Abstract
In this study, the complete mitochondrial genome sequence of Pampus minor has been determined by long polymerase chain reaction and primer walking methods. The mitochondrial genome is a circular molecule of 16,690 bp in length, including the typical structure of 13 protein-coding genes, two ribosomal RNA genes, 22 transfer RNA genes, and two non-coding regions (L-strand replication origin and control region), the gene contents of which are identical to those observed in most bony fishes. The overall base composition of the heavy strand shows 29.9% of T, 24.7% of C, 30.6% of A and 14.7% of G, with a slight A + T rich feature (60.5%). Within the control region, we identified the termination-associated sequence domain (TAS), and the conserved sequence block domains.
Pampus minor (Liu and Li 1998) belongs to the order Perciformes, the family Stromateidae, and lives in warm temperate zone. This species is commercially important fish in the Indo-Pacific region. Until now, there are some researches focused on its identification and distribution, but only a few studies are about its genetic characteristics. Therefore, we determined the complete mitochondrial genome sequence of P. minor using 38 pairs of primers in order to provide basic information for the genetic studies of P. minor. Pampus minor was collected from the coastal waters of Wuyu island (24°19′36.3″N, 118°9′18.1″E), Zhangzhou, Fujian province, China during March 2012. The sample and its DNA were deposited in Fishery Ecology Laboratory of Ocean University of China (FEL, OUC; 36°03′59.5″N, 120°20′19.4″E) and were preserved in alcohol and stored at −80 °C, respectively. Sequence has been deposited in GeneBank with accession number MH037007.
The complete mitochondrial genome of P. minor was sequenced to 16,690 bp and has high similarity on gene content and structure with most vertebrates (Boore Citation1999; Wolstenholme Citation1992). It consisted of 13 typical vertebrate protein-coding genes, 22 tRNA genes, two rRNA genes (12S rRNA and 16S rRNA), and two major non-coding regions (control region and L-strand replication origin). Most mitochondrial genes of P. minor were encoded on the H-strand, while only ND6 and eight tRNA (Gln, Ala, Asn, Cys, Tyr, Ser-UCN, Glu, and Pro) genes encoded on the L-strand. Overall base compositions of P. minor mitochondrial genome were as follows: C, 24.7%; A, 30.6%; T, 29.9%; G, 14.7%, indicating a strand compositional bias characterized by an excess of C relative to G. The total length of 13 protein-coding genes was 11,428 bp, accounting for 68.5% of the complete mitochondrial genome sequences, and contained 3800 amino acids for protein coding. Like other mitochondrial genomes (Inoue et al. Citation2000; Zhao et al. Citation2012), 22 tRNA genes of P. minor mitochondrial genome were detected and interspersed between the rRNA and protein-coding genes and ranged in size from 66 to 75 bp. A small subunit of rRNA (12S rRNA) and a large subunit of rRNA (16S rRNA) were also identified in P. minor mitochondrial genome, which was 957 and 1696 bp, respectively. The largest non-coding region (control region) in P. minor mitochondrial genome, which was located between tRNAPro and tRNAPhe, was determined to be 1001 bp in length. By comparing with the recognition sites in some other bony fishes (Zardoya et al. Citation1995; Inoue et al. Citation2001; Zhao et al. Citation2012), the control region was characterized by the typical tripartite with termination-associated sequence domain, the central conserved sequence block domains and the conserved sequence block domains (Cann et al. Citation1984). The additional non-coding region, the origin of L-strand replication (OL) in P. minor, was 41 bp in size and located between tRNAAsn and tRNACys in the WANCY region, almost identical with other Stromateidae fishes.
Phylogenetic relationship was constructed using neighbor-joining (NJ) algorithm among six Pampus species based on 12 H-strand mitochondrial protein-coding genes, 22 tRNA and two rRNA genes (). This phylogenetic tree shows that P. minor is more closely related to P. echinogaster.
Figure 1. Phylogenetic relationship using NJ algorithm among same family species based on 12 H-strand mitochondrial protein-coding genes, 22 tRNA and two rRNA genes. Peprilus triacanthus were used to root the trees.
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The authors declare that there are no conflicts of interest and authors are solely responsible for the contents and writing of the paper.
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References
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