Identification of the complete mitochondrial genome of Garra pingi pingi (Cypriniformes, Cyprinidae)
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TECHNICAL NOTE
Identification of the complete mitochondrial genome of Garra pingi pingi (Cypriniformes, Cyprinidae) Yuan‑Chao Zou1,2 · Mei Chen1 · Chuan‑Jie Qin1 · Yong‑Ming Wang1 · Rui Li1 · Ze‑Min Qi1 · Zheng‑Yong Wen1
Received: 21 September 2017 / Accepted: 13 October 2017 © Springer Science+Business Media B.V. 2017
Abstract Garra pingi pingi, an endemic species to China, is mainly distributed in the upper Yangtze River and its tributaries. In present study, the complete mitochondrial genome of G. pingi pingi was first determined using the next-generation sequencing technology and annotated using bioinformatic tools. The circular mitochondrial genome was 16,599 bp long, contained 13 protein-coding genes, 2 ribosomal RNA genes (rRNA), 22 transfer RNA (tRNA) genes, an origin of light-strand replication ( OL) and one displacement loop locus (D-loop). Most mitochondrial genes were encoded on the heavy strand, except for ND6 and eight tRNA genes. The total nucleotide composition was 31.48% A, 25.79% T, 26.66% C, 16.07% G, with 57.27% AT, respectively. Phylogenetic analysis based on the tandem 13 coding protein genes nucleotide sequences indicated that G. pingi pingi showed a close relationship with G. imberba. These data provide fundamental information not only for unravelling the population structure and differentiation, but also for further conservation genetics studies on Labeonini species. Keywords Garra pingi pingi · Mitochondrial genome · Phylogenetic analyses Garra pingi pingi, belonging to the subfamily Labeoninae in Cypriniformes, is an important economic freshwater fish, * Zheng‑Yong Wen [email protected] 1
College of Life Sciences, Conservation and Utilization of Fishes Resources in the Upper Reaches of the Yangtze River Key Laboratory of Sichuan Province, Neijiang Normal University, Neijiang 641100, Sichuan, China
School of Life Sciences, Southwest University, Chongqing 400700, China
2
which mainly distributed in the upper Yangtze River and its tributaries (Chu and Cui 1987). It’s an important commercial fish due to its good taste and high nutrition. However, its natural populations declined rapidly in recent years due to overfishing, dam construction in the Yangtze River (Zhao et al. 2011). In this study, the complete mitochondrial DNA sequence was first determined by the next generation sequencing. The specimens were obtained from the Conservation and Utilization of Fishes resources in the Upper Reaches of the Yangtze River Key Laboratory of Sichuan Province, Neijiang Normal University. A 30–40 mg fin clip was collected and preserved in 95% ethanol at 4 °C. Total genomic DNA was extracted with a Tissue DNA Kit (OMEGA E.Z.N.A.) following the manufacturer’s protocol. Subsequently, the genomic DNA was sequenced using the next-generation sequencing, and then the mitogenome was assembled using G. kempi as reference. The complete mitochondrion genome of G. pingi pingi was a circular molecule with 16,599 bp in length (Fig. 1). It composed of 13 protein-coding genes, 22 transfer RNA (tRNA)
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