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We sequenced and annotated the complete mitochondrial genome for the freshwater water flea Moina macrocopa (Straus, 182. This is the first mitogenome for the family Moinidae. The complete mitogenome of M. macrocopa is 16,072 bp, with 35.8% A, 17.6% C, 12.8% G, and 33.8% T. The mitogenome comprises 13 protein-coding genes (PCGs), two ribosomal RNA (rRNA) genes, 22 transfer RNA (tRNA) genes, and a non-coding region. Phylogenomic analysis based on 28 in-group taxa belonging to the orders Anostraca, Diplostraca, and Notostraca is congruent
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