Xiaoxiao Jin

Complete mitochondrial genome of Trypauchen vagina (Perciformes, Gobioidei)

The complete mitochondrial genome of Trypauchen vagina was determined first. The genome is 16,686 bp in length and consists of 13 protein-coding genes, 22 tRNA genes, 2 ribosomal RNA genes, and 2 main non-coding regions [the control region (CR) and the origin of the light strand replication], the gene composition and order of which was similar to most other vertebrates. The overall base composition of T. vagina is T 27.6%, C 27.6%, A 29.5%, and G 15.3%, with a slight A+T bias of 57.1%. In addition to the discrete and conserved sequence blocks, an incomplete tandem repeat unit is detected within the CR. This mitogenome sequence data would play an important role in population genetics and phylogenetic analysis of the Gobioidei.

Complete mitochondrial genome of the yellow drum Nibea albiflora (Perciformes, Sciaenidae).

The yellow drum, Nibea albiflora, is a commercially important perciform fish species in China (Zhu et al. 1963). The wild resource of N. albiflora has sharply decreased recently due to overfishing and water pollution, prompting aquaculture development of this species. Intensive studies have been carried out in the areas of embryonic development, pre-larva morphology, and seed production (Sun et al. 2005; Yu et al. 2005); few reports are available on its genetic characteristics (Han et al. 2006, 2007; Xing et al. 2009). Therefore, it is very important to characterize the complete mitochondrial genome (mitogenome) of this species, which can be utilized in research on taxonomic resolution, population genetic structure and phylogeography, and phylogenetic relationships (Avise 1986; Miya et al. 2003; Bremer et al. 2005; Garber et al. 2005; Paine et al. 2008). In the present study, the complete mitogenome of N. albiflora was determined (GenBank accession number: HQ890947). Its characteristics are presented in Table I. The genome content (13 protein-coding genes, 2 rRNA genes, and 22 tRNA genes), gene order, and gene coding strand of N. albiflora mitogenome conform to the vertebrate consensus. The overall base composition is 25.9% T; 30.8% C; 26.4 A%; and 16.9% G. The AT content is higher than GC content, which is similar to other fishes. An anti-G bias was observed in the third position of protein-coding genes as reported in other vertebrate mitogenomes. All 21 tRNA genes can fold into a typical cloverleaf structure except for tRNA (AGY), which lacks a dihydrouridine arm. The three tRNA clusters (IQM, WANCY, and HSL) are well conserved in N. albiflora as those of typical vertebrate mitogenomes. The two ribosomal RNA genes (12S and 16S) are located between tRNA and tRNA (949 bp), and between tRNA and tRNA (UUR) (1704bp), respectively. Two reading frame overlaps occur on the same strand: atp8 and atp6 overlap by 10 nt, and nd4 l and nd4 overlap by 7 nt. All of the protein-coding genes begin with an ATG start codon, with the exception of nd4, which begins with GTG as an initiation codon. Seven protein-coding genes end with complete termination codons, TAA (atp8, atp6, nd4 l, nd5, and nd6), TAG (nd1), and AGA (cox1), the remaining six genes end with incomplete termination codons, either TA (nd2, cox3) or T (cox2, nd3, nd4, and cytb), and these incomplete termination codons are presumably completed as TAA via post-transcriptional polyadenylation (Ojala et al. 1981). The control region was determined to be 823 bp and exhibits the typical tripartite structure with extended termination associated sequence domain, central conserved sequence block (CSB) domain (CSB-D, CSB-E, and CSB-F), and CSB domain (CSB-1, CSB-2, and CSB-3), although some Sciaenidae species lack these conserved motif (such as CSB-D, CSB-E, and CSB-F). The origin of L-strand replication was identified and it can fold into a stem-loop secondary structure with the conserved motif 50-GCCGG-30. We expect that the present result will facilitate further

Complete mitochondrial genome of the Walking goby Scartelaos histophorus (Perceformes, Gobiidae)

The Walking goby Scartelaos histophorus (Perciformes, Gobiidae) is an amphibious gobioid fish. In this paper, the complete mitochondrial genome of S. histophorus was first determined. The genome is 16,496 bp in length and consists of 13 protein-coding genes, 22 tRNA genes, 2 ribosomal RNA genes, and 1 control region. The overall base composition of S. histophorus is 27.5% for T, 28.0% for C, 28.3% for A, and 16.1% for G, with a slight A+T bias of 55.8%. It has the typical vertebrate mitochondrial gene arrangement.

Complete mitochondrial genome of the striped sandgoby Acentrogobius pflaumii (Perciformes, gobiidae)

The striped sandgoby, Acentrogobius pflaumii (Perciformes, Gobiidae), is a widespread goby inhabiting shallow sandy–muddy bottoms in temperate riverine estuaries and inner bays. In this study, the complete mitochondrial genome of A. pflaumii was firstly determined. The genome is 16,515 bp in length and consists of 13 protein-coding genes, 22 tRNA genes, 2 ribosomal RNA genes, and 2 main non-coding regions (the control region and the origin of the light-strand replication). The overall base composition of A. pflaumii is 25.8% for T, 29.3% for C, 26.6% for A, and 18.3% for G, with a slight A+T bias of 52.4%. It has the typical vertebrate mitochondrial gene arrangement.

