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The first complete mitochondrial genome and phylogenetic analysis of Clypeaster virescens (Clypeasteroida, Clypeasteridae)

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Abstract

The complete mitochondrial genome of Clypeaster virescens was sequenced and analyzed to clarify its genomic features and evolutionary placement within Echinoidea. The 15,781 bp circular mitogenome encoded 37 mitochondrial genes, including 13 protein-coding genes, 22 tRNA genes, and 2 rRNAs, along with one control region. The nucleotide composition of the mitochondrial genome exhibits a high A + T content, with negative A-T skew and G-C skew. Using a 35-taxon dataset (34 echinoids and one holothuroid outgroup), phylogenetic analyses based on the complete mitochondrial genome robustly placed C. virescens within a well-supported Clypeasteroida clade alongside S. mai and A. mannii. The recovered topology also resolved major echinoid orders with strong support, including the early divergence of Echinothurioida and Diadematoida and the close relationship between Clypeasteroida and Spatangoida. These findings provide the first complete mitogenome for C. virescens, expand available molecular resources for Clypeasteroida, and establish a stable phylogenetic framework for future evolutionary and comparative studies on irregular echinoids.

Data availability

The data that support the findings of this study are freely available in GenBank of NCBI (https://www.ncbi.nlm.nih.gov/), with accession number PQ838327.

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Funding

The study was supported by the Fundamental Research Funds for Zhejiang Provincial Universities and Research Institutes (2024J002); National Natural Science Foundation of China (NSFC) (NO.42576115); Zhejiang Provincial Natural Science Foundation of China (LY22D060001&LY20C190008); Key research and development projects in Xizang (XZ202301ZY0012N).

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Authors and Affiliations

  1. Marine Science and Technology College, Zhejiang Ocean University, Zhoushan, 316022, China

    Jinghua Wu, Mingzhe Han, Luxiu Gao, Shuaishuo Kang, Xinyi Niu, Bingjian Liu & Tianming Wang

  2. National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, Zhejiang Ocean University, Zhoushan, 316022, China

    Luxiu Gao

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  1. Jinghua Wu
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  2. Mingzhe Han
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  3. Luxiu Gao
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Contributions

JHW, BJL and TMW conceived and designed the research. JHW, MZH, LXG, SSK, XYN, BJL and TMW conducted experiments, analyzed data, and wrote the manuscript. All authors have read and agreed to the published version of the manuscript.

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Bingjian Liu or Tianming Wang.

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Wu, J., Han, M., Gao, L. et al. The first complete mitochondrial genome and phylogenetic analysis of Clypeaster virescens (Clypeasteroida, Clypeasteridae).
Sci Rep (2026). https://doi.org/10.1038/s41598-025-33261-7

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Keywords

  • Clypeasteroida

  • Clypeaster virescens
  • Mitogenome
  • Phylogenetic

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