Mitochondrial genome of Ying hybrid carp (Russian scattered scale mirror carp ♀ × carp-goldfish nucleocytoplasmic hybrid ♂).

The complete mitogenomes of Ying hybrid carp (Russian scattered scale mirror carp ♀ × Carp-goldfish nucleocytoplasmic hybrid ♂) was sequenced by PCR-based method. The total of the mtDNA was 16,581 bp, and consisted of 13 protein-coding genes, 22 tRNAs, 2rRNA genes, and 1 control region (D-loop region). The overall base composition was as follows: A: 31.9%, T: 24.8%, C: 27.5%, and G: 15.8%, respectively. The overall AT and GC skew were found to be 0.125 and -0.271, respectively. A majority of the genes used ATG as the start codon, except that the codon GTG was found to initiated the CO I gene. Most of the genes ended with the complete stop codon TAA or TAG, while the COII, ND3, ND4, and Cytb genes terminated with the incomplete stop codons 'T--'.

Russian scattered scale mirror carp is a traditional and important domestic freshwater fish for food. Except the traditional variety, a novel nuclear-cytoplasmic hybridized fish was produced by Chinese scientist, in which the blastulae nucleus of purse red carp (Cyprinus carpio var. wuyuannensis) was transplanted into the cytoplasm of the Yangtze River crucian carp (Carassius auratus) (Tung 1980; Hu et al. 2014). Using Russian scattered scale mirror carp and carp-goldfish nucleocytoplasmic hybrid as parents, one commercial hybrid of common carp were produced, named Ying hybrid carp, which have quite high growth and survival rate compared to their parents. In the present study, the Ying hybrid carp were collected from Yaowan Experimental Station, Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, China to examine the functional role of mitochondrial DNA in the heterosis.

The complete mitochondrial genome sequence of Ying hybrid carp (Genbank no. KX710076) was determined to be 16,581 bp in length. Similar to other common carp varieties (Hu et al. 2016a,b), the mitochondrial genome of Ying hybrid carp comprised of 37 genes including 13 protein-coding genes, 22 transfer RNA genes, 2 ribosomal RNA genes (16sRNA and 12sRNA), and 2 main non-coding regions involved in replication and transcription processes: D-loop and the light-strand replication origin in QL. The overall base composition was as follows: A: 31.9%, T: 24.8%, C: 27.5%, G: 15.8%, and the A + T content 56.7%, respectively. The overall AT and GC skew were found to be 0.125 and −0.271, respectively. The protein-coding gene organization of Ying hybrid carp was conformed to that of other common carp varieties. A majority of the genes used the ATG as the start codon, except that the codon GTG was found to initiated the CO I gene. Most of the genes ended with the complete stop codon TAA or TAG, while the COII, ND3, ND4, and Cytb genes terminated with the incomplete stop codons ‘T––’. Moreover, ATP8-ATP6, ATP6-COIII, ND4L-ND4, and ND5-ND6 were overlapped by seven, one, seven, and four nucleotide, respectively. In addition, there are 70 bp intergenic nucleotides in the whole mitogenome, ranging from 1 to 33 bp. Similar to other teleost, except for ND6 gene and eight tRNA genes (tRNA-Gln, Ala, Asn, Cys, Tyr, Ser, Glu, and Pro), all other genes were encoded on the H-strand. The two ribosomal RNA genes, 12S rRNA gene (955 bp) and 16S rRNA gene (1679 bp), were located between tRNA and tRNA and separated by tRNA. The main control region (D-Loop) in Ying hybrid carp was 927 bp long and located between tRNA and tRNA.

To validate the phylogenetic position of Ying hybrid carp, MEGA6 software (Tamura et al. 2013) was used to construct a maximum-likehood tree containing complete mitogenomes of 11 common carp varieties. Grass carp (Ctenopharyngodon idella) was used as an outgroup member for tree rooting. Result showed that Ying hybrid carp is closely related to their parents Russian scattered scale mirror carp (Figure 1), which confirmed the maternal mode of inheritance for the mtDNA.

Figure 1.

Molecular phylogeny of Ying hybrid carp and other common carp varieties based on complete mitogenome. The complete mitogenome is downloaded from GenBank and the phylogenic tree is constructed by maximum-likelihood method with 500 bootstrap replicates.