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Article

First Genomic Survey of Pleurocryptella fimbriata Provides Preliminary Insights into Genome Characteristics and Evolution of a Deep-Sea Parasitic Isopod

by
Aiyang Wang
1,2,3,4,
Min Hui
1,4,* and
Zhongli Sha
1,2,3,4,*
1
Department of Marine Organism Taxonomy & Phylogeny, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
2
Laboratory for Marine Biology and Biotechnology, Qingdao Marine Science and Technology Center, Qingdao 266237, China
3
Shandong Province Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
4
University of Chinese Academy of Sciences, Beijing 100049, China
*
Authors to whom correspondence should be addressed.
Diversity 2025, 17(4), 297; https://doi.org/10.3390/d17040297
Submission received: 24 March 2025 / Revised: 18 April 2025 / Accepted: 19 April 2025 / Published: 20 April 2025
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Abstract

:
Genomic adaptations of parasitic crustaceans in deep-sea extreme environments are poorly understood. This study presents the first genome survey of Pleurocryptella fimbriata, a bopyrid isopod parasitizing deep-sea squat lobsters, using Illumina sequencing. The genome size was estimated to be 1.06 Gb via a K-mer analysis, smaller than its free-living relatives. The repeat content and heterozygosity were 66.31% and 1.14%, respectively, indicating a complex genome. The draft genome assembly yielded 0.93 Gb of scaffolds with an N50 length of 989 bp, and a complete mitochondrial genome of 14,711 bp was obtained. Phylogenetic analyses of 13 mitochondrial protein-coding genes confirmed the monophyly of Bopyridae, supporting Pleurocryptella as the most primitive genus within the group and the key role of deep sea in the origin and diversification of bopyrids. A mitochondrial gene variation analysis identified NAD2 and NAD4 as promising DNA markers for a population genetic study of P. fimbriata. Twenty-four positively selected sites across COX1, NAD2, and NAD4 genes in P. fimbriata explained the genetic basis of its adaptive evolution at the mitochondrial level. These findings provide valuable genomic resources for deep-sea parasitic crustaceans and establish a foundation for further high-quality genome assembly and adaptive mechanism studies of P. fimbriata.

1. Introduction

Bopyrid isopods (Isopoda: Epicaridea: Bopyridae) are specialized parasites of decapod crustaceans, exhibiting extreme sexual dimorphism and a holoparasitic lifestyle that profoundly affects their hosts [1]. These parasites typically trigger distinctive swellings in the gill chambers or carapace of their hosts and alter the hosts’ immune responses, such as reduced total hemocyte counts, gill necrosis, and hepatopancreatic vacuolation [2,3]. Parasitic infections also have detrimental effects on the growth and reproduction of hosts [4]. For instance, the invasive Orthione griffenis on the west coast of the U.S. severely impacts mud shrimp (Upogebia pugettensis), which reduces female fecundity by an average of 68%, leading to significant population declines and even local extinctions in Pacific coast estuaries [5].
Recent research on bopyrids has predominantly centered on molecular phylogenetics, utilizing mitochondrial and nuclear markers to elucidate evolutionary relationships within this group [6,7,8,9]. Pleurocryptella fimbriata is one of the bopyrid species, which parasitizes the branchial chambers of the deep-sea squat lobsters belonging to Galatheoidea, Anomura [10]. This specific parasitic interaction, set against the backdrop of extreme deep-sea environments, renders P. fimbriata an exemplary model for an adaptive evolution study.
Decoding the genome is essential for elucidating the evolutionary processes and adaptative mechanisms of organisms residing in extreme environments. In the parasitic polychaete Branchipolynoe longqiensis, from deep-sea hydrothermal vents, an expansion of single-domain hemoglobin and a unique formation of tetra-domain hemoglobin via tandem duplications have been revealed to be related to its adaptation to the hypoxic environment through a comparative genomic analysis [11]. Thus far, only two genomes of deep-sea crustaceans have been reported, the hadal amphipod Hirondellea gigas [12] and the giant isopod, Bathynomus jamesi [13], both showing large genome sizes. Our preliminary investigation of the genome of the alvinocaridid shrimp Shinkaicaris leurokolos provides initial genome data and the genome characteristics of crustaceans from deep-sea hydrothermal vents [14]. However, parasitic isopods, especially deep-sea species, remain genomically underexplored, which greatly limits our deeper understanding of the parasitic mechanism in an extreme environment.
Genome survey sequencing (GSS) using next-generation sequencing (NGS) enables the efficient assessment of genome characteristics (e.g., genome size estimations and complexity assessments) [14,15,16,17]. In this study, the P. fimbriata infesting Shinkaia crosnieri were collected from a deep-sea cold seep (Site F) in the South China Sea. Based on the genome sequencing of P. fimbriata, we aimed to estimate the genome characteristics of this deep-sea parasitic isopod and assemble a draft genome as well as a complete mitochondrial genome (mitogenome). The phylogenetic position of P. fimbriata and the genetic basis of its adaptive evolution were also explored at the mitogenome level.

