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

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.