Origin Of Light Strand Replication Research Articles

The complete mitochondrial genome sequence of Acentrogobius caninus (Gobiiformes: Gobiidae)

At present, only several species of genus Acentrogobius were described and information of mitochondrial DNA were also just focused on two species. Here, the complete mitochondrial genome of Acentrogobius caninus was completely sequenced by high throughput sequencing method. The complete mitochondrial genome was 16,614 bp in length, consisted of 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes, 1 large non-coding control region, and 1 light-strand replication origin. Overall base composition values for the mitochondrial genome were 28.24, 29.20, 16.77, and 25.79% for A, C, G, and T, respectively. The gene arrangement is identical to those in typical fishes. Phylogenetic tree based on 13 protein-coding genes shows that three species of genus Acentrogobiu did not cluster into one clade.

The complete mitogenome of Bagrid catfish Chrysichthys nigrodigitatus (Siluriformes: Claroteidae)

We here report the complete mitochondrial genome of Chrysichthys nigrodigitatus, which is 16,514 bp in length. Mitogenome of C. nigrodigitatus showed the conserved 13 protein-coding genes, 22 tRNA genes, two rRNA genes, and two noncoding regions including the light-strand replication origin (OL) and a putative control region (CR). All tRNA genes were predicted to fold into the typical cloverleaf secondary structures with the typical base-pairing except for tRNA-Ser(AGC). Phylogenetic analysis with currently known complete mitogenome sequences in Siluriformes showed that C. nigrodigitatus is most closely related to Auchenoglanis occidentalis forming a family Claroteidae cluster.

Complete mitochondrial DNA genome of grey pomfret Pampus cinereus (Bloch, 1795) (Perciformes: Stromateidae)

In this study, we sequenced the complete mitochondrial genome of Pampus cinereus (Bloch, 1795). This mitochondrial genome, consisting of 16,540 base pairs (bp), contains 13 protein-coding genes, two ribosomal RNAs, 22 transfer RNAs, and two mainly noncoding regions (control region and origin of light-strand replication) as those found in other vertebrates. Control region with 846 bp in length, is located between tRNAPro and tRNAPhe. The overall base composition of the heavy strand shows 27.4% of T, 27.5% of C, 30.0% of A, and 15.2% of G, with a slight A + T rich bias (57.4%). The complete mitochondrial genome data will provide useful genetic markers for the studies on the molecular identification, population genetics, phylogenetic analysis and conservation genetics.

The complete mitochondrial genome of Sarcocheilichthys davidi and its phylogeny

Sarcocheilichthys davidi is a small-size ornamental freshwater species. In the present study, the complete mitochondrial genome of S. davidi was first determined using the next-generation sequencing technology. The result showed that the circular mitogenome was 16,675 bp in length, contained 13 protein-coding genes (PCGs), two ribosomal RNA (rRNA) genes, 22 transfer RNA (tRNA) genes, and two non-coding regions: origin of light-strand replication (OL) and displacement loop locus (D-loop). In addition to ND6 and eight tRNA genes, most mitochondrial genes were encoded on the heavy strand. Furthermore, the overall base composition was 29.97% A, 26.12% T, 26.86% C, 17.04% G, respectively, and showed AT-rich feature (56.09%). Moreover, phylogenetic analysis based on the tandem 13 PCGs nucleotide sequences indicated that S. davidi had a close relationship with S. snigripinnis and S. variegatus wakiyae. The complete mitogenome sequence of S. davidi would contribute to the better understanding of molecular systematics, selection, conservation, species identification and evolution of this species.

The complete mitochondrial genome of Microhyla fissipes (Amphidia, Anura, Microhylidae) from Taiwan

The complete mitochondrial genome sequence of Microhyla fissipes from Yi-Lan, Taiwan was determined through Sanger sequencing. The total length was 16,729 nucleotide base pairs. The genome included distinctive 37 genes, one light-strand replication origin and one control region. Regardless indels the non-coding genes were more conserved than the coding genes within Microhyla, as well as in Kaloula. The abnormal high differences in ND5 (0.2316) and ND6 (0.2406) between Taiwan and China samples is interesting for further studies.