2. Materials and Methods

2.1. Sample Collection

Specimens of S. crosnieri were collected from the Site F cold seep (119°17.140′ E, 22°06.930′ N, and 1119 m depth) in the South China Sea during a cruise of the RV KEXUE (Institute of Oceanology, Chinese Academy of Sciences) in May 2020 (Figure 1). They were retrieved using the remotely operated vehicle (ROV) Quasar MkII (Soil Machine Dynamics, UK) and put into a temperature-controlled bio-box made by the Institute of Oceanology, Chinese Academy of Sciences, which maintained the same low temperature as the seabed. Once on board, S. crosnieri individuals displaying pronounced branchial chamber swelling suggestive of parasitism were selected, and bopyrid isopods were carefully extracted from their branchial chambers. Using a morphological classification [10], the isopods were identified as P. fimbriata. All P. fimbriata specimens were immediately flash-frozen in liquid nitrogen and stored at −80 °C.

2.2. DNA Extraction, Library Construction, and Sequencing

For genome sequencing, a female P. fimbriata was selected due to the larger body size (Figure 1). Total DNA was extracted from the entire body using the standard phenol-chloroform method [18]. DNA integrity was assessed via 1% agarose gel electrophoresis and purity was measured using a NanoDrop 2000 spectrophotometer (Thermo Fisher, Wilmington, DE, USA). The concentration was determined using a Qubit 2.0 fluorometer (Thermo Fisher, Waltham, MA, USA).
Sequencing libraries were prepared using a TruSeq Nano DNA HT Sample Preparation Kit (Illumina, San Diego, CA, USA) following the manufacturer’s protocol. Genomic DNA was fragmented into 350 bp using a Covaris sonicator (Covaris, Woburn, MA, USA). The resulting fragments were end-polished, A-tailed, and ligated with full-length adapters for Illumina PE150 sequencing, followed by further size selection and PCR amplification. PCR products were purified using an AMPure XP system and quantified using real-time PCR. The libraries were then sequenced using the Illumina HiSeq platform.

2.3. K-Mer Analysis and Genome Assembly

After filtering low-quality reads, the clean data were subjected to a K-mer analysis using Jellyfish v2.3.0 with a K-mer size of 17 [19], and the results were evaluated via GenomeScope [20]. The clean reads were assembled into contigs using SOAPdenovo v2.40 [21] with a K-mer size of 41, employing a de Bruijn graph-based approach. Subsequently, paired-end information was utilized to link the unique contigs into scaffolds.

2.4. Mitogenome Assembly and SNP Screening

The mitogenome of P. fimbriata was assembled de novo using Novoplasty v4.3.1 [22], with the published COX1 sequence of P. fimbriata (GenBank accession no. MH398102) as the seed sequence. The annotation for the mitogenome was performed using the automated mitochondrial gene annotators Geseq [23] and Geneious Prime v2025.0.2.0 [24], followed by rigorous manual verification.
To identify variations in the P. fimbriata mitogenome, SNP recovery was carried out. The previously published incomplete P. fimbriata mitogenome (GenBank accession no. MG729628) served as the reference. Sequence alignment between the two mitogenomes was performed using MEGA 11 [25], and the variant sites were considered to be candidate SNPs.

