Whole Mitochondrial Genome Sequencing and Phylogenetic Tree Construction for Procypris mera (Lin 1933).

Simple Summary: As a fish under second-class protection in China, the structure and characteristics of the mitochondrial genome Procypris mera (Lin, 1933) have not been reported. We reported three mitochondrial genomes of P. mera from three sites and conducted a detailed analysis of their characteristics, which were employed to infer phylogenetic relationships. These findings revealed that the mitochondrial genomes of P. mera from the different sites exhibited considerable similarity. Furthermore, the phylogenetic tree constructed from amino acid sequences supported the original phylogenetic relationships of the subfamily Cyprininae in China, suggesting that the genus Puntioplites is sister to all other genera of the subfamily Cyprinidae of China; the genus Procypris forms a monophyletic group; and the genera Carassioides, Carassius, and Cyprinus form a monophyletic group. Procypris mera (Lin, 1933), also known as the Chinese ink carp, currently has a second-class protection status in China. Understanding the structure and characteristics of mitochondrial genes provides essential information for resource conservation and phylogenetic studies of P. mera. Here, we sequenced the mitochondrial genomes of three P. mera (WYL1-3) from three sites and performed phylogenetic analysis. The generated three genomes were 16,587 bp in length, comprising 13 protein-coding genes (PCGs), 22 tRNAs, two rRNAs, and two non-coding regions (control region (CR), D-loop, and light-stranded replication start OL), with a preference for codons ending in A or C. The mitochondrial genomes of WYL2 and WYL3 were identical, differing from that of WYL1 by only five single-nucleotide polymorphisms (SNPs). All mitochondrial PCGs had Ka/Ks ratios of less than one, suggesting purifying selection. Phylogenetic tree analysis based on amino acid sequences suggested that the genus Puntioplites is sister to all other genera of the subfamily Cyprinidae of China; the genus Procypris forms a monophyletic group; and the genera Carassioides, Carassius, and Cyprinus form a monophyletic group. This study contributes to our understanding of the phylogenetic relationships in subfamily Cyprininae in China and lays the foundation for resource conservation and management of P. mera. [ABSTRACT FROM AUTHOR]