Complete mitochondrial genome of Oxuderces dentatus (Perciformes, Gobioidei)

The complete mitochondrial genome (mitogenome) of Oxuderces dentatus was determined first. The genome was 17,116 bp in length and consisted of 13 protein-coding genes, 22 tRNA genes, 2 ribosomal RNA genes, and 2 main non-coding regions [the control region (CR) and the origin of the light strand replication], the gene composition and order of which was similar to most other vertebrates. The overall base composition of the heavy strand was T 27.9%, C 26.8%, A 30.2%, and G 15.1%, with a slight A+T bias of 58.1%. In addition to the discrete and conserved sequence blocks, unusual long tandem repeat unit (three 150-bp tandem repeat units and an incomplete copy of 146 bp) was also detected within CR. This mitogenome sequence data would play an important role in population genetics and phylogenetic analysis of the Gobioidei.

UNIVERSAL PRIMERS FOR AMPLIFICATION OF THE COMPLETE MITOCHONDRIAL CONTROL REGION IN MARINE FISH SPECIES

Through multiple alignment analysis of mitochondrial tRNA-Thr and tRNA-Phe sequences from 161 fishes, new universal primers specially targeting the entire mitochondrial control region were designed. This new primer set successfully amplified the expected PCR products from various kinds of marine fish species, belonging to various families, and the amplified segments were confirmed to be the control region by sequencing. These primers provide a useful tool to study the control region diversity in economically important fish species, the possible mechanism of control region evolution, and the functions of the conserved motifs in the control region.

Complete mitochondrial genome of the Asian freshwater goby Synechogobius ommaturus (Perciformes, Gobioidei)

The Asian freshwater goby, Synechogobius ommaturus (Perciformes, Gobiidae) is a big goby inhabiting shallow sandy–muddy bottoms in temperate riverine estuaries and inner bays, mainly distributed in China, Japan, and the Korean Peninsula. In this paper, the complete mitochondrial genome of S. ommaturus was firstly determined. The genome is 16,660 bp in length and consists of 13 protein-coding genes, 22 tRNA genes, 2 ribosomal RNA genes, and 2 main non-coding regions (the control region and the origin of the light strand replication). The overall base composition of S. ommaturus is 26.9% for T, 27.9% for C, 27.7% for A, and 17.4% for G, with a slight A+T bias of 54.6%. It has the typical vertebrate mitochondrial gene arrangement.

Mitochondrial genome of Cryptocentrus yatsui (Perciformes, Gobioidei) and phylogenetic consideration within the genus Cryptocentrus.

The complete mitochondrial genome (mitogenome) of Cryptocentrus yatsui was first determined. The genome was 16,584 bp in length and consisted of 13 protein-coding genes, 22 tRNA genes, 2 ribosomal RNA genes, and 2 main noncoding regions (the control region and the origin of the light strand replication), the gene composition and order of which were similar to most other vertebrates. The overall base composition values of the heavy strand are 26.0% for T, 29.9% for C, 26.4% for A, and 17.7% for G, with a slight A+T bias of 52.4%. To clarify the phylogenetic relationships of C. yatsui within the genus Cryptocentrus, 18 sequences, which were generated from COI region of six species, were used to construct the neighbor-joining phylogenetic tree. And we found that C. yatsui was rooted with the other Cryptocentrus species and has a distant relationship with others.

Complete mitochondrial genome sequence and structure of control region of the Amoya chusanensis (Perciformes, Gobioidei)

Amoya chusanensis is a small benthonic fish, which inhabits the near shore area of freshwater and brackish, especially the hole of the intertidal zone, and is an endemic species of China which is mainly distributed in the East China Sea. In this study, firstly the complete mitochondrial genome of A. chusanensis was determined. The genome is 16,486 bp in length and consists of 13 protein-coding genes, 22 tRNA genes, 2 ribosomal RNA genes, and 2 main noncoding regions (the control region and the origin of the light strand replication). The complete mitochondrial genome base composition is 26.4% for T, 28.7% for C, 29.0% for A, and 15.9% for G, with a slight A+T bias of 55.4%. Within the control region, the termination-associated sequence, central, and conserved sequence block domains were found.

The complete mitochondrial genome of silver croaker Argyrosomus argentatus (Perciforems; Sciaenidae): Genome characterization and phylogenetic consideration

The complete mitochondrial genome (mitogenome) sequence of the silver croaker, Argyrosomus argentatus, was obtained by using LA-PCR and sequencing. The mitogenome is 16485 bp in length, consists of 13 protein-coding genes, two ribosomal RNAs, 22 transfer RNAs, and a non-coding control region like those found in other vertebrates, with the gene order similar to that of typical teleosts. Most of the genes of A. argentatus 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. The reading frames of two pairs of genes overlapped: ATPase8 and 6 and ND4L and ND4 by ten and seven nucleotides, respectively. The origin of L-strand replication in A. argentatus was in a cluster of five tRNA genes (WANCY) and was 46 nucleotides in length. The conserved motif (5′-GCGGG-3′) was found at the base of the stem within the tRNACys gene. Within the control region, we identified all of the conserved motifs except for CSB-F.