2.5. Phylogenetic Analysis

To reconstruct the phylogeny of Epicaridea, the mitogenome sequences of 10 species within the suborder were analyzed, including Portunion sp., Portunion conformis, Orthione mesoamericana, Gyge ovalis, Aparapenaeon japonica, Parapenaeon diatropa, Parasymmetrorbione bicauda, Parapenaeonella distincta, P. expansa, and P. fimbriata. Ichthyoxenos japonensis and Elthusa poutassouiensis were selected as outgroup species (Table 1). The nucleotide sequences of 13 PCGs from all mitogenomes were extracted using PhyloSuite v1.2.3 [26]. These sequences were aligned using MAFFT v7.313 [27] with default parameters and concatenated into a single supergene for each species. The optimal partitioning strategy and the best-fit evolutionary model for each partition were determined using PartitionFinder v2.1.1 [28], employing the Bayesian information criterion (BIC) and a greedy search scheme in PhyloSuite v1.2.3.
Phylogenetic relationships among the 12 species were inferred using maximum likelihood (ML) and Bayesian inference (BI) methods based on the concatenated nucleotide sequences of the 13 PCGs. The ML tree was constructed using IQ-TREE v2.2.0 [35] in PhyloSuite v1.2.3 with 1000 bootstrap replicates. The BI analysis was performed using MrBayes v3.2.7 [36], with four Markov chain Monte Carlo (MCMC) chains running simultaneously for 20 million generations and sampling every 1000 generations. Bayesian posterior probability (BPP) was calculated using a majority-rule consensus tree after discarding the first 25% of samples as burn-in. The phylogenetic trees were visualized and edited using the online tool Interactive Tree Of Life (iTOL) [37].

2.6. Positive Selection Analysis

For the positive selection analysis, we exclusively targeted the bopyrid species included in the phylogenetic tree. Within this group, P. fimbriata was distinguished as the only deep-sea species, while the other bopyrid species predominantly occupied shallow-sea habitats. The CodeML program in the PAML package [38] was employed to detect positively selected genes (PSGs) among the 13 PCGs, with a particular focus on the deep-sea P. fimbriata.
The ratio of nonsynonymous to synonymous substitution rates (ω) was a key parameter in detecting the selection pressure, where ω > 1 indicated positive selection, ω = 1 suggested neutral selection, and ω < 1 implied purifying selection [39]. First, the one-ratio model (M0) was applied to estimate ω, assuming uniform selection pressure across all branches. Next, the two-ratio model (M2) was used to test for positive selection by comparing the foreground lineage (P. fimbriata) with background lineages. A free-ratio model (M1) was then implemented to allow ω to vary among branches, facilitating comparisons of selection pressure across the Bopyridae clade. Likelihood ratio tests (LRTs) were conducted to compare the one-ratio and two-ratio models, assessing if P. fimbriata experienced elevated selection pressure relative to other bopyrid species.
Additionally, branch-site Model A [40] was applied to detect positively selected sites within the P. fimbriata lineage. Sites where ω > 1 were identified as being under positive selection, with significance determined by a Bayes Empirical Bayes (BEB) analysis [41] requiring posterior probabilities ≥0.95.

3. Results

3.1. Characteristics of P. fimbriata and S. crosnieri Specimens

A total of 90 S. crosnieri specimens (carapace length: 4.0–7.5 cm; carapace width: 2.0–5.0 cm) were collected from the Site F cold seep. Of these, eight individuals exhibited pronounced swelling in either the left or right branchial chamber, showing an infection rate of approximately 8.9%. A sexually dimorphic pair of P. fimbriata in each infected host (male length: 3–7 mm; female length: 10–20 mm) was dissected from the branchial chamber. The male P. fimbriata was observed attaching itself to the dorsal surface of the female, while the female directly attached itself to the branchial cuticle of the host.

3.2. Sequencing and Quality Evaluation

High-throughput sequencing of P. fimbriata yielded 136.21 Gb of raw data, providing a sequencing depth of 128×. After stringent filtering, 134.09 Gb of high-quality clean reads were retained, representing an effective rate of 98.45%. A sequencing quality assessment showed that 94.94% and 89.56% of bases reached the Q20 score (≥99% accuracy) and Q30 score (≥99.9% accuracy), respectively. The GC content of the clean reads was 32.40%.

3.3. K-Mer-Analysis-Based Genome Characteristics

The 17-mer frequency distribution plot for P. fimbriata revealed three distinct peaks. The peak at a depth = 16 was a heterozygous peak, the peak at a depth = 32 was the main peak, and the repetitive peak was at a depth = 64 (Figure 2). The estimated genome size of P. fimbriata was 1,056,738,515 bp, with a heterozygosity of 1.14% and a repeat content of 66.31%.

3.4. Genome Assembly Statistics

The genome of P. fimbriata was initially assembled into 2,289,701 contigs, yielding a total length of 888,848,407 bp, with a maximum length of 137,550 bp and an N50 length of 726 bp. A subsequent scaffold assembly integrated these contigs, resulting in 1,960,944 scaffolds with a total length of 927,035,547 bp, accounting for 87.73% of the genome size, and a maximum length of 266,030 bp. The N50 length of the scaffolds was 989 bp and the GC content was 35.09% (Table 2).

