Mitochondrial genome sequencing and evolutionary analysis of geoduck clam Panopea japonica

Geoduck clam ( Panopea japonica ), a large burrowing bivalve species, is primarily distributed in the Yellow Sea and Bohai Sea of China, Korean coastal waters, and marine areas near Hokkaido, Japan. Notably, wild populations in China's Yellow-Bohai Sea region have become commercially extinct. To elucidate the mitochondrial genomic characteristics and phylogenetic relationships of the geoduck clam, we conducted comprehensive assembly and characterization of its complete mitochondrial genome. The mitochondrial genome of the P. japonica measured 16,005 bp in length and encodes 37 genes, including 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes, and a non-coding control region (D-Loop region). The genomic GC-content was determined to be 35.9%, indicating a distinct AT bias. Analyses confirmed structural conformity with bivalve mitochondrial standards in gene order, promoter/terminator positions, and codon usage. The length of the D-loop region was identified as 837 bp. Intraspecific genetic distance ( P. japonica ) ranged 0.012–0.087, while interspecific distances ( Panopea genus) spanned 0.105–0.188. Phylogenetic congruence was observed across coxI - and mitogenome-based trees, genetic distance evaluations, and codon usage-based clustering analyses. This study establishes fundamental genetic data for P. japonica conservation and germplasm restoration.