L-strand Replication Origin Research Articles

Complete mitochondrial genome of Qingyang donkey (Equus asinus)

The present study aimed to report the entire mitochondrial genome of Qingyang donkey (Equus asinus). Donkeys play an important role in the daily lives of human beings. The population of Chinese donkey breeds has undergone an enormous decline with the advance of agricultural mechanization, rapid development of transportation and introduction of new different breeds over the past few decades. As a result, a large number of donkey breeds are close to extinction, especially Qingyang donkey. Mitochondrial DNA is used as a molecular tool in research on biodiversity conservation and sustainable utilization of biological resources. The circular genome sequenced using the Illumina Hiseq 2500 platform was 16,568 base pairs (bp), containing 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes and a non-coding control region. The initiation site of the L-strand replication origin, 32 bp in length, was between tRNA-Asn and tRNA-Cys. The base composition of the genome was A (32.4%), C (28.7%), G (13.2%) and T (25.7%) with an A+T content of 58.1%. Molecular phylogeny demonstrated two separated clades in Equidae and the presence of a distant relationship between the domestic donkey breeds and Asian wild asses, indicating that domestic donkeys might not probably have originated from Asian wild asses. However, African wild asses were grouped as a sister to domestic donkeys. This study presented the complete mitochondrial genome of E. asinus, providing the important genetic background of protection and adequate utilization of domestic donkey breeds.

The complete mitochondrial genome of Protobothrops kaulbacki (Squamata: Viperidae)

Protobothrops kaulbacki is a new record in China, and in this study, the complete mitochondrial genome sequence of P. kaulbacki had been determined. The length of mitogenome is 17,237 bp, including 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes (12S and 16S rRNA), 1 origin of L-strand replication (OL), and 2 control regions (CRs). The maximum-likelihood (ML) tree based on the whole mitogenome shown that P. kaulbacki belongs to the genus Protobothrops.

Complete mitochondrial genome and phylogeny of Microhyla butleri (Amphibia: Anura: Microhylidae)

The whole mitochondrial genome of Microhyla butleri was determined by next-generation sequencing of mitochondrial DNA. It had a total length of 16,720 bp, consisting of 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes and 2 non-coding regions (L-strand replication origin and control region). The control region (1338 bp) was flanked by cob and trnL1 genes. The start codons included 11 ATG, 1 ATA and 1 GTG. Three PCGs had TAA, 3 had AGG, 1 had TAG and 6 had incomplete T stop codons. The cloverleaf structure for trnS1 lacked the DHU-stem, and that of trnC lacked the DHU-loop. Molecular phylogeny based on 12 protein-coding genes (without nad6 on L-strand) was congruent with 13 protein-coding genes. It was not concordant with 37 mitochondrial genes and rrnL and rrnS genes. In all mitochondrial markers, M. butleri was basal to its congeners. The genera Microhyla and Kaloula of Microhylidae were monophyletic. The whole mitogenome of M. butleri will serve as a useful dataset for studying the genetics, systematics and phylogenetic relationships of the Microhyla species in particular, and Microhylidae in general.

The complete mitochondrial genome of Pholis nebulosus (Perciformes: Pholidae)

In this study, the complete mitochondrial genome (mitogenome) sequence of Pholis nebulosus has been determined by long polymerase chain reaction and primer-walking methods. The mitogenome is a circular molecule of 16 524 bp in length, including the typical 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), the gene contents of which are identical to those observed in most bony fishes. Within the control region, we identified the termination-associated sequence domain (TAS), and the conserved sequence block domain (CSB-F, CSB-E, CSB-D, CSB-C, CSB-B, CSB-A, CSB-1, CSB-2, CSB-3).