3.5. Mitogenome Features and Candidate SNPs

The complete mitogenome of P. fimbriata was assembled as a closed circular molecule that was 14,711 bp in length (Figure 3 and Table 3), with a base composition of A (29.18%), T (33.84%), G (20.65%), and C (16.33%). The A+T content (63.02%) exceeded the G+C content (36.98%), showing a pronounced AT bias. Annotation identified 34 mitochondrial genes, comprising 13 PCGs, 19 transfer RNA (tRNA) genes, and 2 ribosomal RNA (rRNA) genes. The gene arrangement was compact, featuring 8 non-coding regions and 13 gene overlaps. The largest non-coding region, a 431 bp control region, was located between tRNA-Ser and CYTB.
A further comparison of the mitochondrial PCGs between the P. fimbriata incomplete mitogenome (previous published in NCBI) and the one in this study identified 24 candidate SNPs. Of these, the majority were synonymous substitutions (19 out of 24 SNPs), while only five mutations were nonsynonymous substitutions, occurring in COX2 (G→W), ATP6 (K→S; M→L), NAD5 (I→T), and NAD4L (L→I). Notably, COX1, ATP8, and NAD1 exhibited no detectable SNPs, highlighting their high conservation within P. fimbriata’s mitogenome (Table 4). NAD2 and NAD4 showed higher intraspecific mutation rates (0.30%) and suitable sequence lengths for the primer design, representing promising molecular markers for a population genetics study of P. fimbriata.

3.6. Phylogenetic and Selective Pressure Analyses of Mitochondrial PCGs

The phylogenetic reconstruction of Epicaridea using ML and BI methods produced identical topologies that were strongly supported at most nodes (Figure 4). The phylogenetic analysis confirmed the monophyly of the family Bopyridae as all included species formed a well-supported clade (ML bootstrap = 100; BPP = 0.95). Within Bopyridae, P. fimbriata and O. mesoamericana were resolved as sister taxa, forming a distinct subclade. Notably, P. fimbriata occupied a basal position within Bopyridae, indicating that it represented one of the most primitive lineages within this family.
A branch-specific model analysis revealed that the average ω ratio for each of the 13 mitochondrial PCGs in P. fimbriata and its shallow-sea Bopyridae relatives was less than 1, as estimated by the one-ratio model (M0) (Table 4). This indicated strong purifying selection and functional constraints across these genes, consistent with their critical roles in mitochondrial respiration, oxidative phosphorylation, and electron transport [42]. To further explore the selective pressures, we used the two-ratio model (M2), where P. fimbriata was designated as the foreground branch and other shallow-water Bopyridae as background branches, and detected significantly elevated ω values (p < 0.05) in the COX1 and CYTB genes of P. fimbriata (Table 5). These findings suggested a relaxation of purifying selection in P. fimbriata compared with its shallow-sea relatives.
A branch-site model analysis comparing Model A with the Null model detected significant signals of positive selection (p < 0.05) in the PCGs COX1, NAD2, and NAD4 along the P. fimbriata lineage (Table 6). The BEB analysis identified a total of 24 positively selected residues (posterior probability >0.95) across these genes, with NAD2 and NAD4 harboring the highest numbers of positively selected sites (11 in each). This suggested that positive selection acted on specific mitochondrial genes in P. fimbriata.

4. Discussion

4.1. Characteristics of the Parasitic P. fimbriata Genome

In this study, an Illumina-based genome survey of P. fimbriata generated high-quality sequencing data (Q20 = 94.94%; Q30 = 89.56%) exceeding the Illumina platform quality thresholds (Q20 > 90%; Q30 > 85%) [43]. The GC content (32.4%) fell within the optimal range (25–65%) for avoiding sequence bias in Illumina platforms [44]. These metrics confirmed the robust sequencing quality, providing a reliable foundation for subsequent genomic analyses.
It has been shown that the estimated genome size of P. fimbriata (1.06 Gb) is markedly smaller than that of the free-living deep-sea giant isopod Bathynomus jamesi (5.90 Gb) [13]. Similar findings have been found in other studies, where parasitic species often exhibit reduced genome sizes compared with their free-living counterparts, likely due to distinct selective pressures [45,46]. For example, the plant-parasitic nematode Meloidogyne hapla has a compact genome of 54 Mb, significantly smaller than that of the free-living Caenorhabditis elegans (106.4 Mb) [47,48]. The orthonectid parasite Intoshia variabili exhibits an even more striking case, with a genome of just 15.3 Mb, the smallest known among metazoans [49]. It has been proposed that a smaller genome in parasitic organisms confers several adaptive advantages, such as reduced energy demands for transcription and translation, potentially allowing resource allocation to other critical processes [46]. Additionally, smaller genomes are often correlated with a reduced cell size and developmental complexity [50], which could enhance the ability of parasitism [51].
The draft genome assembly of P. fimbriata presented here provides foundational insights into its genomic characteristics. However, a chromosome-level genome with the advantages of high integrity, coherence, and accuracy [52] may provide a more comprehensive understanding of the molecular mechanisms underlying its sexual dimorphism and deep-sea parasitic adaptations. Based on a high-quality genome assembly and multi-omics analysis, expanded and contracted gene families in the P. fimbriata genome are expected to be revealed, and sex-differentiation-related genes differently expressed between females and males may be identified. To this end, we are currently assembling and analyzing a chromosome-level genome for P. fimbriata based on advanced sequencing techniques, including PacBio long-read sequencing and Hi-C technology, with results forthcoming.