The complete mitochondrial genome of the horned lizard Phrynosoma blainvillii (Squamata: Phrynosomatidae) from California, USA

Analysis of Phrynosoma blainvillii Gray from Marina, Monterey County, California, using 150 bp paired-end Illumina sequences (Illumina, San Diego, CA) resulted in the assembly of its complete mitogenome. The mitogenome is 16,946 bp in length and contains a putative origin of light strand replication (OL), control region, 22 tRNA, 2 rRNA, and 13 protein-coding genes. Its content and organization are similar to other Squamata. Phylogenetic analysis of P. blainvillii resolves it in a clade with P. sherbrookei Nieto-Montes de Oca, Arenas-Moreno, Beltrán-Sánchez & Leaché, sister in position to Uma notata Baird. Mitochondrial marker analysis of P. blainvillii from Marina shows that it belongs to a coastal Santa Lucia Mountain Range haplogroup that is distinct from other populations of P. blainvillii in California.

The complete mitochondrial genome of Gymnogobius Petschiliensis (Gobiiformes; Gobiidae; Gobionellinae) and its phylogenetic implications

Of the goby fishes, many Gymnogobius species have been poor recognized mainly because of the absence of enough molecular information and clear phylogenetic framework. In this study, the complete mitochondrial genome of Gymnogobius petschiliensis was determined and described. The mitogenome is 16,422 bp in length and consists of 22 tRNAs, 13 protein-coding genes, two rRNAs, one control region and a light strand replication origin (OL). The arrangement of this mitogenome is identical to that of the typical teleost. The overall base composition is 27.5%, 29.5%, 26.1%, and 16.9%, for A, T, C, and G, respectively, with a slight bias on A + T content (57.0%). The 13 protein-coding genes use the initiation codon ATG except COI, which uses GTG. Most of them use TAA or TAG as the stop codon, while COII, COIII, and Cyt b use an incomplete T or TA and ND4 uses an unusual AGA. The maximum-likelihood phylogeny tree of 19 Gobionellinae species demonstrated that G. petschiliensis had a very closely relationship with the same genus G. urotaenia. This study is expected to contributing to the phylogenetic evolution of G. petschiliensis and further phylogenetic relationship of Gobionellinae and Gobiiformes.

Identification of the complete mitochondrial genome of Garra pingi pingi (Cypriniformes, Cyprinidae)

Garra pingi pingi, an endemic species to China, is mainly distributed in the upper Yangtze River and its tributaries. In present study, the complete mitochondrial genome of G. pingi pingi was first determined using the next-generation sequencing technology and annotated using bioinformatic tools. The circular mitochondrial genome was 16,599 bp long, contained 13 protein-coding genes, 2 ribosomal RNA genes (rRNA), 22 transfer RNA (tRNA) genes, an origin of light-strand replication (OL) and one displacement loop locus (D-loop). Most mitochondrial genes were encoded on the heavy strand, except for ND6 and eight tRNA genes. The total nucleotide composition was 31.48% A, 25.79% T, 26.66% C, 16.07% G, with 57.27% AT, respectively. Phylogenetic analysis based on the tandem 13 coding protein genes nucleotide sequences indicated that G. pingi pingi showed a close relationship with G. imberba. These data provide fundamental information not only for unravelling the population structure and differentiation, but also for further conservation genetics studies on Labeonini species.

Characterization and phylogenetic analysis of the complete mitochondrial genome of Bodianus oxycephalus (Perciformes, Labridae)

Bodianus oxycephalus is a fish species at a high risk of extinction and is included in the International Union for Conservation of Nature Red List of Threatened Species. This study determined for the first time the complete mitochondrial genome (mitogenome) of B. oxycephalus. The mitogenome is 16514 nucleotides long, consisting of 13 protein-coding genes, 2 ribosomal RNA genes, 22 tRNA genes, and 2 main non-coding regions. The overall base composition of B. oxycephalus mitogenome includes C (30.3%), A (26%), T (25.3%), and G (18.4%). Moreover, the gene arrangement, base composition, and tRNA structures of the mitogenome are similar to those of other teleosts. The conserved motif 5′-GCCGG-3′ was identified in the origin of light strand replication. In addition, terminal-associated sequences and conserved sequence blocks were detected in the control region. Phylogenetic analysis showed that B. oxycephalus and Choerodon schoenleinii clustered in a clade and formed a sister relationship.

