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. 2025 Aug 8;10(9):800–803. doi: 10.1080/23802359.2025.2544685

The complete mitochondrial genome of Protankyra verrilli Théel, 1886 (Apodida: Synaptidae)

Wendan Mu 1,✉, Jie Chen 1, Changle Li 1
PMCID: PMC12337721  PMID: 40792196

Abstract

In this study, we sequenced and annotated the complete mitochondrial genome of Protankyra verrilli. The 16,970 bp mitogenome contains 13 protein-coding genes, 22 transfer RNA genes (duplications of trnL and trnS), and two ribosomal RNA genes. The phylogenetic analysis of the 13 protein-coding genes in echinoderms indicated that P. verrilli has a close evolutionary relationship with Euapta godeffroyi (Apodida: Synaptidae).

Keywords: Protankyra verrilli, mitochondrial genome, phylogenetic analysis

Introduction

Species in the order of Apodida are distributed from shallow to deep oceanic waters and are usually nocturnal deposit feeders (Pawson et al. 2010; Sun et al. 2021; Pu et al. 2024), and there are few studies reporting the genetic information of the genus Protankyra. Hence, investigations of its genomes will fill in such knowledge gaps and further provide genetic material for studying phylogenetic relationships and identifying taxonomic units as demonstrated in other rarely studied marine organisms (Kilpert and Podsiadlowski 2006; Jia et al. 2020). Here, we reported the complete mitochondrial genome of the sea cucumber Protankyra verrilli Théel, 1886, and investigated the phylogenetic position of the genus Protankyra in Holothuroidea.

Materials and methods

The specimens of P. verrilli were collected and preserved in 95% ethanol from the Beibu Gulf (21°8′53.52″N, 109°3′21.24″E) at the depth of 23.3 m in August 2020. This animal was deposited as voucher specimen at the Fourth Institute of Oceanography, Ministry of Natural Resources (No. IDXB3, Wendan Mu, muwendan@4io.org.cn) (Figure 1). Total genomic DNA was extracted from preserved subcutaneous muscle tissue samples using the TIANGEN Marine Animal DNA kit (TIANGEN, Beijing, China) and stored at −20 °C. The complete mitochondrial genome of P. verrilli was sequenced on an Illumina NovaSeq6000 platform (San Diego, CA) using the paired-end technology with an average read length of 350 bp. The reads were assembled using SPAdes Genome Assembler (v3.14.1). The completeness of the mitogenome was validated by assessing sequencing depth coverage data using BAMStats, which were obtained through the alignment of raw sequencing reads to the reference mitogenome map (Supplementary Figure S1). The average depth of coverage was 40.16. ORFfinder (http://www.ncbi.nlm.nih.gov/projects/gorf/orfig.cgi) and BLAST (http://blast.ncbi.nlm.nih.gov/Blast.cgi) were used to identify the protein-encoding genes and ribosomal RNA (rRNA) genes. The transfer RNA (tRNA) genes were identified by MITOS webserver (http://mitos2.bioinf.uni-leipzig.de/index.py) (Bernt et al. 2013) and tRNAscan-SE 2.0 (http://lowelab.ucsc.edu/tRNAscan-SE/) (Chan et al. 2021). Sequences of 13 partitioned amino acid sequences of protein-coding genes from 12 Holothuroidea species and two outgroup species from Crinoidea were aligned by MAFFT v7.037b (Katoh and Standley 2013). Ambiguously aligned regions were removed using Gblocks ver. 0.91b (Castresana 2000) with the default option. ProtTest version 3.4 (Darriba et al. 2011) was used to select the best-fit substitution models for each data partition. Phylogenetic reconstruction was performed using maximum-likelihood (ML) and neighbor-joining (NJ) methods in MEGA 5.0 (Tamura et al. 2011) with 1000 bootstrap replicates.

Figure 1.

Figure 1.

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Photograph of Protankyra verrilli, captured by Wendan Mu.

