Termination-associated Sequence Research Articles

Sequencing and analysis of the complete mitochondrial genome of tundra shrew (Sorex tundrensis) from China

The complete mitogenome sequence of tundra shrew (Sorex tundrensis) was determined using long PCR. The genome was 17,444 bp in length and contained 13 protein-coding genes, 2 ribosomal RNA genes, 23 transfer RNA genes, 1 origin of L strand replication and 1 control region. The overall base composition of the heavy strand is A (32.9%), C (24.8%), T (29.0%), and G (13.3%). The base compositions present clearly the A–T skew, which is most obviously in the control region and protein-coding genes. The extended termination-associated sequence domain, the central conserved domain and the conserved sequence block domain are defined in the mitochondrial genome control region of tundra shrew. Mitochondrial genome analyses based on MP, ML, NJ and Bayesian analyses yielded identical phylogenetic trees. The three Sorex species formed a monophyletic group with the high bootstrap value (100 %) in all examinations.

Sequencing and analysis of the complete mitochondrial genome of Gloydius saxatilis (Squamata: Viperidae: Crotalinae)

The mitochondrial genome sequence of Gloydius saxatilis is analyzed and presented for the public for the first time. The genome was 17,218 bp in length and contained 13 protein-coding genes, 2 ribosomal RNA genes, 22 transfer RNA genes and 2 control regions. The overall base composition was A (32.3%), C (28.9%), T (25.8%), and G (13.0%). The base compositions presented clearly the A-C skew, which was most obviously in the protein-coding genes. The extended termination-associated sequence domain, the central conserved domain and the conserved sequence block domain are defined in the mitochondrial genome control region of G. saxatilis. Mitochondrial genomes analyses based on MP, ML, NJ and Bayesian analyses yielded identical phylogenetic trees, indicating a close phylogenetic affinity of the thirteen Crotalinae species. It appeared that no less than two major phyletic lineages were present in Crotalinae. The main clades within the Crotalinae supported are: A clade including the Protobothrops. A clade (G. brevicaudus, G. ussuriensis, G. intermedius, G. saxatilis) with the Ovophis as the sister taxon to Protobothrops and was supported by bootstrap values of 88%. The four Gloydius species formed a paraphyletic group with the high bootstrap value (100%) in all examinations.

Complete mitochondrial genome of Acrossocheilus parallens (Cypriniformes, Barbinae)

The omnivorous fish Acrossocheilus parallens (Cypriniformes, Barbinae) is endemic to China. In this paper, the complete mitochondrial genome sequence of A. parallens was firstly determined. The circle genome (16,592 bp) comprises 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes and 1 control region. The overall base composition of A. parallens is 31.0% for A, 24.7% for T, 28.0% for C, and 16.3% for G, with a slight A + T bias of 55.7%. The termination-associated sequence and conserved sequence block domains were found in the control region. It has the typical vertebrate mitochondrial gene arrangement.

Complete mitochondrial genome of Argentine shortfin squid (Illex argentines)

In this study, we determined the complete mitochondrial genome of the Illex argentinus. The genome was 20,278 bp in length and contained 18 protein-coding genes, 23 transfer RNA genes, 2 ribosomal RNA genes and 3 main non-coding regions. The composition and order of genes were different to some other invertebrates. The overall base composition of I. argentinus was A 39.23%, C 17.50%, T 33.71% and G 9.56%, with a highly A + T bias of 72.94%. All of the three control regions (CR) contained termination-associated sequences and conserved sequence blocks. This mitogenome sequence data would play an important role in the taxonomic resolution and phylogeography of the Ommastrephidae.

Complete mitochondrial genome of the Loligo opalescence

In this study, we determined the complete mitochondrial genome of the Loligo opalescence. The genome was 17,370 bp in length and contained 13 protein-coding genes, 22 transfer RNA genes, 2 ribosomal RNA genes and 3 main non-coding regions. The composition and order of genes, were similar to most other invertebrates. The overall base composition of L. opalescence is A 38.62%, C 19.40%, T 32.37% and G 9.61%, with a highly A + T bias of 70.99%. All of the three control regions (CR) contain termination-associated sequences and conserved sequence blocks. This mitogenome sequence data would play an important role in the investigation of phylogenetic relationship, taxonomic resolution and phylogeography of the Loliginidae.

The complete mitochondrial genome of Coilia grayii (Clupeiformes: Engraulidae)

In this study, the complete mitochondrial genome (mitogenome) sequence of Coilia grayii has been determined by long polymerase chain reaction and primer walking methods. The mitogenome is a circular molecule of 16,851 bp in length and contains 37 mitochondrial genes including 13 protein-coding genes, 2 ribosomal RNA (rRNA), 22 transfer RNAs (tRNAs) 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).

