Characterization of the complete mitochondrial genome of Gymnocypris scleracanthus (Teleostei: Cyprinidae)
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TECHNICAL NOTE
Characterization of the complete mitochondrial genome of Gymnocypris scleracanthus (Teleostei: Cyprinidae) Fei Tian1,2,3 · Yongtao Tang1,2,4 · Kai Zhao1,2,3
Received: 8 August 2017 / Accepted: 11 August 2017 © Springer Science+Business Media B.V. 2017
Abstract Gymnocypris scleracanthus (Teleostei: Cyprinidae) is an endangered fish species, and distributes in a small glacial lake Langcuo in the Qinghai-Tibetan Plateau. The natural population of G.scleracanthus has been dramatically decreased during recent years. In the present study, we report the complete mitochondrial genome of G. scleracanthus, and explore its phylogenetic position using concatenated 13 protein-coding genes (PCGs). The mitochondrial genome of G. scleracanthus is 16,679 bp in length, containing 27.33% of T, 26.01% of C, 28.52% of A and 18.14% of G. Besides the D-loop control region, the mitochondrial genome encodes 13 PCGs, 22 transfer RNAs (tRNAs), and two ribosomal RNAs (rRNAs). The phylogenetic analysis demonstrates G. scleracanthus and Gymnocypris dobula are most closely related. Keywords Gymnocypris scleracanthus · Mitochondrial genome · Phylogenetics
Fei Tian and Yongtao Tang have contributed equally to the work. * Kai Zhao [email protected] 1
Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, No. 23 Xinning Road, Xining 810008, Qinghai, China
2
Laboratory of Plateau Fish Evolutionary and Functional Genomics, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, Qinghai, China
3
Qinghai Key Laboratory of Animal Ecological Genomics, Xining, Qinghai, China
4
University of Chinese Academy of Sciences, Beijing, China
Gymnocypris scleracanthus belongs to family of Schizothoracinae, and inhabits exclusively in a small, nutrition-limited glacial lake of Langcuo in the Qinghai-Tibetan Plateau with the altitude about 4300 m (Cao Wenxuan et al. 1981). Human activities and the global warming make the native habitat for G. scleracanthus gradually decreased, which results in the dramatic reduction of its natural population. Currently, G. scleracanthus is defined as a vulnerable species by IUCN Red List of Threatened Species (IUCN 2017). Understanding the genetic information helps to develop the effective strategy to maintain and recover the population of G. scleracanthus. However, genetic studies on G. scleracanthus are rare. To facilitate the genetic research and conservation on G. scleracanthus, we sequence, assemble and annotate its mitochondrial genome. The annotated mitochondrial genome is deposited in NCBI Genbank with the Accession Number MF598300. The genomic DNA was extracted from the pooled tissue samples of liver, muscle, brain, kidney, heart, ovary and testis using standard phenol–chloroform method. The DNA library was constructed and sequenced with Illumina Hiseq 2500™ (Illumina, USA). The 125-bp raw reads were trimmed and assembled using MITobin v1.8 with default parameters (Hahn et al. 2013). The c
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