atp8 - ATP synthase F0 subunit 8
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Pubmed
Journal: Mitochondrial DNA
February/2/2014
Abstract
Liobagrus nigricauda is endemic to the Yangtze River system (Ding 1994, The fishes of Sichuan province. pp. 470-78) and listed as an endangered species (IUCN 2012, Red list of threatened species. http://www.iucnredlist.org ). In this study, the complete mitochondrial genome sequence of L. nigricauda has been obtained with polymerase chain reaction (PCR), which contains 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes, and a noncoding control region with the total length of 16,512 bp. The gene arrangement and composition are similar to that of other vertebrates. Most of the genes are encoded on heavy strand, except for eight tRNA and ND6 genes. Just like most other vertebrates, the bias against G has a universality in different statistics results. The mitogenome sequence of L. nigricauda would contribute to better understand population genetics and to protect its genetic diversity.
Pubmed
Journal: Mitochondrial DNA
March/28/2016
Abstract
Liachirus melanospilos (Pleuronectiformes: Soleidae) is characterized by both eyes on the right side of the body and pale brown color with black dots, small irregular, brown spots and large vague ocelli. In this study, the complete mitogenome sequence of this carpet sole has been determined. The total length is 17,001 bp, including 13 protein-coding genes, 22 tRNA genes and 2 rRNA genes (12S and 16S), as well as one control region and one L-strand replication origin (OL). Gene contents, locations and arrangements are identical to those of typical bony fishes. The nucleotide composition of the genome is 30.9%, 27.8%, 15.9% and 25.5% for A, C, G and T, respectively, with a slight bias of A + T content (56.4%). The determination of L. melanospilos complete mitogenome sequence could contribute to a better understanding of the systematic evolution of Soleidae and Pleuronectiformes.
Pubmed
Journal: Acta biochimica et biophysica Sinica
September/29/2008
Abstract
We determined the complete nucleotide sequence of the mitogenome from Chinese oak silkmoth, Antheraea pernyi (Lepidoptera: Saturniidae). The 15,566 bp circular genome contains a typical gene organization and order for lepidopteran mitogenomes. The mitogenome contains the lowest A+T content (80.16%) among the known lepidopteran mitogenome sequences. An unusual feature is the occurrence of more Ts than As, with a slightly negative AT skewness (-0.021), in the composition of the major genome strand. All protein-coding genes are initiated by ATN codons, except for cytochrome oxidase subunit I, which is proposed by the TTAG sequence as observed in other lepidopterans. All transfer RNAs (tRNAs) have a typical clover-leaf structure of mitochondrial tRNA, except for tRNASer(AGN), the DHU arm of which could not form a stable stem-loop structure. Two aligned sequence blocks with a length of more than 50 bp and 90% of the sequence identity were identified in the A+T-rich region of the Saturniidae and Bombycoidae species.
Pubmed
Journal: Mitochondrial DNA
April/10/2016
Abstract
The complete mitochondrial genome of S. caldwelli was determined in this study. The gene composition, arrangement and transcriptional orientation in S. caldwelli mitogenome were identical to most vertebrates. Two start codon patterns (ATG and GTG) and three stop codon patterns (TAG, TAA and T) were found in protein-coding genes. Only the tRNA-Ser2 could not fold into a typical clover-leaf secondary structure for lacking the dihydrouridine arm. Sequences alignment results suggest that the complete mitogenome of S. caldwelli is an efficient tool to check species identification by comparing different gene sequences.
