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

• Published in: Animals (Basel) Vol. 14; no. 18; p. 2672
• Main Authors: Li, Zhe, Han, Yaoquan, Li, Yusen, Wu, Weijun, Lei, Jianjun, Wang, Dapeng, Lin, Yong, Wang, Xiaoqing
• Format: Journal Article
• Language: English
• Published: Switzerland MDPI AG 13.09.2024; MDPI
• Subjects: Amino acids; Bats; Cyprininae; DNA sequencing; Endangered & extinct species; Fishes; Genes; Genetic diversity; Genetic testing; Genomes; Genomics; Mitochondrial DNA; mitochondrial genome; Nucleotide sequencing; phylogenetic relationships; Phylogenetics; Phylogeny; Procypris mera; Software; Transfer RNA; Wildlife conservation; China; United States > US; Cyprininae; mitochondrial genome; phylogenetic relationships; Procypris mera
• ISSN: 2076-2615; 2076-2615
• DOI: 10.3390/ani14182672

(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 . Here, we sequenced the mitochondrial genomes of three (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 is sister to all other genera of the subfamily Cyprinidae of China; the genus forms a monophyletic group; and the genera , , and 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 .