Unexpectedly low variability of mitochondrial control region in the Whitespotted Bambooshark ( Chiloscyllium plagiosum )

The mitochondrial protein-coding genes (PCGs) are generally less variable than control region (CR) in vertebrate mitogenomes. Conversely, an unexpected mitochondrial variation pattern in the Whitespotted Bambooshark (Chiloscyllium plagiosum) was observed in this study. Comparative analyses based on 17 mitogenome assemblies detected a total of 62 variable sites, most of which (50/62, 80.65%) were located in PCGs, whereas only three were in the CR, indicating unexpectedly low variability of the CR. In addition, most variations in PCGs were categorized as synonymous substitutions (40/50, 80%), suggesting relaxed purifying selection acting on these genes. Selection tests further confirmed purifying selection as a major driving force. We further sequenced CR and Cyt b gene fragments of 144 individuals for population-scale comparison: two variable sites and extremely low genetic diversity (π = 0.00072) were observed based on CR sequences, while 12 variable sites were detected in the Cyt b gene (π = 0.00324), suggesting Cyt b was more suitable for population genetics studies than CR. Our results uncovered an unusual mitochondrial variation pattern of C. plagiosum at the mitogenome level, deepening the understanding of mitochondrial variation and evolution of chondrichthyans. Further studies on mitochondrial genetic variation in other cartilaginous fish species will help elucidate the universality of this unusual variation pattern.