Termination-associated Sequence Research Articles

The complete mitochondrial genome of Coilia nasus (Clupeiformes: Engraulidae) from the coast of Ningbo in China

In this study, the complete mitochondrial genome (mitogenome) sequence of Coilia nasus has been determined by long polymerase chain reaction and primer walking methods. The mitogenome is a circular molecule of 16,896 bp in length and contains 37 mitochondrial genes including 13 protein-coding genes, 2 ribosomal RNA (rRNA), 22 transfer RNA (tRNA) and a control region as other bony fishes. Within the control region, we identified the termination-associated sequence domain (TAS), the central conserved sequence block domains (CSB-F, CSB-E and CSB-D), and the conserved sequence block domains (CSB-1, CSB-2 and CSB-3).

Characteristics of complete mitogenome of Pampus sp. nov. (Perciformes: Stromateidae)

Pampus sp. nov. is a new species in genus Pampus and different from six reported Pampus species at the molecular level. Long PCR and primer walking methods are employed for determining the complete mitochondrial genome sequence of the new species. The mitogenome is a circular molecule of 16,560 bp in length including the 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). Within the control region, we identify the termination-associated sequence domain (TAS), central conserved domain (CSB-F, CSB-E and CSB-D), and three conserved sequence blocks (CSB-1, CSB-2 and CSB-3).

The complete mitochondrial genome of Nibea coibor (Perciformes: Sciaenidae)

In this study, the complete mitochondrial genome (mitogenome) sequence of Nibea coibor has been determined by long polymerase chain reaction and primer walking methods. The complete mitochondrial genome is 16,509 bp in length and contains 37 mitochondrial genes (13 protein-coding genes, 2 ribosomal RNA (rRNA), 22 transfer RNA (tRNA)) and a control region as other bony fishes. Within the control region, we identified the termination-associated sequence domain (TAS), the central conserved sequence block domains (CSB-F, CSB-E, CSB-D and CSB-C), and the conserved sequence block domains (CSB-2, CSB-3).

The complete mitochondrial genome of Saurida umeyoshii (Aulopiformes: Synodontidae)

In this study, the complete mitochondrial genome (mitogenome) sequence of Saurida umeyoshii has been determined by long polymerase chain reaction and primer walking methods. The complete mitochondrial genome is 16,546 bp in length and contains 37 mitochondrial genes (13 protein-coding genes, 2 ribosomal RNA (rRNA), 22 transfer RNA (tRNA)), and a control region as other bony fishes. Within the control region, we identified the termination-associated sequence domain (TAS), the central conserved sequence block domains (CSB-F, CSB-E, CSB-D, CSB-C, CSB-B and CSB-A), and the conserved sequence block domains (CSB-1, CSB-2 and CSB-3).

Mitochondrial genome of the tomato clownfish Amphiprion frenatus (Pomacentridae, Amphiprioninae)

The complete mitochondrial (mt) genome of the tomato clownfish Amphiprion frenatus was obtained in this study. The circular mtDNA molecule was 16,774 bp in size and the overall nucleotide composition of the H-strand was 29.72% A, 25.81% T, 15.38% G and 29.09% C, with an A + T bias. The complete mitogenome encoded 13 protein-coding genes, 2 rRNAs, 22 tRNAs and a control region (D-loop), with the gene arrangement and translation direction basically identical to other typical vertebrate mitogenomes. The D-loop included termination associated sequence (TAS), central conserved domain (CCD) and conserved sequence block (CSB), and was composed of 6 complete continuity tandem repeat units and an imperfect tandem repeat unit.

The complete mitochondrial genome of Saurida undosquamis (Aulopiformes: Synodontidae)

In this study, the complete mitochondrial genome (mitogenome) sequence of Saurida undosquamis has been determined by long polymerase chain reaction and primer walking methods. The complete mitochondrial genome is 16,550 bp in length and contains 37 mitochondrial genes (13 protein-coding genes, 2 ribosomal RNA (rRNA), 22 transfer RNA (tRNA)), and a control region as other bony fishes. Within the control region, we identified the termination-associated sequence domain (TAS), the central conserved sequence block domains (CSB-F, CSB-E, CSB-D, CSB-C, CSB-B and CSB-A), and the conserved sequence block domains (CSB-1, CSB-2 and CSB-3).