Pubmed
Journal: Gene
January/25/2017
Abstract
Complete mitochondrial genomes of five syllids (Streptosyllis sp., Eusyllis blomstrandi, Myrianida brachycephala, Typosyllis antoni and Typosyllis sp.) have been obtained using Illumina sequencing. Together with two previous studied taxa (Ramisyllis multicaudata and Trypanobia cryptica), the analysed sequences represent most of the main lineages within the family Syllidae (Anoplosyllinae, Eusyllinae, Autolytinae and Syllinae). The genomic features, gene order and phylogenetic relationships are examined. Unusual for annelids, syllid mitochondrial genomes are highly variable in their gene order. Considering genomic features, such as length, skewness, gene content, and codon bias, most similar to the rest of annelids are the genomes of E. blomstrandi and M. brachycephala, while Streptosyllis sp. and the analysed sylline taxa (R. multicaudata, T. cryptica, T. antoni and Typosyllis sp.) are the most dissimilar. Two methionine tRNA's (trnM) have been found in T. antoni and Typosyllis sp. The mt genomes of these latter taxa are the longest with numerous non-coding regions. The 13 protein coding genes, as well as the rRNA's are used to perform phylogenetic analyses that recovered the relationships within the family explored before by previous authors. The gene order in Syllidae shows very different patterns. E. blomstrandi and M. prolifera show a similar pattern to the one found in Pleistoannelida; however this might have changed at least twice within Syllidae: in Streptosyllis sp. and within Syllinae. All analysed Syllinae show different gene orders, thereby illustrating more variability as all other pleistoannelids analysed so far. The information provided herein allows a more accurate reconstruction of the possible evolutionary scenarios in Syllidae.
Pubmed
Journal: Genetics
February/7/1996
Abstract
We have determined the complete nucleotide (nt) sequence of the mitochondrial genome of an oligochaete annelid, the earthworm Lumbricus terrestris. This genome contains the 37 genes typical of metazoan mitochondrial DNA (mtDNA), including ATPase8, which is missing from some invertebrate mtDNAs. ATPase8 is not immediately upstream of ATPase6, a condition found previously only in the mtDNA of snails. All genes are transcribed from the same DNA strand. The largest noncoding region is 384 nt and is characterized by several homopolymer runs, a tract of alternating TA pairs, and potential secondary structures. All protein-encoding genes either overlap the adjacent downstream gene or end at an abbreviated stop codon. In Lumbricus mitochondria, the variation of the genetic code that is typical of most invertebrate mitochondrial genomes is used. Only the codon ATG is used for translation initiation. Lumbricus mtDNA is A + T rich, which appears to affect the codon usage pattern. The DHU arm appears to be unpaired not only in tRNAser(AGN), as is typical for metazoans, but perhaps also in tRNAser(UCN), a condition found previously only in a chiton and among nematodes. Relating the Lumbricus gene organization to those of other major protostome groups requires numerous rearrangements.
Pubmed
Journal: Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis
October/15/2017
Abstract
In this study, the first complete mitochondrial genome (mitogenome) sequence of Cacopsylla coccinae was determined by long PCR and primer walking methods. The complete mitochondrial genome is 14,832 bp in length and contains 13 protein-coding genes, 2 ribosomal RNA genes, 22 transfer RNA genes as well as a control region. The overall base composition of the genome is A (38.16%), T (33.88%), C (17.95%) and G (10.01%). Stop codon was incomplete for coxII gene and ND1 gene. The gene overlaps were suggested between 13 pairs of the contiguous genes in C. coccinae. The mitogenome would contribute to resolving phylogenetic position and interrelationships of Cacopsylla.
Pubmed
Journal: Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis
October/15/2017
Abstract
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.
Pubmed
Journal: Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis
October/15/2017
Abstract
In this study, the complete mitochondrial DNA (mtDNA) sequence of Polytremis nascens (Lepidoptera: Hesperiidae) was determined. The 15,392 bp mitogenome with GenBank accession number KM981865 contained 13 protein genes, 22 tRNAs, 2 rRNAs, and a non-coding control region (D-loop). All the 37 typical animal mitochondrial genes were found. The overall base composition was 39.7% A, 40.7% T, 7.7% G and 11.9% C, with a high A + T content (80.4%). This complete mitogenome of P. nascens provides a basic data for studies on species identification, molecular systematics and conservation genetics.
