Whitetail Angelfish (Centropyge flavicauda) and Orangeback Angelfish (Centropyge acanthops) are known as pygmy angelfish due to their small body size (usually less than two inches). In this study, we used the next-generation sequencing method to deduce two complete mitogenomes of C. flavicauda and C. acanthops for the first time. The assembled mitogenome, consisting of 16 747 bp and 16 748 bp, was showing 99.2% identity each other. Both mitogenome follow the typical vertebrate arrangement, including 13 protein coding genes, 22 transfer RNAs, two ribosomal RNAs genes and a non-coding control region of D-loop. D-loop contains 895 bp in C. flavicauda and 896 bp in C. acanthops and locates between tRNA-Pro and tRNA-Phe. The overall GC content is 46.4% for C. flavicauda and C. acanthops. Complete mitogenomes of C. flavicauda and C. acanthops provide essential and important DNA molecular data for phylogenetic and evolutionary analysis for marine angelfish.
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