4.2. Phylogeny-Based Insights into the Origin and Evolution of Bopyrids

Our phylogenetic results strongly support the current classification system on Epicaridean isopods and the monophyly of different genera. Most importantly, we found that P. fimbriata was located at the base of the phylogenetic tree. This validates a long-standing morphological hypothesis, which supposes Pleurocryptella to be the earliest diverging genus in Bopyridae. This perspective is supported by several ancestral morphological traits retained in this genus: females preserve seven oostegites, including rudimentary oostegites on pereomeres VI and VII (lacking in all other bopyrids), males with lamellar pleopods and uropods (the latter being a rare feature found in only a few other bopyrid genera), and both sexes possessing bisegmented maxilliped palps (an uncommon trait within the family) [53,54].
The discovery of a rich deep-sea marine biota prompts basic questions on their origin and evolution. Studies using phylogenetic approaches to classify current species ranges as shallow or deep have yielded inconsistent findings, with some revealing an onshore–offshore macroevolutionary pattern [55,56] and others indicating the opposite [57,58]. The genus Pleurocryptella is now known to be distributed at a wide depth range, with the deepest record being 5130 m (P. altalis). The samples of P. fimbriata in this study were taken from a deep-sea cold seep with a depth of more than 1000 m. Therefore, the basal position of deep-sea P. fimbriata on the phylogenetic tree and its ancestral morphological traits suggest that deep sea might play a key role in driving the evolution and diversification of bopyrid species.

4.3. Adaptations of the Mitochondrial Genome to Deep-Sea Environments in P. fimbriata

The deep-sea cold seep ecosystem is extremely high-pressure, low in oxygen, and rich in toxic substances like methane [59,60,61]. It is significant to classify the adaptive mechanisms of deep-sea organisms. Mitochondria are often referred to as the “powerhouses” of the cell, with the primary function of generating ATP, which is the cell’s main energy source. Positive selection at specific sites within the COX1, NAD2, and NAD4 genes in P. fimbriata indicates the adaptive evolution of its mitochondrial genome in response to the harsh deep-sea environment. NADH dehydrogenase is the first and largest enzyme complex in the mitochondrial respiratory chain [62]. In P. fimbriata, as the subunit of the NADH dehydrogenase complex, NAD2 exhibited positive selection at 11 sites (42G, 54G, 100M, 114N, 124I, 153G, 174V, 207K, 243T, 266M, and 278L) as well as NAD4 (11 sites: 45S, 68N, 70L, 176S, 225S, 230H, 285W, 358G, 368Y, 369M, and 401W) (Table 6). These residue substitutions in NADs likely alter proton-pumping efficiency [63,64] and may enhance the energy metabolism of the species under harsh deep-sea conditions, as suggested in studies for deep-sea mussels, clams, shrimps, and anomurans [65,66,67,68,69]. Additionally, two residues (397K and 456Y) in the COX1 gene encoding cytochrome c oxidase were also found to be under positive selection (Table 6). As another critical component of the respiratory chain, the positive selection of COX1 in P. fimbriata may also facilitate its adaptation to the extreme environments of deep sea and its parasitic lifestyle, as revealed in other studies [65,67,69,70,71].

