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. 2025 Sep 13;10(10):948–952. doi: 10.1080/23802359.2025.2559710

Characterization and phylogenetic analysis of the complete mitochondrial genome of Benthodytes gosarsi Gebruk 2008 (echinodermata: holothuroidea: elasipodida) from deep-sea environments

Wendan Mu a,✉, Changle Li a, Jun Liu b, Haibin Zhang b
PMCID: PMC12434848  PMID: 40959689

Abstract

Deep-sea organisms exhibit remarkable adaptations to extreme environmental conditions. It is important to elucidate the survival mechanisms of deep-sea life by exploring their genetic characteristics and origins. This study reports the complete mitochondrial genome of a deep-sea holothurian species (Benthodytes gosarsi). The mitochondrial genome of B. gosarsi is 17,133 bp in length and encodes 13 PCGs, 2 rRNAs, and 22 tRNAs. The heavy strand of B. gosarsi mtDNA consists of 31.62% A, 13.30% G, 37.38% T, and 17.70% C bases. Phylogenetic analysis with 18 mitogenomes from five sea cucumber orders determined the phylogenetic position of B. gosarsi within Holothuroidea. This study provides new insights into the genetic structure and phylogenetic relationships of B. gosarsi, contributing to a better understanding of deep-sea adaptation in holothurians.

Keywords: Mitochondrial genome, holothuroidea, Benthodytes gosarsi, phylogenetic analysis

Introduction

Holothuroidea (sea cucumbers) is one of the five extant classes of echinoderms, with approximately 1,700 species (Paulay 2023). These marine organisms inhabit diverse environments ranging from polar regions to the deepest ocean trenches (Mark O’Loughlin et al. 2011; Gallo et al. 2015). Deep-sea environments represent the largest ecosystem on Earth, encompassing over 50% of the planet’s surface (Woolley et al. 2016). Deep-sea habitats are known for extreme conditions, such as low temperatures, steady darkness, high hydrostatic pressure, and scarce food resources (Sanders and Hessler 1969). Despite substantial progress in biological sciences, research on deep-sea organisms remains relatively limited compared to studies of other ecosystems (Danovaro et al. 2014). Complete mitochondrial genomes provide genomic characteristics for studying species evolution and phylogenetic relationships (Cai et al. 2006; Lei et al. 2010; Mu et al. 2018). In the present study, we sequenced the complete mitochondrial genome of Benthodytes gosarsi Gebruk 2008 and examined its phylogenetic position within Holothuroidea.

Materials and methods

Benthodytes gosarsi was collected from the South China Sea (18.199595°N, 114.353466°E, at 3529 m depth) (Figure 1), by the human occupied vehicle (HOV) “shenhaiyongshi” in June 2018, and preserved at −80 °C. The specimen has been deposited at the Institute of Deep-sea Science and Engineering, CAS, with the assigned voucher number SQW137 (Wendan Mu, muwendan@4io.org.cn). The complete mitochondrial genome of B. gosarsi was amplified via polymerase chain reaction (PCR) using four specific primer pairs, followed by sequencing through the application of Sanger dideoxy sequencing technology (see details in Supplementary Figure S1 and Table S1). The PCR cycling conditions were set up as follows: an initial denaturation step at 94 °C for 5 min, followed by 35 cycles consisting of denaturation at 94 °C for 30 s, annealing at 55 °C for 1 min (as detailed in Table S1), and extension at 72 °C for a duration of 2–7 min, depending on the expected length of the PCR products. The process was completed by subjecting the mixture to a final extension at 72 °C for 10 min. Genomic DNA was extracted from preserved muscle tissue samples using the TIANGEN Marine Animal DNA kit (TIANGEN, China). The base calling was performed using Phred software (Ewing et al. 1998; Ewing and Green 1998) with a quality score of 20. Manual adjustments were conducted to correct erroneous or low-quality assemblies using the Consed software (Gordon et al. 1998). Protein-coding genes (PCGs) and ribosomal RNA genes were identified using ORFfinder (http://www.ncbi.nlm.nih.gov/orffinder), and BLAST alignments (http://www.ncbi.nlm.nih.gov/BLAST). Transfer RNA genes were predicted using tRNAscan-SE 2.0 (http://lowelab.ucsc.edu/tRNAscan-SE/) (Lowe and Chan 2016) and MITOS webserver program (http://mitos.bioinf.uni-leipzig.de/index.py) (Bernt et al. 2013). MEGA 5.0 was utilized to analyze codon usage bias (Tamura et al. 2011). The mitochondrial gene map was generated using GenomeVx (Conant and Wolfe 2008).