Complete sequence and characterization of the paradise fish Macropodus erythropterus (Perciformes: Macropodusinae) mitochondrial genome

Macropodus erythropterus is a small well-known aquarium fish. In the present study, the complete mitochondrial DNA (mtDNA) sequences of M. erythropterus were first determined. The mtDNA of M. erythropterus (GenBank accession no. KU215670) was a circular molecule of 16 495 bp in length with two ribosome RNA (rRNA) genes, 13 protein-coding genes, 22 transfer RNA genes, an L-strand replication origin and a control region (CR). The entire mitogenome nucleotide acid was 15.71% for G, 29.66% for A, 28.37% for T and 26.26% for C with an A + T content of 58.03%. And the A + T contents of 12S rRNA, 16S rRNA and CR were 55.63%, 57.66% and 66.79%, respectively. This study provides basic molecular data for studying the conservation biology, phylogenetic and evolutionary analysis of Macropodusinae fishes.

The complete mitochondrial genome sequence of Ptyas mucosus

The complete mitochondrial genome sequence of the Ptyas mucosus was sequenced and reported for the first time using muscle tissue. The total length is 17 151 bp and sequence analysis showed its structure is in accordance with other snakes. The complete mitochondrial genome contains 2 rRNA genes, 21 tRNA genes, 13 protein-coding genes (PCGs), 2 control regions and 1 putative origin of L-strand replication. The gene order and nucleotide composition of P. mucosus are very similar with E. bimaculata, E. anomala and E. schrenckii. A phylogenetic tree of mitochondrial genomes indicated P. mucosus had the most closely relationship with E. bimaculata, and formed a monophyletic group with E. bimaculata, E. anomala and E. schrenckii.

Sequencing and analysis of mitochondrial genome of Elaphe carinata(Reptilia, Squamata, Colubridae)

The complete mitochondrial genome of Elaphe carinata was sequenced and analysed using muscle tissue for the first time. The genome is 17 154 bp in length. The complete mitochondrial genome contains 22 tRNA genes, 13 protein-coding genes (PCGs), two rRNA genes, two control regions (CRI and CRII) and one putative origin of L-strand replication. The gene order and nucleotide composition of E. carinata are very similar with E. davidi, E. schrenckii, E. anomala and E. bimaculata. A phylogenetic tree of mitochondrial genomes analyses of 16 species snakes of Colubridae was made based on the Neighbour-Joining (NJ) method, E. carinata has the most closely relationship with E. davidi, while E. poryphyracea and Euprepiophis perlacea are special species.

Mitochondrial genome and phylogenetic position of the tawny nurse shark (Nebrius ferrugineus)

The complete mitochondrial genome of the tawny nurse shark (Nebrius ferrugineus) was first presented in this study. It was 16 693 bp in length with the typical gene order in vertebrates. The overall base composition was 33.6% A, 25.6% C, 12.7% G and 28.1% T. Two start (ATG and GTG) and two stop (TAG and TAA/T––) codons were found in the protein-coding genes. The size of 22 tRNA genes ranged from 67 to 75 bp. The origin of L-strand replication could form a hairpin structure. All nodes strongly supported that N. ferrugineus was placed as sister to Rhincodon typus in the Bayesian tree.

Complete mitochondrial genome of the Yellow-spotted skate Okamejei hollandi (Rajiformes: Rajidae)

The complete mitochondrial genome of the Yellow-spotted skate Okamejei hollandi was determined in this study. It is 16,974 bp in length and contains 13 protein-coding genes, two rRNA genes, 22 tRNA genes, and one putative control region. The overall base composition is 30.5% A, 27.8% C, 14.0% G, and 27.8% T. There are 28 bp short intergenic spaces located in 12 gene junctions and 31 bp overlaps located in nine gene junctions in the whole mitogenome. Two start codons (ATG and GTG) and two stop codons (TAG and TAA/T) were used in the protein-coding genes. The lengths of 22 tRNA genes range from 68 (tRNA-Ser2) to 75 (tRNA-Leu1) bp. The origin of L-strand replication (OL) sequence (37 bp) was identified between the tRNA-Asn and tRNA-Cys genes. The control region is 1311 bp in length with high A + T and poor G content.