Complete mitochondrial genome of the Loliolus (Nipponololigo) uyii

In this study, we determined the complete mitochondrial genome of the little squid (Loliolus (Nipponololigo) uyii). The genome was 17,134 bp in length and contained 13 protein-coding genes,22 transfer RNA genes, 2 ribosomal RNA genes and 3 main non-coding regions. The composition and order of genes were similar to most other invertebrates. The overall base composition of L. uyii is A 39.98%, C 18.65 %, T 32.39% and G 8.98%, with a high A + T bias of 72.37%. All of the three control regions (CR) contain termination-associated sequences and conserved sequence blocks. These mitogenome sequence data would play an important role in the investigation of phylogenetic relationship, taxonomic resolution and phylogeography of the Loliginidae.

The complete mitochondrial genome of the hybrid of Pelteobagrus fulvidraco (♀) × Pelteobagrus vachelli (♂)

In the present of study, we have reported the complete mitochondrial DNA sequence of the hybrid of Pelteobagrus fulvidraco (♀) × Pelteobagrus vachelli (♂) that is obtained by artificial hybridization. The total length of the mitochondrial genome is 16,527 bp, with the base compositions of 30.84% A, 25.54% T, 28.22% C, and 15.40% G. It contains two ribosomal RNA genes, 13 protein-coding genes, 22 transfer RNA genes, and a major non-coding control region (D-loop region). The arrangement of these genes is same as that observed in the teleosts. All protein initiation codons are ATG, except for COX1 that begins with GTG. The complete mitogenome of the hybrid of P. fulvidraco (♀) × P. vachelli (♂) provides an important data set for the exploration of mitochondrial inheritance mechanism. The termination-associated sequence and critical central conserved sequences (CSB-D, CSB-E and CSB-F) are also detected.

Seven complete mitochondrial genome sequences of bushtits (Passeriformes, Aegithalidae, Aegithalos): the evolution pattern in duplicated control regions

The control region (CR) of the mitochondrial DNA exhibits important functions in replication and transcription, and duplications of the CR have been reported in a wide range of animal groups. In most cases, concerted evolution is expected to explain the high similarity of duplicated CRs. In this paper, we present seven complete mitochondrial genome sequences from the bushtits (genus Aegithalos), in which we discovered two duplicated CRs, and try to survey the evolution pattern of these duplicated CRs. We also found that the duplicated CRs within one individual were almost identical, and variations were concentrated in two sections, one located between a poly-C site and a potential TAS (termination associated sequence) element, the other one located at the 3′ end of the duplicated CRs. The phylogenetic analyses of paralogous CRs showed that the tree topology were depending on whether the two high variable regions at the upstream of TAS element and the 3′end of duplicated CRs: when they were concluded, the orthologous copies were closely related; when they were excluded, the paralogous copies in the same lineages were closely related. This may suggest the role of recombination in the evolution of duplicated CRs. Consequently, the recombination was detected, and the breakpoints were found at ∼120 bp (the upstream of the potential TAS element) and ∼1150 bp of the alignment of duplicated CRs. According to these results, we supposed that homologous recombination occurred between paralogous CRs from different mtDNA molecule was proposed as the most suitable mechanism for concerted evolution of the duplicated CRs, and the recombination took place in every replication cycle, so that most part of the duplicated regions remain identical within an individual, while the 5′ and 3′end of the duplicated CRs were not involved in recombination, and evolved independently.

Complete mitochondrial genome of the Indonesian whaler shark Carcharhinus tjutjot

In this study, we first present the complete mitochondrial genome of the Indonesian whaler shark Carcharhinus tjutjot. It is 16,705 bp in length and encodes 37 mitochondrial genes with the typical gene order and transcriptional direction in vertebrates. The overall nucleotide base content is 31.6% A, 26.4% C, 13.0% G and 29.0% T. A total of 33 bp short overlaps and 22 bp short intergenic spaces were found at 9 and 11 gene junctions, respectively. Two initiated codon types (ATG and GTG) and three terminal codon types (TAA, TAG and AGG) were used in the protein-coding genes. The tRNA-Ser2 replaced the DHU arm by a simple loop and could not be folded into the typical secondary structure. The origin of L-strand replication (OL) was identified between the tRNA-Asn and tRNA-Cys genes. The termination-associated sequence (TAS) was found near the tRNA-Pro in the control region.

Complete mitochondrial genome sequence of Labeo fimbriatus (Bloch, 1975)

The complete mitochondrial genome of Labeo fimbriatus, the fringe-lipped carp, was determined for the first time. The genome was 16,614 bp in length and consisted of 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes and one control region. Organization of genes and their order are in accordance with other vertebrates. The overall base composition on the plus strand was A: 32.35%, G: 15.46%, C: 27.54%, T: 24.647%, and the A + T content 57%. The control region contains a microsatellite, (TA)12, a putative termination-associated sequence and three conserved sequence blocks. This mitogenome sequence data would play an important role in population genetics and phylogenetics of cultivable carps of India.

Complete mitochondrial genome of the Cyclemys dentata and phylogenetic analysis of the major family Geoemydidae.