The complete mitochondrial genome sequence of Jinshaia abbreviata (Cypriniformes, Balitoridae)

Jinshaia abbreviata, belonging to the family Balitoridae in Cypriniformes, is endemic to the Upper Yangtze River with most population distributed in the Jinsha River. In this study, the complete mitochondrial genome of J. abbreviata was sequenced with its structure analyzed. The mitochondrial genome of J. abbreviata is similar to those of the typical vertebrates, 16,567 bp in length, including 13 protein-coding genes, two ribosomal RNA genes, 22 transfer RNA genes, and one non-coding control region (D-loop). The D-loop of J. abbreviata was characterized by one termination-associated sequence with two pair of motifs and six conserved sequence blocks (CSB-F, CSB-E, CSB-D, and CSB I-III). The mitogenome sequence of J. abbreviata could contribute to estimate the phylogenetic relationship of the Balitoridae. And further investigations with more Jinshaia species and individuals included need to be performed to better understand the speciation process and evolutionary history of the genus Jinshaia.

The complete mitochondrial genome of snubnose pompano Trachinotus blochii (Teleostei, Carangidae)

The complete mitochondrial genome of Trachinotus blochii was determined using the polymerase chain reaction. The complete mitochondrial DNA sequence is 16,558 bp in length. It consists of 13 protein-coding genes, 22 transfer RNA genes, two rRNA genes and two non-coding regions. Overall base composition of its mitochondrial genome is estimated to be 29.21% for A, 15.74% for G, 26.49% for T, 28.56% for C, respectively, with a high A + T content (55.70%). The control region contains three conserved sequence blocks, a termination-associated sequence and a TATA box. The complete mitochondrial genome sequence of T. blochii can provide a basic data for the studies on population structure, molecular systematic, stock evaluation and conservation genetics. It is also helpful to develop the rational management strategies for T. blochii resource.

Complete mitochondrial genome of the blacktip reef shark Carcharhinus melanopterus (Carcharhiniformes: Carcharhinidae)

The complete mitochondrial genome of the blacktip reef shark Carcharhinus melanopterus is determined for the first time in this study. The gene composition and order in the mitogenome of C. melanopterus is identical to most vertebrates. The overall base composition is 31.3% A, 25.3% C, 13.3% G and 30.1% T. There are 29 bp overlaps and 21 bp short intergenic spaces in the mitogenome. Two start codons and three stop codons were found in protein-coding genes. The dihydrouridine arm of tRNA-Ser2 was replaced by a simple loop and the other tRNAs could be folded into the typical cloverleaf structure. The termination associated sequence (TAS) and the conserved sequence blocks (CSB1-3) are found in the control region.

The complete mitochondrial genome of Grammistes sexlineatus (Perciformes, Serranidae)

The complete mitochondrial genome of Grammistes sexlineatus was first determined and studied in the present study. The mitochondrial genome was 16,502 nucleotides that contained 13 protein-coding genes, 22 tRNA genes, 2 ribosomal RNA genes and one putative control region. The overall base composition of G. sexlineatus was T 23.74%, C 31.05%, A 28.79%, and G 16.42%, with a slight A + T bias of 52.53%. The gene order and composition of G. sexlineatus mitogenome was similar to the most vertebrate. Meanwhile, a termination-associated sequence (TAS) and the conserved sequence blocks (CSB-2 and CSB-3) were determined in G. sexlineatus control region. The mitochondrial genome would play key role in phylogenetics analysis of the Serranidae.