The complete mitochondrial genome of Pseudorhombus dupliocellatus (Pleuronectiformes: Paralichthyidae)

The Pseudorhombus dupliocellatus belongs to family Paralichthyidae of Pleuronectiformes. In this study, the complete mitochondrial genome of P. dupliocellatus is determined and described. The mitogenome is 16 621 bp in length and consists of 13 protein-coding genes, 22 tRNAs, 2 rRNAs, a control region, and a L-strand replication origin. The arrangement of the mitogenome is identical to that of the typical teleost. The overall base composition is 26.9%, 25.3%, 31.0%, and 16.8% for A, T, C, and G, respectively, with a slight bias on A+T content (52.2%). The phylogenetic tree of 13 species all in Pleuronectiformes demonstrated that P. dupliocellatus, as well as the other Paralichthyidae fishes containing Paralichthys olivaceus and Pseudorhombus cinnamoneus, clustered in a clade and had a closer relationship with Pleuronectidae species than Bothidae ones. This study is expected to contributing to the systematic evolution of Paralichthyidae and further Pleuronectiformes.

The complete sequence of mitochondrial genome of Sinibotia pulchra (Cypriniformes: Cobitidae)

Sinibotia pulchra (Cypriniformes: Cobitidae) is a small cyprinid fish. In this study, the complete mitochondrial genome sequence of S. pulchra is sequenced. The S. pulchra complete mitochondrial genome (GenBank accession no. KT362179) was a circular molecule of 16 568 bp in length, with 13 protein-coding genes (PCGs), 2 ribosome RNA (rRNA) genes, 22 transfer RNA (tRNA) genes, an L-strand replication origin (OL) and a control region (D-loop). The nucleotide acid composition of the entire mitogenome was 31.69% for A, 25.63% for T, 26.94% for C and 15.74% for G, with an AT content of 57.32%. The AT content of 12S rRNA, 16S rRNA and D-loop was 50.21%, 56.86% and 66.74%, respectively.

The complete mitochondrial genome of Sinibotia robusta (Cypriniformes: Cobitidae)

The Sinibotia robusta mitochondrial genome (GenBank accession no. KP979711) was a circular molecule of 16 575 bp in length, with two rRNA genes, 13 protein-coding genes, 22 tRNA genes, an l-strand replication origin (OL), and a control region (D-loop). The nucleotide acid composition of the entire mitogenome was 31.91% for A, 26.90% for C, 15.56% for G, and 25.63% for T, with an A + T content of 57.54%. And the A + T content of 12S rRNA, 16S rRNA, and D-loop was 51.26%, 56.17%, and 67.73%, respectively.

The complete mitochondrial genome sequence of Tylototriton taliangensis (Amphibia: Caudata)

Tylototriton taliangensis was listed as a Near Threatened amphibian in IUCN red list. In this study, we sequenced the complete mitochondrial (mt) genome of this species (GenBank: KP979646) and found it contains 16,265 base pairs, which encode 13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNA), 2 ribosomal RNA genes (rRNA) and 1 control region (CR). We also found that almost all PCGs and tRNA genes are located on the H-strand, except for ND6 subunit gene and eight tRNA genes, which were distributed on the L-strand. The PCGs used “ATG” and “GTG” as the start codon, while used four types of stop codons. Almost all tRNA genes were folded into typical cloverleaf secondary structures. The L-strand replication origin (OL) and a non-coding region were also found. The new mitogenomic phylogenetic tree confirms the reciprocally monophyly of the genus Tylototriton, Echinotriton and Pleurodeles with high bootstrap value. The present study will provide information for future studies on the conservation genetics and phylogeny of this species and its relatives.

The complete mitochondrial genome of Botia lohachata (Cypriniformes: Cobitidae)

In this study, the complete mitochondrial genome of Botia lohachata was determined (GenBank accession number KP729183). The mitochondrial genome sequence of B. lohachata was a circular molecule with 16,594 bp in length, and it contained 37 typical animal mitochondrial genes: 2 ribosomal RNA genes, 13 protein-coding genes, 22 transfer RNA genes, an L-strand replication origin (OL) and a control region (D-loop). The nucleotide acid composition of the entire mitogenome was 26.53% C, 15.63% G, 31.98% A and 25.86% T, with an AT content of 57.83%.