5. Conclusions

This study presents the first genomic survey of P. fimbriata, a deep-sea parasitic isopod from cold-seep ecosystems. Key genomic features of P. fimbriata were uncovered, which showed a smaller genome size, high heterozygosity, and repetitive sequence content. Based on successfully assembling the complete mitochondrial genome and a phylogenetic analysis, the basal position of deep-sea P. fimbriata on the phylogenetic tree and its ancestral morphological traits suggested that deep sea was critical in the origin and diversification of bopyrid species. Positive selection was detected in COX1, NAD2, and NAD4, which revealed the adaptive foundation of P. fimbriata to the harsh habitat at the mitochondrial genome level. The identification of candidate mitochondrial molecular markers provided tools for a population genetic investigation of P. fimbriata. Further studies of P. fimbriata incorporating transcriptomics, chromosome-level genome assemblies, and comparative genomics will deepen our understanding for the molecular mechanisms of deep-sea parasitism.

Author Contributions

Conceptualization: M.H. and Z.S.; methodology: A.W. and M.H.; formal analysis: A.W. and M.H.; writing—original draft preparation: A.W.; writing—review and editing: M.H. and Z.S.; supervision: M.H. and Z.S.; funding acquisition: M.H. and Z.S. All authors have read and agreed to the published version of the manuscript.

Funding

This research was funded by the National Science Foundation of China (NSFC) for Distinguished Young Scholars, grant number 42025603; the NSFC Innovative Group Grant, grant number 42221005; and the NSFC, grant number 42376143. The APC was funded by the NSFC for Distinguished Young Scholars, grant number 42025603.

Institutional Review Board Statement

Not applicable.

Data Availability Statement

The clean data from the genome survey have been deposited in the NCBI Sequence Read Archive (SRA) under accession number SRR27941652. The complete mitochondrial genome of P. fimbriata has been deposited in the NCBI GenBank database under accession number PV243289.

Acknowledgments

The samples were collected by RV KEXUE. The authors wish to thank the crew for their help during the collection of the samples.

Conflicts of Interest

The authors declare no conflicts of interest.

