Abstract
Acrossocheilus jishouensis is an endemic south China stream-dwelling cyprinid species. Its complete mitochondrial genome is 16,587 bp in length, consisting of 13 protein-coding genes, 22 tRNA genes (ranging from 67 bp in tRNACys to 76 bp in tRNALeu and tRNALys), two rRNA genes (956 bp in 12S rRNA and 1673 bp in 16S rRNA), and one control region (942 bp). Its overall base composition is A: 31.2%, C: 27.6%, G: 16.2%, and T: 25.1%. The complete mitogenome of the Chinese barred species of Cpynidae could provide a basic data for further phylogenetics analysis.
Keywords: Barred species, mitogenome, Acrossocheilus jishouensis, next generation sequencing
Acrossocheilus jishouensis is a barred cyprinid species from the Yuan-Jiang of Hunan Province in China, a tributary flowing to Dongting Lake connected to the middle Yangtze River (Zhao et al. 1997). This species differs from the congenus with a combination of characters: six vertical bars on the flanks 1–2 scales wide and not beyond the lateral line in the adults, a longitudinal stripe along the lateral line, two thick lateral lobes of the lower lip, last unbranched dorsal-fin ray slim and unserrated along its posterior margin, membranes between the dorsal-fin rays oblong with black blotches. However, ontogenetic changes and/or sexual dimorphism in body colouration and mouthpart structures usually confuse researchers when delineating these barred species. Thus, combination of mitochondrial DNA data and morphological traits will help for the species identification of taxonomic validity and phylogenetic position of the species.
The sample caught from the Jinping county (Qingshui Jiang, flowing to Yuan Jiang basin) of Guizhou Province in China was deposited in the collection of the Zhejiang Museum of Natural History under the accession number ZMNH 2015030001. The complete mitogenome of A. jishouensis has been obtained from high-throughput sequencing on whole genomic DNA with HiSeq 2000 platform (Illumina, San Diego, CA). We used next generation sequencing to perform low-coverage whole genome sequencing according to previous protocol (Shen et al. 2016). The complete mitogenome of A. jishouensis is 16,587 bp in length (GenBank KY131974), includes 13 protein-coding genes, 22 tRNA genes (ranging from 67 bp in tRNACys to 76 bp in tRNALeu and tRNALys), two rRNA genes (956 bp in 12S rRNA and 1673 bp in 16S rRNA), and one D-loop control region (942 bp). Its overall base composition is A: 31.2%, C: 27.6%, G: 16.2%, and T: 25.1% which shows AT bias, with the AT content of 57.4%. The complete mitogenome of A. jishouensis shows 95% identities to A. parallens (GenBank KP274878) after BLAST search against NCBI nr/nt database.
To validate the phylogenetic position of A. jishouensis, we used MEGA6 software (Tamura et al. 2013) to construct a maximum likelihood tree (with 500 bootstrap replicates and Kimura 2-parameter model) containing complete mitogenomes of 11 species derived from Acrossocheilus genus. Onychostoma gerlachi (Cheng et al. 2016) derived from Onychostoma genus was used as outgroup for tree rooting. The resultant phylogeny shows that the A. jishouensis is closely related to A. parallens with high bootstrap value supported (Figure 1). The resultant phylogeny showed that the sister pair A. parallens and A. hemispinus were sister to A. jishouensis, with the basal position of the group occupied by A. jishouensis. The Kimura-2-parameter distance was 0.055 between A. jishouensis and A. parallens, and was 0.057 between A. jishouensis and A. hemispinus, much higher than that between the sister pair A. parallens and A. hemispinus (0.022) in the same group. The complete mitogenome of A. jishouensis which is deduced in this study provides a basic data for further phylogenetic and conversational analysis of the Chinese barred species in Cyprinidae.
Figure 1.
Molecular phylogeny of Acrossocheilus jishouensis and related species based on complete mitogenome. The complete mitogenomes is downloaded from GenBank and the phylogenic tree is constructed by Maximum likelihood method with 500 bootstrap replicates. The gene's accession number for tree construction is listed behind the species name.
Acknowledgements
Our sincere thanks are given to Xue Wang and Liang Cao for their assistance in data analysis and Zhuo-Cheng Zhou, Qing-Yun Huang, and Xiao-Lu Yu for helping with field work. We also thank Dr. Chung-Der Hsiao from Chung Yuan Christian University in Taiwan for his help on Bioinformatic analysis of NGS data.
Disclosure statement
The authors report no conflicts of interest. The authors alone are responsible for the content and writing of the paper.
References
- Cheng Q, Chen F, Huang DM, Wang HY.. 2016. The complete mitochondrial genome of the Onychostoma gerlachi (Cypriniformes: Cyprinidae). Mitochondrial DNA A. 27:3210–3211. [DOI] [PubMed] [Google Scholar]
- Shen KN, Yen TC, Chen CH, Li HY, Chen PL, Hsiao CD.. 2016. Next generation sequencing yields the complete mitochondrial genome of the flathead mullet, Mugil cephalus cryptic species NWP2 (Teleostei: Mugilidae). Mitochondrial DNA A DNA Mapp Seq Anal. 27(3):1758–1759. [DOI] [PubMed] [Google Scholar]
- Tamura K, Stecher G, Peterson D, Filipski A, Kumar S.. 2013. MEGA6: Molecular Evolutionary Genetics Analysis version 6.0. Mol Biol Evol. 30:2725–2729. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Zhao J, Chen X, Li W.. 1997. A new species of the genus Acrossocheilus from Hunan Province, China (Cypriniformes: Cyprinidae). Syst Zool. 18:243–246. [Google Scholar]