The complete mitochondrial genome of Ambastaia sidthimunki (Cypriniformes: Cobitidae)

Ambastaia sidthimunki is a beautiful small-sized fish and it was categorized as Endangered B2ab (iii,v) in the IUCN Red List. In this study, we reported the complete mitochondrial genome of the A. sidthimunki. The mitochondrial genome sequence was a circular molecule with 16,574 bp in length, and it contained 2 ribosomal RNA genes, 22 transfer RNA genes, 13 protein-coding genes, an L-strand replication origin (OL) and a control region (D-loop). The nucleotide acid composition of the entire mitogenome was 26.94% for C, 15.55% for G, 31.84% for A and 25.67% for T, with an AT content of 57.51%. This research contributes new molecular data for the conservation of this Endangered species.

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.

The complete mitochondrial genome of leopard cat, Prionailurus bengalensis chinensis (Carnivora:Felidae)

The full-length of the mitochondrial (mt) genome of Prionailurus bengalensis chinensis was first determined in this study and consisted of a 16,990 bp fragment, including 13 protein-coding genes, two rRNA genes, 22 tRNA genes, a control region (CR), and an origin of L-strand replication (OLR). The total base composition of the heavy strand was A, 33.0%; G, 13.6%; C, 26.0%; and T, 27.4%, with a slight AT bias of 60.4%. The complete mitogenomic data of P. b. chinensis may provide an important data set for further phylogenetic and taxonomic analyses of Genus Prionailurus species.

Complete mitochondrial genome of the Endangered Narrow Sawfish Anoxypristis cuspidata (Rajiformes: Pristidae)

In this study, we describe the first complete mitochondrial sequence for the Endangered Narrow Sawfish Anoxypristis cuspidata. It is 17,243 bp in length and contains 13 protein-coding genes, two rRNA genes, 22 tRNA genes, and a control region with the common vertebrate mitogenomic organization. A total of 30 bp overlaps and 28 bp short intergenic spaces are located between all genes. The overall base composition is 32.7% A, 25.7% C, 12.9% G, and 28.6% T. Two start codons (ATG and GTG) and two stop codons (TAG and TAA/T) were used in all protein-coding genes. The origin of L-strand replication (OL) sequence (38 bp) formed a hairpin structure (13 bp stem and 12 bp loop) to initiate the replication of L-strand.

The complete mitochondrial genome of the black-tailed brush lizard Urosaurus nigricaudus (Reptilia, Squamata, Phrynosomatidae)

Previous studies using mitochondrial DNA (mtDNA) genes suggest the black-tailed brush lizard, Urosaurus nigricaudus, which is a small-sized lizard from the peninsula of Baja California, Mexico, has 4 deeply isolated mtDNA lineages with sequence divergence ranging from 4% to 11.2%. We present its complete mitochondrial genome. This genome is 17,298 bp long and comprises 2 rRNAs, 22 tRNAs, 13 protein-coding genes, 1 L-strand origin of replication and 1 control region. The overall nucleotide content is A = 34.2%; C = 26.8%; G = 13.5%; T = 25.5%. The gene organization and features agree with the general vertebrate organization and that found in other lizards. The control region is 1909 bp long and is located between tRNAPro and tRNAPhe.

Полный митохондриальный геном павлиньего морского языкаPardachirus pavoninus(Pleuronectiformes: Soleidae) и сравнительный анализ контрольной области у 13 видов морских языков

The complete mitogenome of the peacock sole Pardachirus pavoninus (Lacepède, 1802) was determined. The total length is 16 536 bp, containing 13 protein-coding genes, 22 tRNA genes and two rRNA genes, as well as one control region (CR). The L-strand replication origin (OL), which is typically located in the WANCY cluster, is lost in P. pavoninus. The gene arrangement is identical to that in most teleosts. Comparison of the CR sequences among 13 soles reveals that a 211-bp fragment at the 5'-end of the CR is lost in the P. pavoninus mitogenome, responsible for its short sequence with a length of 872 bp. All typical conservative blocks (TAS, CSB-F, E, D, C, B, A, CSB-1, 2, 3) are identified. Seven out of 13 soles contain tandem repeats in the CR and the possible mechanisms of their formation are discussed. These results may provide the consensus sequences of the conserved units in the sole CR as well as molecular data for phylogenetic studies on Soleidae and Pleuronectiformes.