Pubmed
Journal: Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis
October/15/2017
Abstract
The complete sequence of the mitochondrial genome was determined for Asio flammeus, which is distributed widely in geography. The length of the complete mitochondrial genome was 18,966 bp, containing 2 rRNA genes, 22 tRNA genes, 13 protein-coding genes (PCGs), and 1 non-coding region (D-loop). All the genes were distributed on the H-strand, except for the ND6 subunit gene and eight tRNA genes which were encoded on the L-strand. The D-loop of A. flammeus contained many tandem repeats of varying lengths and repeat numbers. The molecular-based phylogeny showed that our species acted as the sister group to A. capensis and the supported Asio was the monophyletic group.
Pubmed
Journal: Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis
October/15/2017
Abstract
The complete mitochondrial genome of the wolf spider Wadicosa fidelis was determined. It is a circular molecule of 14,741 bp in length and contains a standard set of 13 protein-coding genes, 2 ribosomal RNAs, 22 transfer RNAs and a control region. The A + T content of the overall base composition of majority strand (J-strand) is 76.1% (T: 43.0%; C: 8.2%; A:33.1%; G: 15.7%). Start codons in all 13 protein-coding genes (PCGs) follow the ATN rule, except of four genes (COII, COII, ND4 and ND6), which have TTG start codon. The usual termination codons (TAA and TAG) are found from nine PCGs. However, COI, ND1, ND4L, ND5 had an incomplete termination codon (T). The control region (D-loop) is 1071 bp long with 67.9% A + T content, and contains a long tandem repeat region, which is comprising three full 215 bp copies and a partial fourth (87 bp) copy.
Pubmed
Journal: Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis
October/15/2017
Abstract
In this work, we reported the complete mitochondrial genome sequence of the Schizothorax nukiangensis Tsao for the first time. The complete mtDNA genome sequence of S. nukiangensis Tsao was 16 585 bp in length, which contains 22 transfer RNA genes, 2 rRNA genes, 13 protein-coding genes, an origin of light-strand replication (OL) and a control region (D-Loop). The overall base composition of the mitogenome was calculated to be 29.6% for A, 27.0% for C, 17.9% for G and 25.5% for T. The complete mitogenome of the S. nukiangensis Tsao can provide an important data set for further studies on population history, molecular systematics, phylogeography and stock assessment.
Pubmed
Journal: Mitochondrial DNA
October/20/2015
Abstract
In the present study, the complete mitochondrial genome of the bluefin driftfish Psenes pellucidus was determined first. The genome was 16,572 bp in length and consisted of 13 protein-coding genes, 22 tRNA genes, 2 ribosomal RNA genes and 2 main non-coding regions. The mitochondrial genome of bluefin driftfish had common features about gene arrangement, base composition and tRNA structures compared with those of most of the bony fishes. In the control region, a termination-associated sequence, the central conserved block (CSB-F, CSB-E and CSB-D) and the conserved sequence blocks (CSB-1, CSB-2 and CSB-3) were determined. Meanwhile, the conserved motif 5'-GCCGG-3' was identified in the origin of light strand replication of bluefin driftfish. This mitogenome sequence data would play key role in phylogenetic analysis of Stromateoidei.
Pubmed
Journal: Mitochondrial DNA
October/20/2015
Abstract
Abstract The complete mitochondrial genome of Filchnerella beicki Ramme, 1931, which was collected from the Ningxia Hui Autonomous Region of China, is reported here. It is 15,658 bp in length and contains 72.3% AT. All Filchnerella beicki protein-coding sequences start with a typical ATN codon, excluding cox1. The usual termination codon (TAN) and incomplete stop codons (T) were found from 13 protein-coding genes. All tRNA genes could be folded into the typical cloverleaf secondary structure, excluding trnS(AGN) which forms another structure. The sizes of the large and small ribosomal RNA genes are 1315 and 853 bp, respectively. The AT content of the A+T-rich region is 83.1%.
Pubmed
Journal: Mitochondrial DNA
December/16/2015
Abstract
The freshwater mussel Solenaia oleivora is considered threatened due to anthropogenic habitat modification and pollution. The complete F-type mitochondrial genome (mitogenome) of S. oleivora was first determined (GenBank accession no. KF296320). The length of this mitogenome is 16,392 bp with an AT content of 59.9%. There are 37 typical animal mitochondrial genes and a putative control region. Within the control region, 5 tandem repeats of a 106 bp element were identified. The gene order rearrangement of cox2-rrnS in F-type mitogenome compared to that of other freshwater mussels, is not unique for S. oleivora, but is shared with all other available freshwater mussels in the subfamily Gonideinae. The complete mitogenome can provide a basic data for the further studies on molecular taxonomy, phylogenetic analyses and conservation genetics.