Complete mitochondrial genome and the phylogenetic position of the Mugilogobius myxodermus: an endemic freshwater gobiid fish in China

The Mugilogobius myxodermus is an endemic freshwater fish in china. Herein, we sequenced and assembled the first complete mitogenome of M. myxodermus. The total length of the mitogenome is 16,495 bp, containing 13 protein-coding genes, two ribosomal RNAs (rRNA), two non-coding regions (control region and origin of light-strand replication), and 22 transfer RNAs (tRNA). The overall base composition of M. myxodermus is 26.76% T, 28.97% C, 27.81% A, and 16.45% G, respectively. A phylogenetic tree showed that M. myxodermus clustered closest to M. abei. The complete mitogenome of M. myxodermus provides a resource for studies on biogeography and evolution of this gobiid fish.

The complete mitochondrial genome of Pseudocrossocheilus bamaensis (Cypriniformes: Cyprinidae: Labeoninae)

Pseudocrossocheilus bamaensis is endemic to the upstream of Xijiang River, Guangxi, China and its natural population has been declining due to overfishing and habitat destruction. Here, we first report the complete mitogenome of this species, which is 16,594 bp in length, containing 13 protein-coding genes, 22 tRNA genes, two rRNA genes, as well as a putative light strand origin of replication (OL) and a putative control region (D-loop). The overall base composition is 31.8% of A, 15.7% of G, 26.8% of T and 25.7% of C, with a high A + T content (58.6%). Phylogenetic analysis suggests that P. bamaensis is closely related to Ptychidio jordani and Rectoris posehensis. These results will contribute to the molecular evolution and phylogenetic research of Labeoninae and further protection of its fish species.

Characterization of the complete mitochondrial genome of the hybrid Epinephelus moara♀ × Epinephelus lanceolatus♂, and phylogenetic analysis in subfamily epinephelinae

This study presents the complete mitochondrial genome of the hybrid Epinephelus moara♀× Epinephelus lanceolatus♂. The genome is 16886 bp in length, and contains 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes, a light-strand replication origin and a control region. Additionally, phylogenetic analysis based on the nucleotide sequences of 13 conserved protein-coding genes using the maximum likelihood method indicated that the mitochondrial genome is maternally inherited. This study presents genomic data for studying phylogenetic relationships and breeding of hybrid Epinephelinae.

Mitochondrial genome of the sand goby Acentrogobius caninus (Acentrogobius, Gobiidae)

In this study, we first determined and described the complete mitochondrial genome of Acentrogobius caninus, a member of the Family Gobiidae. The complete mitogenome sequence is 16,616 bp in length containing 13 protein-coding genes, two rRNA genes, 22 tRNA genes, a putative control region (CR), and a light-strand replication origin (OL). Phylogenetic analysis suggests that A. caninus boasts a close relationship with other two species of the genus Acentrogobius. Our results are expected to provide useful molecular information for species identification and further phylogenetic studies of the Gobiiformes family.

The complete mitochondrial genome of Xiphister atropurpureus (Perciformes: Stichaeidae)

Analysis of the marine black prickleback Xiphister atropurpureus Kittlitz using 76 bp paired-end Illumina sequences resulted in the assembly of its complete mitogenome. The mitogenome is 16,518 bp in length and contains an origin of light strand replication (OL), control region, 22 tRNA, 2 rRNA, and 13 protein-coding genes. Content and organization of the X. atropurpureus mitogenome is consistent with other teleost. Phylogenetic analysis of X. atropurpureus resolves it in a clade with another member of the Stichaeidae, Chirolophis japonicus Herzenstein.

The complete mitochondrial genome of the greater green snake Cyclophiops major (Reptilia, Serpentes, Colubridae)

The greater green snake Cyclophiops major is a protected and colubrid species. Here, we investigated the complete mitochondrial genome of C. major. The genome is 17,217bp in size, including 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes, 2 control regions, and an origin of light-strand replication. All genes are distributed on the heavy strand, except for ND6 gene and 8 tRNA genes. The AT content of the overall base composition of light strand is 59.83%, showing AT bias. Phylogenetic tree was built based on the genome of C. major and other related snakes to analyze their phylogenic relationship.

