Mitochondrial Genomes of Micropterus cataractae, Micropterus henshalli, and Micropterus punctulatus: Expanded Genetic Resources for Management

The shoal bass (SHB; Micropterus cataractae) and the Alabama bass (ALB; Micropterus henshalli) are species of freshwater fish in the Centrarchidae family of the order Centrarchiformes native to many states in the southeastern United States. Shoal bass currently face the threat of introgression with introduced black bass species in their native range. Conversely, Alabama bass have been introduced both intentionally by state resource managers and illegally by anglers outside of their native range throughout the United States, which could cause introgression with largemouth bass (M. nigricans) and other black bass species. In this study, we establish the first reference mitogenomes of ALB, SHB and spotted bass (SPB; M. punctulatus) for mitochondrial phylogenetics and (meta-)barcoding, which will also facilitate further variant detection in this clade by population-level resequencing. Total lengths of the ALB, SHB, and SPB mitogenomes are 16,480 bp (G + C; 47.1%), 16,487 bp (G + C; 46.6%) and 16,486 bp (G + C; 46.7%), respectively. The mitogenomes are consistent with those of other Micropterus spp. in respect of coding region content and organization. Primer sets targeting the 12S rRNA and 16S rRNA genes commonly used in environmental DNA (eDNA) metabarcoding applications were evaluated, and those suitable to discriminate species-level identification of these species were identified. The information presented here can be applied to inform SHB conservation efforts in their native range and the biosurveillance and control of introduced ALB.