Figure 1.

Figure 1.

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Photograph of Benthodytes gosarsi, captured by deep-sea human-occupied vehicle (HOV) “shenhaiyongshi.”

To determine the phylogenetic position of B. gosarsi within Holothuroidea, we conducted a comparative analysis using mitochondrial genome sequences for 17 holothuroid species from the NCBI database and the one obtained in this study. Two echinoid species (Strongylocentrotus purpuratus NC_001453 and Paracentrotus lividus NC_001572) were used as outgroups. Both maximum likelihood (ML) and Bayesian inference (BI) molecular phylogenetic analyses were conducted using 13 PCGs. These genes were aligned using MAFFT v7.526b (Katoh and Standley 2013), and ambiguous regions were moved using Gblocks v0.91b (Castresana 2000). The optimal evolutionary model for each data partition was identified using ProtTest v3.4 (Darriba et al. 2011). Then, ML analysis was carried out in IQ-Tree (Minh et al. 2020) with 1,000 bootstrap replicates. Bayesian inference analysis was performed using MrBayes v3.2.6 (Ronquist et al. 2012), with Markov chain Monte Carlo (MCMC) simulations running for 50,000,000 generations, sampling every 1,000 generations. After discarding the first 25,000 sampled trees as burn-in, a subsequent set of 25,000 trees was employed to calculate Bayesian posterior probabilities (BPP) and construct a 50% majority-rule consensus tree.

Result and discussion

The mitochondrial genome of B. gosarsi is 17,133 bp in length, containing 13 PCGs, 22 tRNA genes (including duplicate trnL and trnS), and two rRNA genes (Figure 2). The B. gosarsi mitogenome has been deposited in the GenBank database (GenBank accession: MK617317). The nucleotide composition of the heavy strand is 31.62% adenine (A), 13.30% guanine (G), 37.38% thymine (T), and 17.70% cytosine (C). Among the 13 PCGs, nad6 is the only gene encoded on the light strand and terminates with a TAG stop codon, while the remaining 12 PCGs are encoded on the heavy strand and terminate with TAA stop codons. Collectively, these PCGs encode 3,786 amino acids. The 16S rRNA gene is 1,434 bp in length with an A + T content of 70.43%, and the 12S rRNA gene is 833 bp in length with an A + T content of 66.03%. Two putative control regions (CRs) have been identified in the mitogenome of B. gosarsi: CR1 is 818 bp in length (A + T% = 72.49) and is flanked by trnE and trnA, while CR2 is 890 bp in length (A + T% = 73.15) and is flanked by trnT and 16S. Sequence similarity of CR1 and CR2 was 90.90%. Among the published mitochondrial genomes of sea cucumbers, duplicated CRs have also been found in the mitogenomes of Benthodytes marianensis, Benthodytes sp. Gxx-2023, and Cucumaria miniata (Mu et al. 2018). Numerous studies support the hypothesis that mitogenomes containing duplicated CRs may exhibit enhanced replication efficiency compared to those with a single CR (Kumazawa et al. 1996; Arndt and Smith 1998; Umeda et al. 2001). The mechanisms by which these duplicated CRs originated and the evolutionary patterns of mitogenomes harboring duplicated CRs in sea cucumbers remain fascinating but largely unresolved issues.

Figure 2.

Figure 2.

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Circular map of the Benthodytes gosars mitochondrial genome. Different colors indicate different types of genes and regions.

Over the past two decades, numerous studies on mitochondrial gene arrangements in Holothuroidea have been published (Boore 1999; Perseke et al. 2008; Shen et al. 2009; Perseke et al. 2010; Mu et al. 2018). In this study, a comparative analysis of gene order between B. gosarsi and the two currently available Benthodytes mitogenomes, B. marianensis and Benthodytes sp. Gxx-2023 reveals consistent genomic features (Mu et al. 2018; He et al. 2024). Phylogenetic analyses using BI and ML methods generated similar tree topologies, with most clades receiving strong support (posterior probability ≥0.95, bootstrap support ≥80; Figure 3). Mitogenomic phylogeny indicated that B. gosarsi clusters with B. marianensis, forming the Psychropotidae clade. This clade further groups with Peniagone sp. YYH-2013 and Scotoplanes sp. TT-2017 formed the Elasipodida clade. Subsequently, the order Elasipodida clusters with Dendrochirotida, Holothuriida, and Synallactida, which is supported by previously published research (Smirnov 2012; Miller et al. 2017).