Results

The complete mitogenome sequence of P. verrilli is 16,970 bp (GenBank accession number: ON018239) and is highly AT-biased (21.32% A, 11.17% C, 24.45% G, and 43.06% T). The P. verrilli contains 13 protein-coding genes, 22 tRNA genes (duplication of trnL and trnS), two rRNA genes, and one control region (Figure 2). Except for cytb, 12S rRNA and nine tRNAs are encoded in the light strand (L-strand), and the other 26 genes are distributed in the heavy strand (H-strand). Phylogenetic analysis was conducted using the amino acid sequences of 13 concatenated mitochondrial protein-coding genes to infer evolutionary relationships (Figure 3). Phylogenetic analyses using ML and NJ methods yielded highly congruent tree topologies, with nearly all inferred phylogenetic relationships supported by high bootstrap values (ML/NJ: 98–100) (Figure 3). Mitogenomic phylogenetic analyses revealed that P. verrilli clustered with Euapta godeffroyi within the Apodida clade (Figure 3).

Figure 2.

Figure 2.

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Genome map and annotation of Protankyra verrilli complete mitochondrial genome. Genes out of the circle encode on positive strand (direction 5′ → 3′) and genes inner of the circle encode on negative strand (direction 3′ → 5′). Different colors indicate different types of genes and regions.

Figure 3.

Figure 3.

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Phylogenetic trees based on complete mitogenomes of Protankyra verrilli (ON018239) and 13 other species. The following sequences were used: Apostichopus nigripunctatus NC_013432 (Sasaki and Hamaguchi, unpublished), Apostichopus japonicus NC_012616 (Sun et al. 2010), 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), Cucumaria miniata NC_005929 (Scouras et al. 2004), Phyllophorella liuwutiensis NC_057437 (Yang et al. 2020), Benthodytes marianensis NC_040968 (Mu et al. 2018), Peniagone sp. YYH-2013 KF915304 (Huo et al. unpublished), Euapta godeffroyi LC704718 (Ogawa et al. 2022), Antedon mediterranea NC_010692 (Perseke et al. 2008), and Florometra serratissima NC_001878 (Scouras and Smith 2001). The branch length was determined by the ML analysis. ML/NJ bootstrap values are given at each node for branching.

Discussion and conclusions

A comparative analysis of the gene order between P. verrilli and the currently available Synaptidae mitogenome, E. godeffroyi, reveals that several tRNA genes and three protein-coding genes have undergone rearrangements (Ogawa et al. 2022). The Apodida represented a monophyletic group and together with the sister groups Elasipodida, Dendrochirotida, Holothuriida, and Synallactida clustered with the holothuroids group, which supported the classification of Holothuroidea (Miller et al. 2017).

This study characterized the complete mitochondrial genome of P. verrilli for the first time. We analyzed the mitogenome features and phylogenetic relationships of P. verrilli. Our study provides molecular evidence for future phylogenetic analysis of Protankyra.

Supplementary Material

Figure S1.jpg
TMDN_A_2544685_SM3946.jpg (578KB, jpg)

Acknowledgments

Thanks to the responsible editor and the reviewers for their work, which has significantly improved this paper.

Funding Statement

This study was supported by 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, Guangxi Major Science and Technology Special Project (GuiKe AA24206044) awarded to JC.

Ethical approval

The study did not involve the study of vertebrates or regulated invertebrates, and samples were 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 specimen). All the research meets ethical guidelines and adheres to the legal requirements of the study country.

Disclosure statement

No potential conflict of interest was reported by the author(s).

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 ON018239. The associated Bio-Sample, SRA, and BioProject numbers are SAMN28649446, SRR19426740, and PRJNA842447, respectively.

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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.jpg
TMDN_A_2544685_SM3946.jpg (578KB, jpg)

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 ON018239. The associated Bio-Sample, SRA, and BioProject numbers are SAMN28649446, SRR19426740, and PRJNA842447, respectively.

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