Pubmed
Journal: Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis
September/13/2016
Abstract
The taxonomy of genus Anodonta is rather ambiguous, as it has great variation on the shell shape. Anodonta lucida is an endemic species of freshwater mussel in China, characterized by shining epidermis. The complete maternal mitochondrial genome of freshwater mussel A. lucida was first determined (GenBank accession no. KF667529). The genome is 16,285 bp long with an AT content of 64.02%. All the 37 typical animal mitochondrial genes are found, including 13 protein-coding genes, 22 tRNA genes, and 2 rRNA genes. The genome also contains 24 unassigned regions, ranking from 1 to 830 bp in length, the largest of which is the putative control region (CR). The base composition of the genome is A (36.32%), G (13.01%), T (27.70%) and C (22.98%). Gene order is identical to other species of Unionidae except Gonideinae.
Pubmed
Journal: Mitochondrial DNA
August/13/2013
Abstract
The complete mitochondrial genome of Dichocrocis punctiferalis (Lepidoptera: Pyralidae) was determined (GenBank accession number JX448619). The genome is 15,355 bp long with 37 typical animal mitochondrial genes and an A+T-rich region. As in other sequenced mitochondrial genomes of Lepidoptera, trnM was rearranged to the upstream of trnI-trnQ-trnM cluster compared with the pupative ancestral arrangement of insects. All protein-coding genes start with ATN start codon except for the gene cox1, which uses CGA as in other lepidopteran species. Seven protein-coding genes stop with termination codon TAA. Four protein-coding genes use incomplete stop codons TA and two use T. The A+T-region is located between rrnS and trnM with a length of 338 bp. This is the first completely sequenced mitochondrial genome from the family Pyralidae.
Pubmed
Journal: Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis
October/15/2017
Abstract
Dixidae, meniscus midges, belong to the suborder Nematocera of the order Diptera. The family includes 197 known species classified in nine genera. The complete mitochondrial genome of the Dixella aestivalis (Meigen) from the United Kingdom is reported here, along with its annotation and comparison with the genome of an unidentified species of Dixella from China. The circular genome consists of 16 465 bp and has a gene content consisting of 13 protein-coding genes, 22 transfer RNA genes, two ribosomal RNA genes and a non-coding, A + T-rich, control region. The mitochondrial genome of D. aestivalis can be used to identify genetic markers for species identification, and will be valuable for resolving phylogenetic relationships within the genus, family Dixidae and suborder Nematocera.
Pubmed
Journal: Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis
October/15/2017
Abstract
The complete mitochondrial genome of the Wanieso lizardfish (Saurida wanieso) was determined by using a PCR-based method. The total length of mitochondrial DNA is 16,552 base pairs including 13 protein-coding genes, 2 ribosomal RNA, 22 transfer RNA genes, 1 replication origin region and 1 control region as other Saurida spp. and bony fish. Base composition of the genome is A (25.7%), T (25.2%), C (31.5%), and G (17.6%) with an A + T-rich hallmark as that of other vertebrate mitochondrial genomes.
Pubmed
Journal: Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis
October/15/2017
Abstract
In this study, the complete mitochondrial (mt) genome of the copperband butterflyfish Chelmon rostratus from Beibu Bay, China, was determined. It is one of the most common coral reef fish in South China Sea. The total length of C. rostratus mitogenome is 16,538 bp, which consists of 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes and a control region, with the genome organization and gene order being identical to other typical vertebrate mitogenomes. The overall nucleotide composition of the H-strand is 28.05% A, 28.94% T, 16.22% G and 26.79% C, with an A + T bias. This study will provide the first complete mitochondrial genome of Chelmon rostratus as useful information for the application of fish phylogenetic relationship analysis within the butterflyfish species.
