. 75.

    Dreyer H, Wägele JW. The Scutocoxifera tax. nov. and the information content of nuclear ssu rDNA sequences for reconstruction of isopod phylogeny (Peracarida: Isopoda). J Crust Biol. 2002;22:217–34.

    Article  Google Scholar 

Download references


The authors would like to thank Dr Fabian Kilpert for the assistance in finding the hairpin structure in the mitochondrial control region of Ichthyoxenos japonensis. The authors also would like to thank the editor and the three anonymous reviewers for the time and expertise they invested into reviewing our manuscript, their comments helped us improve it.


This study was funded by the Earmarked Fund for China Agriculture Research System (CARS-45-15), the National Natural Science Foundation of China (31872604, 31572658), and the Major Scientific and Technological Innovation Project of Hubei Province (2015ABA045).

Availability of data and materials

All data are fully available without restriction. The datasets supporting the conclusions of this article are included within the article and its additional files. The mitogenomic sequences of Tachaea chinensis and Ichthyoxenos japonensis were submitted to the GenBank database under accession numbers MF419232 and MF419233, respectively).

Author information




GTW, WXL and CJH designed the study. CJH and HZ conducted the experiments. CJH and DZ conducted the data analysis. CJH and IJ wrote the paper. All authors have revised the manuscript critically for important intellectual content and read and approved the final manuscript.

Corresponding author

Correspondence to Gui T. Wang.

Ethics declarations

Ethics approval and consent to participate

All applicable international, national, and/or institutional guidelines for the care and use of animals were followed.

Consent for publication

Not applicable.

Competing interests

The authors declare that they have no competing interests.

Publisher’s Note

Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Additional files

Additional file 1:

Figure S1. Maximum likelihood tree for the family Cymothoidae based on mitochondrial 16S rRNA sequence data conducted in MEGA7. (TIF 5180 kb)

Additional file 2:

Figure S2. An image of Tachaea chinensis. (TIF 6612 kb)

Additional file 3:

Figure S3. An image of Ichthyoxenos japonensis. (TIF 5659 kb)

Additional file 4:

Table S1. Primers used to amplify and sequence the mitochondrial genomes of the two parasitic cymothoid isopods Ichthyoxenos japonensis and Tachaea chinensis. (XLSX 13 kb)

Additional file 5:

Figure S4. Relative synonymous codon usage of mitochondrial genomes of 17 isopods. Codon families are labelled on the x-axis. Values on the top of the bars refer to amino acid usage. (TIF 570 kb)

Additional file 6:

Figure S5. Comparison of mitochondrial gene arrangements of 17 isopod mt genomes. (TIF 1590 kb)

Additional file 7:

Table S2. Comparison of 17 isopod mitochondrial genomes. (XLSX 13 kb)

Rights and permissions

Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (, which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver ( applies to the data made available in this article, unless otherwise stated.

Reprints and Permissions

About this article

Verify currency and authenticity via CrossMark

Cite this article

Hua, C.J., Li, W.X., Zhang, D. et al. Basal position of two new complete mitochondrial genomes of parasitic Cymothoida (Crustacea: Isopoda) challenges the monophyly of the suborder and phylogeny of the entire order. Parasites Vectors 11, 628 (2018).

Download citation


  • Ichthyoxenos japonensis
  • Tachaea chinensis
  • Mitochondrial genome
  • RNA secondary structure
  • Gene rearrangement
  • Phylogenetic analysis