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This study describes the complete mitochondrial genome sequence of the scyphozoan  Acromitus flagellatus  (Maas, 1903), a blooming jellyfish found in the coastal areas of Hainan, China. Its mitochondrial DNA is 16,779 bp in length and has a linear structure, comprising 13 protein-coding genes (PCGs), two rRNAs (s-rRNA and l-rRNA), and two tRNAs (trna-W-TCA and trna-M-CAT). A + T content was 65.39% (A: 29.27%, C: 16.59%, G: 18.03%, and T: 36.12%). ATG was the start codon in 11 PCGs:  COX1 ,  COX2 ,  ATP8 ,  ATP6 ,  COX3 ,  NAD2 ,  NAD6 ,  NAD4l ,  NAD1 ,  NAD4 , and  COB .  NAD5  and  NAD3  had GTG as the start codon. TAG was the stop codon for  COX2 ,  NAD6 , and  COB . The other 10 PCGs were terminated by TAA. The neighbor-joining phylogenetic tree of the 15 related jellyfish species showed that  A. flagellatus  is closely related to  Nemopilema nomurai  and  Rhopilema esculentum .

Complete mitochondrial genome sequence of Acromitus flagellatus and its phylogenetic relationship with related jellyfish species