Pubmed
Journal: Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis
October/15/2017
Abstract
The Wied's black-tufted-ear marmoset, Callithrix kuhlii, is a New World monkey that lives in tropical and subtropical forests of eastern Brazil. In this study, the mitochondrial genome sequence of this species is determined, which is found to be 16 500 bp in length and consists of 22 transfer RNA genes, 13 protein-coding genes, 2 ribosomal RNA genes and one D-loop control region. The overall nucleotide composition is 32.73% of A, 26.80% of T, 27.04% of C and 13.43% of G, with an AT content of 59.53%. The genome structure about gene order and composition of C. kuhlii mitochondrial genome is similar to those of most other vertebrates. With the exception of the NADH dehydrogenase subunit 6 (ND6) and eight tRNA genes, all the other genes are encoded on the heavy strand. Phylogenetic analysis shows that C. kuhlii and C. jacchus are more closely related to each other than to other marmosets of the genus Callithrix that have its mitochondrial genome published.
Pubmed
Journal: Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis
October/15/2017
Abstract
The complete mitochondrial genome sequence of Hepialus gonggaensis was sequenced for the first time. The complete mtDNA sequence was 15,940 bp in length and contained 13 protein-coding genes, two rRNA genes, 22 tRNA genes, and an AT-rich region, the gene composition and the arrangement of which were identical to other insects of Hepialidae. The overall base composition of the heavy strand was 41.14% A, 40.24% T, 11.17% C, and 7.45% G, with an AT content of 81.37%. The necleotide sequence data of 13 protein-coding genes of H. gonggaensis and other 10 Lepidoptera species were used for constructing the phylogenetic tree. It revealed that H. gonggaensis and other four Hepialidae species were clustered to a clade with high bootstraps values.
Pubmed
Journal: Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis
October/15/2017
Abstract
The complete mitochondrial genome sequence of Carangoides equula (Perciformes: Carangidae) was determined. The size of the genome was 16,588 bp and overall base compositions of the sequence were 26.3% of A, 30.3% of C, 25.3% of T and 18.1% of G, showing an obvious anti G bias commonly observed in teleosts. The genome contained 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes, and 2 non-coding regions (the control region and the light strand replication origin). Gene organization and gene order was similar to that observed in most other vertebrates. The initiation codon GTG was detected in the open reading frames of ATPase subunit 6, which was novel for ATP6 gene in Carangidae species. The mitogenome of C. equula shared 84.1% and 84.0% sequence similarity with two other Carangoides species Carangoides malabaricus and Carangoides armatus, respectively. The complete mitogenome sequence data of C. equula could provide useful information for taxonomic and phylogenetics studies.
Pubmed
Journal: Molecular biology and evolution
June/17/2016
Abstract
The frequency of horizontal gene transfer (HGT) in mitochondrial DNA varies substantially. In plants, HGT is relatively common, whereas in animals it appears to be quite rare. It is of considerable importance to understand mitochondrial HGT across the major groups of eukaryotes at a genome-wide level, but so far this has been well studied only in plants. In this study, we generated ten new mitochondrial genome sequences and analyzed 40 mitochondrial genomes from the Saccharomycetaceae to assess the magnitude and nature of mitochondrial HGT in yeasts. We provide evidence for extensive, homologous-recombination-mediated, mitochondrial-to-mitochondrial HGT occurring throughout yeast mitochondrial genomes, leading to genomes that are highly chimeric evolutionarily. This HGT has led to substantial intraspecific polymorphism in both sequence content and sequence divergence, which to our knowledge has not been previously documented in any mitochondrial genome. The unexpectedly high frequency of mitochondrial HGT in yeast may be driven by frequent mitochondrial fusion, relatively low mitochondrial substitution rates and pseudohyphal fusion to produce heterokaryons. These findings suggest that mitochondrial HGT may play an important role in genome evolution of a much broader spectrum of eukaryotes than previously appreciated and that there is a critical need to systematically study the frequency, extent, and importance of mitochondrial HGT across eukaryotes.
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