The complete mitochondrial genome of Sparus aurata (Perciformes: Sparidae) with phylogenetic consideration

Abstract

The complete mitochondrial genome of the Sparus aurata was presented in this study. The mitochondrial genome is 16,652 bp long and consists of 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes, and a control region. The gene order and composition of S. aurata mitochondrial genome were similar to that of most other vertebrates. The nucleotide compositions of the light strand in descending order is 28.84% of G, 27.26% of A, 26.77% of T and 17.13% of C. With the exception of the NADH dehydrogenase subunit 6 (ND6) and eight tRNA genes, all other mitochondrial genes are encoded on the heavy strand. The phylogenetic analysis by maximum-likelihood (ML) method showed that the Sparus aurata has the closer relationship to the Rhabdosargus sarba in the phylogenetic relationship.

Keywords:

• Mitochondrial genome
• Sparus aurata
• phylogenetic

The Sparus aurata is a commercially important aquaculture fish species, which is mainly distributed in the Eastern Atlantic region, including British Isles, Strait of Gibraltar to Cape Verde and around the Canary Islands; also in the Mediterranean. With the aim of achieving to find new DNA markers for the studies on population genetics of S. aurata, we determined to sequence the complete mitochondrial genome of S. aurata using the next-generation sequencing (NGS) techniques strategy (Xie et al. 2015). The specimen was obtained from the Daya Bay Aquaculture Center, Guangdong, China. Then, the specimen was preserved in 95% ethanol. The total genomic DNA was extracted from the fin of the fresh fish using the salting-out procedure (Howe et al. 1997).

The complete mitochondrial genome of Sparus aurata (Genbank accession number KT805959) is 16,652 bp in length, consisting of 13 protein-coding genes, 2 ribosomal RNA genes (12S rRNA and 16S rRNA), 22 transfer RNA genes (tRNA), and 1 control region, which is similar to the typical vertebrates (Wang et al. 2008). Most of the genes are encoded on the heavy strand, with only the NADH dehydrogenase subunit 6 (ND6) and eight tRNA genes [Gln, Ala, Asn, Cys, Try, Glu, Pro, Ser (GCT)] encoded on the light strand. Overall nucleotide compositions of the light strand are 27.26% of A, 17.13% of C, 26.77% of T, and 28.84% of G. However, the most representative base is G and the bias against C was observed, which is different from the base compositions of mitochondrial genome of other teleosts.

All the protein-coding genes begin with an ATG start codon except for COX1 started with GTG. Five types of stop codons revealed are TAA (ND4L, ND1, ND6, ATP8), TA (ND2, ATP6, COXIII), T (COXII, ND3, ND4, CYTB), AGG (COXI), and TAG (ND5). The 12S and 16S rRNA genes are located between the tRNA-Phe (GAA) and tRNA-Leu (TAA) genes, and are separated by the tRNA-Val gene with the same situation found in other vertebrates. Most genes are either abutted or overlapped. The 22 tRNA genes vary from 66 to 74 bp in length. All these could be folded into the typical cloverleaf secondary structure although numerous non-complementary and T–G base pairs exist in the stem regions. The control region was 984 bp in length, located between tRNA-Pro (TGG) and tRNA-Phe (GAA) gene. The nucleotide composition of the control region was 32.52% of A, 21.75% of C, 14.74% of G, and 31.00% of T.

The phylogenetic position of S. aurata was reconstructed with the complete mtDNA sequences from 17 species of Perciformes using the maximum-likelihood (ML) methods (Kumar et al. 2004). As shown in Figure 1, S. aurata has the closer relationship to Rhabdosargus sarba, which suggested that Rhabdosargus sarba has the closer relationship to S. aurata.

Figure 1. The ML phylogenetic tree of Perciformes species. Numbers on each node are bootstrap values of 100 replicates.

Disclosure statement

No potential conflict of interest was reported by the authors.

Additional information

Funding

This project was supported by the National Science Foundation of China [No. 31201978], the National Natural Science Foundation of China [No. 31260632], the National Natural Science Foundation in Jiangxi Province of China [20122BAB204018], and the National Key Technology Support Program in Jiangxi Province of China [20133BBF60020].