Figure 3.

Figure 3.

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Phylogenetic trees based on complete mitogenomes of Benthodytes gosarsi (MK617317) and 19 other species. The following sequences were used: Parastichopus nigripunctatus NC_013432 (Aasaki and Hamaguchi, unpublished), Apostichopus japonicus NC_012616 (Sun et al. 2010), Parastichopus californicus NC_026727 (Liu, unpublished), Parastichopus parvimensis NC_029699 (Zhang et al. unpublished), Stichopus horrens NC_014454 (Fan et al. 2011), Stichopus sp. SF-2010 NC_014452 (Fan and Hu, unpublished), Holothuria forskali NC_013884 (Perseke et al. 2010), Holothuria scabra NC_027086 (Xia et al. 2016), Colochirus quadrangularis NC_051929 (Wen, unpublished), Ocnus glacialis NC_082941 (Lee and Rhee, unpublished), Cucumaria miniata NC_005929 (Scouras et al. 2004), Phyllophorella liuwutiensis NC_057437 (Yang et al. 2020), Peniagone sp. YYH-2013 KF915304 (Huo et al. unpublished), Scotoplanes sp. TT-2017 LC416624 (Takano et al. 2019), Benthodytes marianensis MH208310 (Mu et al. 2018), Chiridota heheva NC_058250 (Sun et al. 2021), Chiridota sp. SS-2021 MW357262 (Sun et al. 2021), Strongylocentrotus purpuratus NC_001453 (Qureshi and Jacobs 1993), Paracentrotus lividus NC_001572 (Cantatore et al. 1989). The branch lengths are figured out using BI analysis. In the nodes, the first number is Bayesian posterior probability (BPP) and the ML analyses bootstrap probability is the second number.

Conclusion

In this study, the complete mitochondrial genome of B. gosarsi was sequenced for the first time. We analyzed the mitogenome features, codon usage, gene arrangement, and phylogenetic relationships of B. gosarsi. Our study provides valuable molecular evidence for future investigations into deep-sea sea cucumbers.

Supplementary Material

Figure S1.png
TMDN_A_2559710_SM3402.png (354.3KB, png)
Table S1.docx
TMDN_A_2559710_SM3401.docx (11.6KB, docx)

Acknowledgments

The authors·thank·captains and crews of R/V Tansuo 1, and deep-sea Human Occupied Vehicle (HOV) “Shenhaiyongshi” for their technical·support.

Funding Statement

This study was supported by the Youth Science Fund project of Guangxi Natural Science Foundation (2021GXNSFBA220041) awarded to WM, Guangxi Science and Technology Base and talent Special project (GuiKe AD20159002) awarded to WM, the Major scientific and technological projects of Hainan Province (ZDKJ2021036) awarded to HZ.

Ethical approval

The study does not involve the study of vertebrates or regulated invertebrates, and samples are collected in areas available for collection in public areas, in accordance with guidelines provided by the authors’ institutions and national or international regulations (Standards for sampling, detecting and preserving specimens). All the research meets ethical guidelines and adheres to the legal requirements of the study country.

Disclosure statement

No conflict of interest was reported by the authors.

Data availability statement

The genome sequence data that support the findings of this study are openly available in GenBank of NCBI at [https://www.ncbi.nlm.nih.gov/] under the accession number MK617317. The associated BioProject, Bio-Sample, and SRA numbers are PRJNA1221068, SAMN46725849 and SRR32271521, respectively. Additionally, the corresponding chromatogram files are accessible via Science Data Bank at 10.57760/sciencedb.2313.

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Associated Data

This section collects any data citations, data availability statements, or supplementary materials included in this article.

Supplementary Materials

Figure S1.png
TMDN_A_2559710_SM3402.png (354.3KB, png)
Table S1.docx
TMDN_A_2559710_SM3401.docx (11.6KB, docx)

Data Availability Statement

The genome sequence data that support the findings of this study are openly available in GenBank of NCBI at [https://www.ncbi.nlm.nih.gov/] under the accession number MK617317. The associated BioProject, Bio-Sample, and SRA numbers are PRJNA1221068, SAMN46725849 and SRR32271521, respectively. Additionally, the corresponding chromatogram files are accessible via Science Data Bank at 10.57760/sciencedb.2313.

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