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Figure 1. Sampling location of P. fimbriata at Site F in the South China Sea marked by the red dot. The inset at the lower right shows a photograph of P. fimbriata, with the larger specimen representing the female and the smaller one representing the male. The scale bar represents 1 cm.
Figure 1. Sampling location of P. fimbriata at Site F in the South China Sea marked by the red dot. The inset at the lower right shows a photograph of P. fimbriata, with the larger specimen representing the female and the smaller one representing the male. The scale bar represents 1 cm.
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Figure 2. K-mer (K = 17) analysis for the estimation of the genome size of P. fimbriata. The X-axis represents sequencing coverage and the Y-axis represents the frequency of each coverage.
Figure 2. K-mer (K = 17) analysis for the estimation of the genome size of P. fimbriata. The X-axis represents sequencing coverage and the Y-axis represents the frequency of each coverage.
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Figure 3. Gene map of the mitogenome of P. fimbriata. CR: control region; PCG: protein-coding gene; rRNA: ribosomal RNA; tRNA: transfer RNA.
Figure 3. Gene map of the mitogenome of P. fimbriata. CR: control region; PCG: protein-coding gene; rRNA: ribosomal RNA; tRNA: transfer RNA.
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Figure 4. Phylogenetic estimate of relationships within the suborder Epicaridea based on the 13 PCGs using ML and BI analyses. The ML bootstrap support values (left) and BI posterior probability (right) are denoted at each node.
Figure 4. Phylogenetic estimate of relationships within the suborder Epicaridea based on the 13 PCGs using ML and BI analyses. The ML bootstrap support values (left) and BI posterior probability (right) are denoted at each node.
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Table 1. Mitochondrial genome information for the species used in the phylogenetic analysis.
Table 1. Mitochondrial genome information for the species used in the phylogenetic analysis.
SpeciesHostOriginTaxonomic StatusLength (bp)Accession
Number
Pleurocryptella fimbriataMunidopsidae [10]Deep-sea cold seepPleurocryptellinae14,711PV243289
Orthione mesoamericanaUpogebiidae [29]Shallow seaPseudioninae14,377MG729627
Gyge ovalisUpogebiidae [30]Shallow seaPseudioninae14,268KY038053
Aparapenaeon japonicaPenaeoidea [9]Shallow seaOrbioninae14,360MK886810
Parapenaeon diatropaPenaeoidea [9]Shallow seaOrbioninae14,405MG753993
Parasymmetrorbione bicaudaPenaeoidea [9]Shallow seaOrbioninae14,284MK886808
Parapenaeonella distinctaPenaeoidea [9]Shallow seaOrbioninae14,369MH084345
Parapenaeonella expansaPenaeoidea [9]Shallow seaOrbioninae14,384MG807478
Portunion sp.Brachyura [2,31]Shallow seaEntioninae14,604OL677861
Portunion conformisBrachyura [32]Shallow seaEntioninae14,210OP829302
Ichthyoxenos japonensisTeleostei [33]Fresh waterCymothoidae15,440NC039713
Elthusa poutassouiensisTeleostei [34]Shallow and deep seaCymothoidae15,223OR800751
Table 2. Summary of genome assembly statistics for P. fimbriata.
Table 2. Summary of genome assembly statistics for P. fimbriata.
Total Length (bp)Total NumberMaximum Length (bp)N50 Length (bp)GC Content (%)
Contig888,848,4072,289,701137,55072635.09
Scaffold927,035,5471,960,944266,03098935.09
Table 3. Organization of the complete P. fimbriata mitogenome.
Table 3. Organization of the complete P. fimbriata mitogenome.
GeneStart
Position		Stop
Position		Intergenic LengthStart
Code		Stop
Code		Size
(bp)		Strand
COX1115390ACGTTG1539+
tRNA-Leu (TAA)15381595−2 58+
COX2159622760ATTGGT681+
tRNA-Lys (TTT)227723400 64+
tRNA-Asp (GTC)23392397−2 59+
ATP8239825530GTGTAA156+
ATP625473218−7GTGTAA672+
COX332004000−19ATAAGT801+
tRNA-Gly (TCC)400140580 58+
tRNA-Arg (TCG)406141192 59+
NAD34150449730TTGGAA348+
449845570 60+
NAD14572549214GTGTAA921_
tRNA-Leu (TAG)549355540 62_
tRNA-Asn (GTT)55505613−5 64+
12S rRNA561463470 734+
tRNA-Trp (TCA)634864070 60_
Control region640868380 431+
CYTB683979750ATTTAG1137_
tRNA-Thr (TGT)797680340 59_
NAD5803997634ATATAG1725+
tRNA-Phe (GAA)97569819−8 64+
tRNA-His (GTG)98189876−2 59_
NAD4982711,218−50ATGTAA1392_
NAD4L11,33111,633112TTGTAA303_
tRNA-Pro (TGG)11,63411,6970 64_
NAD611,70012,1852ATATAA486+
tRNA-Ser (TGA)12,18412,245−2 62+
16S rRNA12,24713,4301 1184_
tRNA-Val (TAC)13,42913,492−2 64_
tRNA-Gln (TTG)13,49113,551−2 61_
tRNA-Met (CAT)13,55713,6175 61+
NAD213,61814,6160ATCTAA999+
