Abstract
Using Illumina next-generation sequencing (NGS), the complete mitochondrial genome sequence of the hybrid species of Schizothorax oconnori (♀) × Schizothorax waltoni (♂) was described in this study. 16,592bp long circular molecule consisted of 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes, and a control region. This study discovered the 99.8% sequence identity between the hybrid and its female parent, which confirmed the maternal inheritance pattern followed. The phylogenetic tree showed the hybrid was closer relationships with Schizothorax oconnori. The results would be a useful basis for conservation and phylogenetics of this hybrid.
Schizothorax oconnori (Lloyd.1908) and Schizothorax waltoni (Heckel.1838) belong to the subfamily Schizothoracinae, family Cyprinidae and order Cypriniformes. These species are mainly distributed in Yarlung Zangbo River in Tibet, China (Chen and Cao Citation2000). They all live in the deeper areas of clear, fast-flowing rivers and have great economic value in this region (Wu and Wu Citation1992). Recently, due to the damming of rivers and overfishing, the natural resources of those species have dropped significantly. Five schizothoracinae species have been assessed as Endangered by Red List of China’s Vertebrates (Jiang et al. Citation2016).
The specimens were obtained from the Yarlung Zangbo River (N 83°58′34.00″; E 29°41′35.36″) at an altitude of 4579 m in 2017. This specimen was stored in 95% ethanol with accession number: 20170528YL1. The total genomic DNA was extracted from the pelvic fin by a traditional phenol–chloroform method (Sambrook and Russell Citation2001). A total of 4,486,607,281 bp clean data were generated on the Illumina HiSeq4000. The mitochondrial genome was assembled with the soft of SOAPdenovo2.04 (Li et al. Citation2010) and annotated by DOGMA (Wyman et al. Citation2004).
The complete mitochondrial genome (GenBank accession number: MK105912) was a circular molecule with a length of 16,592 bp, including 13 protein-coding, 2 ribosomal RNA (rRNA), and 22 transfer RNA (tRNA) genes, and 1 control region (D-Loop). The arrangement of encoded genes is similar to the other Schizothoracinae. (Rui et al. Citation2018; Zhang et al. Citation2018; Zhou et al. Citation2018) MEGA 7.0 software was used for constructing a maximum likelihood (ML) tree (Kumar et al. Citation2016). The overall base composition of the heavy strain was A (30.8%), T (30.42%), C (19.3%), G (19.49%), and the content of A + T in the complete genome was 61.22%. Most of the genes were encoded on the heavy strand. Only ND6 and 8 tRNA [tRNA–Gln, –Ala, –ASn, –Cys, –Tyr, –Glu, –Pro, and –Ser (TGA)] were encoded on the light strand.
The sequence alignment of mitochondrial genomes between the hybrid and its female parent revealed a total of 26 variable sites, especially 18 sense mutations in 8 PCGs.The phylogenetic tree () was constructed by the maximum-likelihood method using complete mitochondrial genomes of 14 Schizothoracinae species. Our sequence was phylogenetically clustered with S. oconnori, which is consistent with the mitochondrial inheritance mechanism. The complete mitochondrial genome sequence of the hybrid species of S. oconnori (♀) × S. waltoni (♂) provides an important data basis for further study in mitochondrial inheritance mechanism.
Figure 1. The consensus phylogenetic relationship of the hybrid species of S. oconnori (♀) × S. waltoni (♂) with other fishes. Phylogenetic tree based on the complete mitochondrial genome sequences was constructed by maximum-likelihood (ML) model. GenBank accession numbers of mitogenomic sequences for each taxon are shown in parentheses.
Acknowledgements
The authors would like to thank Jiawen Xu for assistance in sample collection and identification.
Disclosure statement
The authors report no conflicts of interest. The authors alone are responsible for the content and writing of the paper.
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References
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