Characterization of the complete mitochondrial genome of Cynoglossus gracilis and a comparative analysis with other Cynoglossinae fishes

Mitochondrial genomes can provide basic information for phylogenetic analysis and evolutionary studies. We present here the mitochondrial genome of Cynoglossus gracilis, which is 16,565bp in length. Numerous distinct regions were identified, including 13 protein-coding genes (PCGs), 22 tRNA genes, two rRNA genes, a light-strand replication origin, and a control region. Interestingly, we detected rearrangement of genes in C. gracilis, including a control region translocation, tRNAGln gene inversion, and tRNAIle gene shuffling. Additionally, a phylogenetic analysis based on the nucleotide sequences of the 13 PCGs using maximum likelihood and Bayesian inference methods reveals that C. gracilis is closely related to Cynoglossus semilaevis. This study provides important mitogenomic data for analyzing phylogenetic relationships in the Cynoglossinae.

Complex mitochondrial DNA rearrangements in individual cells from patients with sporadic inclusion body myositis

Mitochondrial DNA (mtDNA) rearrangements are an important cause of mitochondrial disease and age related mitochondrial dysfunction in tissues including brain and skeletal muscle. It is known that different mtDNA deletions accumulate in single cells, but the detailed nature of these rearrangements is still unknown. To evaluate this we used a complementary set of sensitive assays to explore the mtDNA rearrangements in individual cells from patients with sporadic inclusion body myositis, a late-onset inflammatory myopathy with prominent mitochondrial changes. We identified large-scale mtDNA deletions in individual muscle fibres with 20% of cytochrome c oxidase-deficient myofibres accumulating two or more mtDNA deletions. The majority of deletions removed only the major arc but ∼10% of all deletions extended into the minor arc removing the origin of light strand replication (OL) and a variable number of genes. Some mtDNA molecules contained two deletion sites. Additionally, we found evidence of mitochondrial genome duplications allowing replication and clonal expansion of these complex rearranged molecules. The extended spectrum of mtDNA rearrangements in single cells provides insight into the process of clonal expansion which is fundamental to our understanding of the role of mtDNA mutations in ageing and disease.

Swinger RNA self-hybridization and mitochondrial non-canonical swinger transcription, transcription systematically exchanging nucleotides

Stem-loop hairpins punctuate mitochondrial post-transcriptional processing. Regulation of mitochondrial swinger transcription, transcription producing RNAs matching the mitogenome only assuming systematic exchanges between nucleotides (23 bijective transformations along 9 symmetric exchanges X<>Y, e.g. A<>G, and 14 asymmetric exchanges X>Y>Z>X, e.g. A>G>C>A) remains unknown. Does swinger RNA self-hybridization regulate swinger, as regular, transcription? Groups of 8 swinger transformations share canonical self-hybridization properties within each group, group 0 includes identity (regular) transcription. The human mitogenome has more stem-loop hairpins than randomized sequences for all groups. Group 2 transformations reveal complementarity of the light strand replication origin (OL) loop and a neighboring tRNA gene, detecting the longtime presumed OL/tRNA homology. Non-canonical G=U pairings in hairpins increases with swinger RNA detection. These results confirm biological relevancy of swinger-transformed DNA/RNA, independently of, and in combination with, previously detected swinger DNA/RNA and swinger peptides. Swinger-transformed mitogenomes include unsuspected multilayered information.

Complete mitochondrial genome of the nurse shark Ginglymostoma cirratum

We determined the complete mitochondrial genome sequence of nurse shark Ginglymostoma cirratum. The circular DNA of 16692 bp comprises 13 protein-coding genes, 22 transfer RNAs, 2 ribosomal RNAs, a non-coding control region and a non-coding origin of light strand replication with typical gene order of vertebrates. The nurse shark formed a well-supported clade that included whale shark Rhincodon typus and zebra shark Stegostoma fasciatum within the Orectolobiformes in a phylogenetic tree constructed with other published mitochondrial genomes of sharks.

The complete mitochondrial genome of Epomophorus gambianus (Chiroptera: Pteropodidae) and its phylogenetic analysis

The Gambian epauletted fruit bat, Epomophorus gambianus, is widely distributed across sub-Saharan Africa. Its assembled and annotated mitochondrial genome (GenBank accession no. KT963027) is 16,702 bases in length, containing 13 protein-coding genes, 22 transfer RNA genes, two ribosomal RNA genes and two non-coding regions: the control region (D-loop) and the origin of light-strand replication (OL). The average base composition is 32.2% A; 27.6% C; 14% G; and 26.1% T. The mitogenome presented a structural composition greatly conserved between members of the Pteropodidae family.