Complete Mitochondrial Genome Characterization of a Traditional Agroecosystem-Derived Natural Mutant Crucian Carp (Carassius auratus)

The mitochondrial genome of a natural mutant crucian carp (Carassius auratus, NMCC), a culturally and ecologically vital species within the FAO-recognized Congjiang Rice-Fish-Duck Complex System, was sequenced and annotated to elucidate its genetic distinctiveness and evolutionary relationships. Phylogenetic analysis of 11 Carassius mitogenomes resolved three major clades, with the Congjiang strain forming a distinct subclade alongside diploid, triploid, and tetraploid crucian carp variants. The findings highlight mitochondrial-nuclear co-evolution as a stabilizing force in polyploid systems and underscore the genetic uniqueness of the NMCC.