Complete sequence of the mitochondrial genome of Uranoscopus tosae: genome characterization and phylogenetic analysis

Abstract

Uranoscopus tosae is a marine fish which some wild populations are in danger, and need urgent conservation. In this study, the complete mitochondrial genome of the U. tosae which is 17,286 base pairs in length, and contained 13 protein-coding genes and 2 ribosomal RNA genes, 22 tRNA genes and 2 main non-coding regions was firstly determined. Most of the genes of U. tosae were encoded on the H-strand, while the ND6 and eight tRNA (Gln, Ala, Asn, Cys, Tyr, Ser (UCN), Glu and Pro) genes were encoded on the L-strand. In addition, the complete mitochondrial genome of U. tosae was used to construct phylogenetic tree, which shows that U. tosae clustered with the species of Howellidae. The mitochondrial genome of U. tosae provides important data for studying on population genetic diversity and genetic conservation.

Keywords:

• Uranoscopus tosae
• mitochondrial genome
• phylogenetic analysis

Uranoscopus tosae belongs to the Uranoscopidae family, which is widely distributed in tropical waters of Indo-West Pacific, including Algoa Bay, South Africa to southern Japan. Many of its wild populations are in danger due to the ecological damages caused by global warming, overfishing, and marine pollution. Now the conservation of U. tosae need to be pays an important attention. In this study, the complete nucleotide sequence for the mitochondrial genome of the U. tosae was presented. The samples were collected from the East China Sea (25.75°N, 123.47°E) and was kept at the Museum of Marine Biology at Zhejiang Ocean University (Index number: MMB-2014-0158).

The mitochondrial DNA of U. tosae is a closed double-stranded circular molecule of 17,286 bp (GenBank accession number: (KX641475) and contained 13 protein genes, 2 rRNA genes, 22 tRNA genes, 1 putative control region (CR) and 1 light strand replication origin (O_L). The base composition of the complete mitochondrial genome was A 24.3%, C 25.5%, G 29.3%, and T 20.9%, with a slight A + T bias of 53.6%, which was similar to other fishes (Xu et al. 2011; Jin et al. 2013). The total base compositions were against G in mitochondrial genome, maybe it was due to a strong bias against the use of G at the third codon position. The two ribosomal RNA genes 12S rRNA and 16S rRNA are located between tRNA^Phe and tRNA^Leu (UUR) genes, and are separated by the tRNA^Phy. Most of protein-coding genes are encoded on the H-strand, except for the ND6. All the protein-coding genes started with ATG, except for COI used GTG as the start codon. The stop codon of five protein-coding genes (ND1, ND2, ATP8, ATP6 and ND4L) is TAA, while COI, ND5 and ND6 end with AGA. The remaining four genes seemed to end in two incomplete stop codons, TA- (COIII) and T- (COII, ND3, ND4 and Cyt b), which were completed via posttranscriptional polyadenylation (Ojala et al. 1981). The 22 tRNA genes, which contains two forms of tRNA^{Ser (UCN and AGY)} and tRNA^{Leu (UUR and CUN)}, scatter throughout the genome and range from 68 to 79 bp in size and the gene arrangement is typically as in most vertebrates. Fourteen tRNA genes were encoded by H-strand, while the remaining eight tRNA genes (tRNA^Gln, tRNA^Ala, tRNA^Asn, tRNA^Cys, tRNA^Tyr, tRNA^Ser, tRNA^Glu and tRNA^Pro) were encoded by L-strand. Three tRNA clusters (IQM, HSL, and WANCY) were well conserved in U. tosae as in other vertebrate mitochondrial genomes (Liu et al., 2013; Wei et al., 2013). The total length of overlaps and intergenic spacers were 7 bp and 773 bp, ranging from 1 to 8 bp and from 1 to 773 bp per location, respectively. As in most vertebrates, two non-coding regions can be found in U. tosae mitogenome, an O_L within the WANCY region including five tRNA genes (tRNA^Trp, tRNA^Ala, tRNA^Asn, tRNA^Cys, and tRNA^Tyr), which can fold into a stemloop secondary structure with the conserved motif 5′-GCCGG-3′. The control region in U. tosae mitogenome is determined between tRNA^Pro and tRNA^Phe and this characterization is consistent with those of other teleost (Cheng et al. 2011, 2012).

To uncover the phylogenetic position of U. tosae among closely related fishes, phylogenetic tree was constructed with other fish using mitochondrial genome sequences. Phylogenetic analysis demonstrated that U. tosae clustered in a clade and formed a sister relationship with other species belong to the Howellidae (Figure 1).

Figure 1. Phylogenetic tree based on the complete mitochondrial genome sequences was constructed using maximum likelihood analyses, all nodes supported with high posterior probabilities (>0.90). The other mitochondrial genome sequences used in phylogenetic analyses were derived from GenBank.

Disclosure statement

No potential conflict of interest was reported by the author(s).