Structure of mitochondrial DNA control region of Pholis fangi and its phylogenetic implication

In this study, the entire mitochondrial DNA (mtDNA) control region (CR) of Pholis fangi was amplified via polymerase chain reaction followed by direct sequencing. The length of the mtDNA CR consensus sequence of P. fangi was 853 bp in length. In accordance with the recognition sites as were previously reported in fish species, the mtDNA CR sequence of P. fangi can be divided into 3 domains, i.e., the extended terminal associated sequence (ETAS), the central conserved sequence block (CSB), and the CSB domain. In addition, the following structures were identified in the mtDNA CR sequence of P. fangi: 2 ETASs in the ETAS domain (TAS and cTAS), 6 CSBs in the central CSB domain (CSB-F to CSB-A), and 3 CSBs in the CSB domain (CSB-1 to CSB-3). These demonstrated that the structure of the mtDNA CR of P. fangi was substantially different from those of most other fish species. The mtDNA CR sequence of P. fangi contained one conserved region from 656 bp to 815 bp. Similar to most other fish species, P. fangi has no tandem repeat sequences in its mtDNA CR sequence. Phylogenetic analysis based on the complete mtDNA CR sequences showed that there were no genetic differences within P. fangi populations of the same geographical origin and between P. fangi populations of different geographical origins.

The complete mitogenome of Pampus argenteus (Perciformes: Stromateidae)

Long PCR and primer walking methods are employed for determining the complete mitochondrial genome sequence of Pampus argenteus. The mitogenome is a circular molecule of 16,544 bp in length including the structure of 13 protein-coding genes, 2 ribosomal RNA genes, 22 transfer RNA genes and 2 non-coding regions (L-strand replication origin and control region). Within the control region, we identify the termination-associated sequence domain (TAS), central conserved domain (CSB-F, CSB-E and CSB-D), and three conserved sequence blocks (CSB-1, CSB-2 and CSB-3).

Complete mitochondrial genome of Florida pompano Trachinotus carolinus (Teleostei, Carangidae)

The complete mitochondrial genome sequence of Florida pompano Trachinotus carolinus was determined by the overlapped polymerase chain reaction. The complete mitochondrial DNA sequence is 16,544 bp in length. It consists of 13 protein-coding genes, 22 transfer RNA genes, two rRNA genes and two non-coding regions. Overall base composition of its mitochondrial genome is estimated to be 28.68% for A, 16.27% for G, 26.00% for T, 29.06% for C, respectively, with a high A+T content (54.68%). The control region contains three conserved sequence blocks, a termination-associated sequence and a TATA box. The sequence data of T. carolinus can provide useful information for the studies on population structure, molecular systematic, stock evaluation and conservation genetics. It is also helpful to develop the rational management strategies for T. carolinus resource.

The complete mitochondrial genome of Pampus chinensis (Perciformes: Stromateidae)

Long PCR and primer walking methods are employed for determining the complete mitochondrial genome (mitogenome) sequence of Pampus chinensis. The mitogenome is a circular molecule of 16,534 bp in length including the structure of 13 protein-coding genes, 2 ribosomal RNA genes, 22 transfer RNA genes and 2 non-coding regions (L-strand replication origin and control region). Within the control region, we identify the termination-associated sequence domain (TAS), central conserved sequence block domains (CSB-F, CSB-E and CSB-D), and conserved sequence blocks (CSB-1, CSB-2 and CSB-3).

Complete mitochondrial genome sequence of northeastern red deer (Cervus elaphus xanthopygus)

The complete mitochondrial genome of the northeastern red deer, Cervus elaphus xanthopygus, was determined by accurate polymerase chain reaction. The entire genome is 16,416 bp in length and contains 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes and 1 control region, all of which are arranged in a typical vertebrate manner. The overall base composition of the northeastern red deer’s mitochondrial genome is 33.3% of A, 24.3% of C, 28.9% of T and 13.5% of G. A termination-associated sequence and several conserved central sequence block domains were discovered within the control region.

