Abstract
The hybrid loach of M. anguillicaudatus (female) and M. bipartitus (male) have the desirable trait of growth performance. Recently, farming scale of this hybrid has been gradually increased in Asia, suggesting a promise of a new variety for loach. In this study, the complete mitochondrial genome of the hybrid loach was obtained by PCR. The genome is 16,647 bp in length, including 2 ribosomal RNA genes. 13 protein-coding genes, 22 transfer RNA genes, and a non-coding control region, the gene composition and order of which was similar to most reported from other vertebrates. Sequence analysis showed that the overall base composition is 29.75% for A, 28.28% for T, 25.61% for C, and 16.36% for G. The phylogenetic tree showed that Misgurnus family got together for one branch, which includes this hybrid loach, and the other loaches had their own branches. Also, the mitochondrial genome sequence of the hybrid loach was aligned by BLAST, compared with Cobitinae the sequence similarity could reach >95%, and the similarity to Misgurnus was >99%. The hybrid loach follows the matrilineal inheritance.
Misgurnus anguillicaudatus (Cypriniformes; Cobitidae), a small-sized freshwater fish species, is a highly valued, aquaculture-relevant food fish in East Asian countries (Zhang et al. Citation2014). M. bipartitus was widely cultivated in the northern part of China. The hybrid loach of M. anguillicaudatus (female) and M. bipartitus (male) have the desirable trait of growth performance. Recently, farming scale of this hybrid has been gradually increased in Asia, suggesting a promise of a new variety for loach. There is no report of the complete genome of this hybrid. Therefore, it is very important to characterize the complete mitogenome of this species, which can be utilized in research on taxonomic resolution, population genetic structure and phylogeography, and phylogenetic relationship (Liu et al. Citation2016).
In this study, we sequenced the complete mitogenome of the hybrid loach of M. anguillicaudatus (famale) and M. bipartitus (male) with a GenBank accession number MK250422. The voucher specimen was collected from Nansi Lake, north latitude 34°66″ and east longitude 117°20″, Jining city, China. They were preserved in 95% alcohol, which were stored in biology herbarium of Heze University. DNA was extracted using Phenol-Chloroform extraction methods and stored at −80 °C in Heze University. The mitogenome was amplified by primers which were initially published (Zeng et al. Citation2012). The entire mitogenome sequence of the hybrid loach was 16,647 bp in length, consisting of 13 protein-coding genes (PCGs), 2 ribosomal RNA (rRNA) genes, 22 transfer RNA (tRNA) genes, one replication origin (OL) and one control region (D-loop). From the base composition analysis, the per cent A + T content was 58.0% (29.75% for A, 28.28% for T, 25.61% for C, and 16.36). Twelve PCGs, 14 tRNA genes and two rRNA genes were located on the heavy strand (H-strand), while one PCG (ND6) and eight tRNA genes (tRNAGln, tRNAAla, tRNAAsn, tRNACys, tRNATyr, tRNASer, tRNAGlu, and tRNAPro) on the light strand (L strand). Eight PCGs (ND1, COI, COII, ATP8, ATP6, ND4L, ND5 and ND6) were terminated with TAA stop codon and three PCGs (ND2, ND3 and ND4) ended with TAG. On the other hand, remaining two PCGs (COIII and CYTB) ended with the incomplete stop codon represented as a single T. Frame overlapping occurred at three pairs of PCGs. ATP8 and ATP6 overlapped by 10 nucleotides (nt), ND4L and ND4 by 7 nt, and ND5 and ND6 (encoded on opposing stand) by 4 nt. Two ribosomal RNA genes, 12S rRNA (953 bp) and 16S rRNA (1679 bp) were located between tRNAPhe and tRNALeu with separation by the tRNAVal as seen in other vertebrate mitogenomes.
To determine the taxonomic status of the hybrid loach, we performed the phylogenetic relationship of the hybrid loach stock with other natural populations in loach as inferred by entire mitogenome (Dai et al. Citation2016). The phylogenetic tree showed that Misgurnus family got together for one branch, which includes the hybrid loach, and the other loaches had their own branches (). Also, the mitochondrial genome sequence of the hybrid loach was aligned by BLAST, compared with Cobitinae the sequence similarity could reach >95%, and the similarity to Misgurnus was >99%. The hybrid loach of M. anguillicaudatus (female) and M. bipartitus (male) follows the matrilineal inheritance.
Figure 1. Phylogenetic relationship of the hybrid loach of M. anguillicaudatus (female) and M. bipartitus (male) stock with other loach as inferred by entire mitogenome. *The hybrid loach (accession number: MK250422) in the position of the evolutionary tree. Trees were reconstructed using MEGA 7 program (Kumar, Tamura, Nei) with neighbour-joining method. Numbers above branches are bootstrap values by 1000 replicates. The phylogenetic tree showed that the hybrid loach to be one of Misgurnus, and the other loaches had their own branches.
Acknowledgements
The authors thank the 13th five-year key laboratory for physiology biochemistry and application of higher education in Shandong province.
Disclosure statement
The authors report no conflicts of interest. The authors are responsible for the content and writing of the manuscript.
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References
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