In the present study, the complete mitochondrial (mt) genome of Cyclemys dentata was determined using PCR reactions. The structural organization and gene order of C. dentata were equivalent to those of most other vertebrates. The mt genome was 16,489 bp in length, has rich A+T content, consisting of 13 protein-coding genes, 2 ribosomal RNA genes, 22 transfer RNA genes, and a control region (D-loop). All protein-coding genes started with ATG, many genes have complete stop codons, except ND2, COX3, ND3, and cyt-b genes had incomplete stop codons of T. The light-strand replication origin (OL) of C. dentata might fold into a stable stem-loop secondary structure, and its loop had 2 nt less than that of the Cyclemys atripons OL sequence. The D-Loop of C. dentata contained a central domain (CD), 2 extended termination associated sequences (ETAS1, ETAS2) and 3 conserved sequence blocks (CSB1, CSB2, CSB3). The average length of 20 turtles' mt genomes was 16,692.5 bp, including 34.1% A, 27.0% T, 26.0% C and 12.9% G. The C. dentata mitochondrial genome could provide useful data for further studies on phylogenetics and conservation genetics of this species. The phylogenetic relationships of the family Geoemydidae were analyzed by maximum-likelihood (ML) and neighbor-joining (NJ) based on concatenated sequences of 13 protein-coding genes from 20 turtle species. The ML and NJ trees had homologous topologies. The results support the existing classification of the genera of Geoemydidae, that C. dentata was a sister species of C. atripons, Pyxidea nested in Cuora, and Chinemys was synonymous with Mauremys.

Complete mitochondrial genome of the Sharpnose stingray Himantura gerrardi (Myliobatiformes: Dasyatidae)

In this study, we presented the complete mitochondrial genome of the Sharpnose stingray Himantura gerrardi for the first time, which was 17,685 bp in length and contained 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes and a putative control region. The overall nucleotide composition was 30.1% A, 27.5% C, 14.5% G and 28.0% T. A total of 22 bp overlaps and 83 bp short intergenic spaces were found in the mitogenome. Two start codons (ATG and GTG) and two stop codons (TAG and TAA/T) were used in the protein-coding genes. The origin of L-strand replication (OL) sequence formed a hairpin structure between the tRNA-Asn and tRNA-Cys genes. The termination associated sequence (TAS) formed a hairpin structure near the tRNA-Pro in the control region.

The complete mitochondrial genome of Sillago aeolus (Perciformes: Sillaginidae)

The long PCR and primer walking methods are used for determining the complete mitochondrial genome sequence of Sillago aeolus. The entire sequence is 16,499 bp in length including 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 identified the termination-associated sequence domain (TAS), central conserved domains (CSB-F, CSB-E, CSB-D, CSB-C, CSB-B and CSB-A), and three conserved sequence blocks (CSB-1, CSB-2 and CSB-3).

The complete mitochondrial genome of Vespertilio sinensis from China

The complete mitogenome sequence of Vespertilio sinensis was determined using long PCR. The genome was 17,146 bp in length and contained 13 protein-coding genes, 2 ribosomal RNA genes, 22 transfer RNA genes and 1 control region. The overall base composition of the heavy strand is A (32.73%), C (23.64%), T (29.72%), and G (13.91%). The base compositions present clearly the A–T skew, which is most obviously in the control region and protein-coding genes. The extended termination-associated sequence domain, the central conserved domain and the conserved sequence block domain are defined in the mitochondrial genome control region of V. sinensis.

The complete mitochondrial genome of Sillago indica (Perciformes: Sillaginidae)

In this study, the complete mitochondrial genome (mitogenome) sequence of Sillago indica has been determined by long polymerase chain reaction and primer walking methods. The complete mitochondrial genome is a circular molecule of 16,647 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-1, CSB-2 and CSB-3).

The complete mitochondrial genome of Lota lota (Gadiformes: Gadidae) from the Burqin River in China

In this study, the complete mitochondrial genome (mitogenome) sequence of Lota lota has been determined by long polymerase chain reaction and primer walking methods. The mitogenome is a circular molecule of 16,519 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 and CSB-D), and the conserved sequence block domains (CSB-1, CSB-2 and CSB-3).

The complete mitochondrial genome of Lota lota (Gadiformes: Gadidae)

In this study, the complete mitochondrial genome (mitogenome) sequence of Lota lota has been determined by long polymerase chain reaction and primer walking methods. The mitogenome is a circular molecule of 16,547 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 and CSB-D), and the conserved sequence block domains (CSB-1, CSB-2 and CSB-3).

The complete mitochondrial genome of Sillago asiatica (Perciformes: Sillaginidae)

In this study, the complete mitochondrial genome (mitogenome) sequence of Sillago asiatica has been determined by long polymerase chain reaction and primer walking methods. The complete mitochondrial genome is a circular molecule of 16,493 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 and CSB-D), and the conserved sequence block domains (CSB-1, CSB-2 and CSB-3).

The complete mitochondrial genome of Coilia nasus (Clupeiformes: Engraulidae) from Ariake Sea

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 16,900 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).