Long-Read Mitogenomes Reveal Hidden Control-Region Architecture in Smeringurus mesaensis and Overlooked Tandem Repeats in Scorpions

Repetitive regions of animal mitochondrial genomes are biologically informative but often difficult to assemble, raising the possibility that structured variation in mitochondrial control regions may be overlooked, especially in short-read datasets. We used Oxford Nanopore long-read sequencing to assemble five complete mitochondrial genomes of the dune scorpion Smeringurus mesaensis and resolve and validate the structure of the mitochondrial control region. In all five individuals, the 1598–1600 bp control region contained six complete 202 bp tandem repeats and one 92 bp terminal partial repeat. Mean control-region coverage ranged from 15.9× to 49.8×, with 10–33 reads spanning the 5′ repeat-array boundary, 14–25 spanning a central repeat junction, and three reads spanning the complete repeat array. Despite this repetitive architecture, the arrays were highly organized: repeats R2–R6 were identical within individuals, whereas R1 and the terminal partial repeat retained consistent positional differences. The 5′ non-repeat region showed significant local similarity to the control regions of Vaejovis mexicanus and V. smithi (72.8% and 69.6% identity), whereas the 202 bp repeat produced only short, nonsignificant matches. This pattern suggests that replication slippage and sequence homogenization have jointly shaped control-region evolution. A comparative survey of published scorpion mitogenomes further indicated that tandem repeats are more widespread and structurally diverse than generally reported. These results demonstrate the value of long reads for direct validation of repeat-rich mitochondrial architecture and highlight control-region structure as an underappreciated feature of scorpion mitogenome evolution.