The mitochondrial genome of the sun anemone shrimp <i>Periclimenes rathbunae</i> (Decapoda: Caridea: Palaemonidae)

The sun anemone shrimp, Periclimenes rathbunae (Decapoda: Palaemonidae), is a small, translucent shrimp broadly distributed across the tropical Western Atlantic that typically inhabits sea anemones in shallow waters. Recent trading of the host sea anemones in the ornamental industry has likely increased stress on the population health of this shrimp. To aid in conservation efforts, the complete mitochondrial genome of P. rathbunae has been assembled and characterized in detail. The mitochondrial genome of P. rathbunae is 15,809 bp long and includes 13 protein-coding genes (PCGs), 22 transfer RNA (tRNA) genes, two ribosomal RNA genes (12S and 16S rRNA), and a 976 bp control region. The gene order is identical to that reported for two other species in family Palaemonidae, but different from the ancestral decapod ground pattern. The overall A + T content is 67.8%, and the codon usage of PCGs exhibits a strong preference for A + T-rich codons. All 13 PCGs exhibited purifying selection, with the strongest selection exhibited in cox1 and the weakest exhibited in atp8. All tRNA genes exhibited the typical cloverleaf secondary structures except for trnT and trnL2, which were missing the TC-loop, trnR missing the D-loop, and trnS1 missing the dihydroxyuridine (DHU) arm. The control region exhibited a high A + T content (74.2%), four dinucleotide microsatellite repeats, a single tandem repeat, and multiple hairpin loops in the predicted Minimum Free Energy (MFE) and Centroid secondary structures. The newly assembled mitochondrial genome will aid in the identification of P. rathbunae and support programs based on environmental DNA (eDNA).