Complete mitochondrial genome of the largest living fish: whale shark Rhincodon typus (Orectolobiformes: Rhincodontidae)

The whale shark Rhincodon typus (Pisces: Chondrichthyes, Orectolobiformes, Rhincodontidae) is the largest living fish on Earth. In this study, we presented its complete mitogenome. It is 16,928 bp in length, contains 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes and one control region with the typical gene order and transcriptional direction in the vertebrates. Overall base composition of the R. typus mitogenome is 33.5% A, 24.3% C, 12.8% G and 29.5% T. Two start codon (GTG and ATG) and two stop codon patterns (TAG and TAA/T) were found in protein-coding genes. The tRNA-Ser2 could not be folded into the typical cloverleaf secondary structure because of the replacement of its dihydrouridine arm by a simple loop. A termination associated sequences (TAS) and three conserved sequence blocks (CSB1-3) were identified in the control region.

The complete mitochondrial genome of Saurida microlepis (Aulopiformes: Synodontidae)

In this study, the complete mitochondrial genome (mitogenome) sequence of Saurida microlepis has been determined by long PCR and primer walking methods. The complete mitochondrial genome is a circular molecule of 16,510 bp in length and contains the same set of 37 mitochondrial genes (13 protein-coding genes, 2 ribosomal RNA (rRNA), 22 transfer RNA (tRNA)), and a control region as other bony fishes. Within the control region, we identified the termination-associated sequence domain (TAS), the central conserved sequence block domains (CSB-F, CSB-E, CSB-D, CSB-C, CSB-B and CSB-A), and the conserved sequence block domains (CSB-1, CSB-2 and CSB-3).

The complete mitochondrial genome of Pampus echinogaster (Perciformes: Stromateidae)

The long PCR and primer walking methods are employed for determining the complete mitochondrial genome sequence of Pampus echinogaster. The mitogenome is a circular molecule of 17,694 bp in length including the structure of 13 protein-coding genes, 2 ribosomal RNA genes, 23 transfer RNA genes and 2 non-coding regions (L-strand replication origin and control region). Two tRNAMet genes are identified in the tRNA-IQM region. Within the control region, we identify the termination-associated sequence domain (TAS), a central conserved domain (CSB-F, CSB-E and CSB-D) and three conserved sequence blocks (CSB-1, CSB-2 and CSB-3). There are 10 copies of tandem repeats of 120–124 bp in the control region, which contain CSB-3.

Complete mitogenome of Hemiculter leucisculus (Cyprinidae: Cultrinae)

The complete mitogenome was first determined for a minnow Hemiculter leucisculus in this study. It is 16,622 bp in length and has 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes and 1 control region. Overall nucleotide base composition is 30.4% A, 27.10% C, 17.10% G and 25.40% T. All the tRNA genes can fold into the typical clover-leaf secondary structures, except the tRNA-Ser2 which loses the dihydrouridine arm and is replaced with one 11 bp loop. The origin of light-strand replication (OL) was found between the tRNA-Asn and tRNA-Cys genes while the termination associated sequence (TAS) and the conserved sequence blocks (CSB1-3) were found in the control region.

Mitochondrial genome of the spotless smooth-hound Mustelus griseus (Carcharhiniformes: Triakidae)

The complete mitochondrial genome of Mustelus griseus was first determined in this study. It is 16,754 bp in length, consisting of 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes and 1 control region with the typical gene order in vertebrates. Overall nucleotide base composition of the mitogenome is 30.7% A, 24.9% C, 14.0% G and 30.3% T. After aligning, it comes to us that the mitogenomic portions of M. griseus are very similar to those of Mustelus manazo, ranging from 86.92% (control region) to 100% (tRNA-His and tRNA-Leu2). The origin of L-strand replication (OL) is identified between tRNA-Asn and tRNA-Cys genes. The control region is located between the tRNA-Pro and tRNA-Phe genes, containing one termination-associated sequence (TAS) and three short conserved sequences (CSB 1-3).