tRNA-Cys (GCA)14,60214,652−15 51_
tRNA-Tyr (GTA)14,65214,711−1 60_
Table 4. Summary of candidate SNPs in the mitochondrial PCGs of P. fimbriata.
Table 4. Summary of candidate SNPs in the mitochondrial PCGs of P. fimbriata.
GeneLength (bp)TransitionTransversionMutation Rates
(%)		Amino Acid Change
COX11559000
COX2726210.44G→W
ATP8156000
ATP6672120.45K→S; M→L
COX3840100.13
NAD3396100.29
NAD1991000
CYTB1137110.18
NAD51725310.24I→T
NAD41392400.30
NAD4L303110.66L→I
NAD6486100.21
NAD2999300.30
Table 5. Selective pressure analyses of the mitochondrial PSGs in P. fimbriata using one-ratio and two-ratio models.
Table 5. Selective pressure analyses of the mitochondrial PSGs in P. fimbriata using one-ratio and two-ratio models.
GeneModellnL2ΔlnLParameter
COX1M0−7860.520 ω0 = 0.019
M2−7858.5903.859 *ω0 = 0.020; ω1 = 0.070
COX2M0−4311.744 ω0 = 0.029
M2−4311.7420.003ω0 = 0.029; ω1 = 0.031
ATP8M0−1127.946 ω0 = 0.207
M2−1126.7672.358ω0 = 0.224; ω1 = 0.003
ATP6M0−4851.615 ω0 = 0.072
M2−4851.6120.006ω0 = 0.072; ω1 = 0.076
COX3M0−5126.943 ω0 = 0.057
M2−5125.8362.214ω0 = 0.060; ω1 = 0.017
NAD3M0−2275.007 ω0 = 0.080
M2−2274.6380.738ω0 = 0.077; ω1 = 0.204
NAD1M0−6009.838 ω0 = 0.068
M2−6008.6012.473ω0 = 0.067; ω1 = 0.155
CYTBM0−6327.929 ω0 = 0.048
M2−6325.3605.138 *ω0 = 0.045; ω1 = 0.110
NAD5M0−9665.997 ω0 = 0.0453
M2−9665.1981.598ω0 = 0.044; ω1 = 0.095
NAD4M0−9551.749 ω0 = 0.052
M2−9551.5250.448ω0 = 0.052; ω1 = 0.011
NAD4LM0−2204.944 ω0 = 0.062
M2−2204.9440.001ω0 = 0.061; ω1 = 0.065
NAD6M0−3834.889 ω0 = 0.071
M2−3834.5780.621ω0 = 0.071; ω1 = 0.005
NAD2M0−7556.800 ω0 = 0.085
M2−7556.5400.521ω0 = 0.086; ω1 = 0.045
Note: * indicates diverged selective pressures between paraphyletic clades of P. fimbriata and other bopyrid species with a statistical significance of a p-value of <0.05 using LRT tests in the branch model.
Table 6. Selective pressure analyses of the mitochondrial PCGs in P. fimbriata using a branch-site model.
Table 6. Selective pressure analyses of the mitochondrial PCGs in P. fimbriata using a branch-site model.
GeneModellnL2ΔlnLParameterPositively Selected Site
COX1Null model−7676.200 P0 = 0.865; P1 = 0.073; P2a = 0.057; P2b = 0.005; ω0 = 0.012; ω1 = 1.000; ω2a = 1.000; ω2b = 1.000
Model A−7679.1905.982 *P0 = 0.877; P1 = 0.076; P2a = 0.043; P2b = 0.004; ω0 = 0.012; ω1 = 1.000; ω2a = 20.550; ω2b = 20.550397 K (0.992); 456 Y (0.994)
NAD2Null model−2405.140 P0 = 0.530; P1 = 0.191; P2a = 0.205; P2b = 0.074; ω0 = 0.070; ω1 = 1.000; ω2a = 1.000; ω2b = 1.000
Model A−2405.3904.502 *P0 = 0.526; P1 = 0.192; P2a = 0.207; P2b = 0.075; ω0 = 0.072; ω1 = 1.000; ω2a = 6.577; ω2b = 6.57742 G (0.996); 54 G (0.974); 100 M (0.975); 114 N (0.985); 124 I (0.973); 153 G (0.965); 174 V (0.991); 207 K (0.997); 243 T (0.984); 266 M (0.978); 278 L (0.964)
NAD4Null model−8918.260 P0 = 0.844; P1 = 0.156; P2a = 0.000; P2b = 0.000; ω0 = 0.053; ω1 = 1.000; ω2a = 1.000; ω2b = 1.000
Model A−8916.40043.675 **P0 = 0.672; P1 = 0.110; P2a = 0.187; P2b = 0.031; ω0 = 0.050; ω1 = 1.000; ω2a = 154.839; ω2b = 154.83945 S (0.994); 68 N (0.989); 70 L (0.956); 176 S (0.993); 225 S (0.968); 230 H (0.961); 285 W (0.970); 358 G (0.981); 368 Y (0.981); 369 M (0.952); 401 W (0.988)
Note: ** and * indicate positive selection in P. fimbriata with a statistical significance of p-values of <0.01 and <0.05, respectively.
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Wang, A.; Hui, M.; Sha, Z. First Genomic Survey of Pleurocryptella fimbriata Provides Preliminary Insights into Genome Characteristics and Evolution of a Deep-Sea Parasitic Isopod. Diversity 2025, 17, 297. https://doi.org/10.3390/d17040297

AMA Style

Wang A, Hui M, Sha Z. First Genomic Survey of Pleurocryptella fimbriata Provides Preliminary Insights into Genome Characteristics and Evolution of a Deep-Sea Parasitic Isopod. Diversity. 2025; 17(4):297. https://doi.org/10.3390/d17040297

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Wang, Aiyang, Min Hui, and Zhongli Sha. 2025. "First Genomic Survey of Pleurocryptella fimbriata Provides Preliminary Insights into Genome Characteristics and Evolution of a Deep-Sea Parasitic Isopod" Diversity 17, no. 4: 297. https://doi.org/10.3390/d17040297

APA Style

Wang, A., Hui, M., & Sha, Z. (2025). First Genomic Survey of Pleurocryptella fimbriata Provides Preliminary Insights into Genome Characteristics and Evolution of a Deep-Sea Parasitic Isopod. Diversity, 17(4), 297. https://doi.org/10.3390/d17040297

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