cox3 - cytochrome c oxidase subunit 3
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Publication
Journal: Malaria journal
August/20/2019
Abstract
Parasites from the genus Plasmodium, the aetiological agent of malaria in humans, can also infect non-human primates (NHP), increasing the potential risk of zoonotic transmission with its associated global public health concerns. In Colombia, there are no recent studies on Plasmodium spp. infecting free-ranging NHP. Thus, this study aimed to determine the diversity of Plasmodium species circulating in fragmented forests in central Colombia, both in Anopheles mosquitoes and in the four sympatric NHP in the region (Ateles hybridus, Cebus versicolor, Alouatta seniculus and Aotus griseimembra), in order to evaluate the risk of infection to humans associated with the presence of sylvatic hosts and vectors infected with Plasmodium spp.Overall, there were collected 166 fecal samples and 25 blood samples from NHP, and 442 individuals of Anopheles spp. DNA extraction, nested PCR using mitochondrial (cox3 gene) and ribosomal (18S rDNA) primers, electrophoresis and sequencing were conducted in order to identify Plasmodium spp. from the samples.Plasmodium falciparum was detected in two fecal samples of Alouatta seniculus, while Plasmodium vivax/simium infected Ateles hybridus, Cebus versicolor and Alouatta seniculus. Co-infections with P. vivax/simium and Plasmodium malariae/brasilianum were found in three individuals. The highest prevalence from blood samples was found for Plasmodium malariae/brasilianum in two Alouatta seniculus while Plasmodium vivax/simium was most prevalent in fecal samples, infecting four individuals of Alouatta seniculus. Seven Anopheles species were identified in the study site: Anopheles (Anopheles) punctimacula, Anopheles (An.) malefactor, Anopheles (Nyssorhynchus) oswaldoi, Anopheles (Nys.) triannulatus, Anopheles (An.) neomaculipalpus, Anopheles (Nys.) braziliensis and Anopheles (Nys.) nuneztovari. Infection with P. vivax/simium was found in An. nuneztovari, An. neomaculipalpus, and An. triannulatus. Furthermore, An. oswaldoi and An. triannulatus were found infected with P. malariae/brasilianum. The effect of fragmentation and distance to the nearest town measured in five forests with different degrees of fragmentation was not statistically significant on the prevalence of Plasmodium in NHP, but forest fragmentation did have an effect on the Minimum Infection Rate (MIR) in Anopheles mosquitoes.The presence of Plasmodium spp. in NHP and Anopheles spp. in fragmented forests in Colombia has important epidemiological implications in the human-NHP interface and the associated risk of malaria transmission.
Publication
Journal: Animal biotechnology
July/30/2018
Abstract
The Indian wild pig is a sub-species (Sus scrofa cristatus) which is different from the other pig breeds and is protected under Schedule-III of the Indian Wildlife (Protection) Act, 1972. In this study, complete mitogenome of two Indian wild pigs was sequenced and characterized by shotgun sequencing and de novo assembly, which revealed sequence size of 16,738 and 16,251 bp, respectively, (Accession no. MG725630 and MG725631). The mitogenome sequence in this study displayed 98% homology with previously reported mitogenome of pigs from different parts of the world. Mitogenome analysis by MITOS Web server revealed similarity of gene organization with the other vertebrates (13 protein-coding, 22 tRNAs, 2 rRNAs genes, and a control region). The mitogenomic sequences of Indian wild pig maintained a separate clade in the phylogenetic tree constructed by using 62 whole mitogenome sequences across the world. The phylogeny derived from mitogenomic sequences revealed distinct separate European-American and Asiatic pig clades. It was concluded that whole mitogenome sequencing using NGS without designing mitogenome-specific primer for amplification, is possible thereby reducing the cost and labor. This study is the first report of complete sequence of mitogenome of Indian wild pig.
Publication
Journal: Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis
October/31/2017
Abstract
The genus Conus sensu lato consists of 500-700 species. However, the mitochondrial genomes of only few species have been fully sequenced and reported so far. In this study, the complete mitochondrial genome of Conus tribblei, a member of the poorly known subgenus Splinoconus is sequenced with the mean coverage of 604×. The mitochondrial genome is 15 570 bp long and consists of genes encoding for 13 respiratory chain proteins, 22 tRNA and 2 rRNA. The gene organization is highly conserved among the Conus species. The longest intergenic region between tRNA-Phe and cytochrome c oxidase subunit III (cox3), which in C. tribblei is 169 bp long and contains a 112 bp long segment of inverted repeat, represents the putative control region. The control regions of Conus species exhibited variability in the length and position of the inverted repeats. Therefore, this region may have the potential to be used as a genetic marker for species discrimination.
Publication
Journal: Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis
October/15/2017
Abstract
Here is a first record for a mitochondrial genome of marine fungus Acremonium fuci and closely related species Emericellopsis sp. One strain for each species, differentiated by morphological features was studied. Complete mitochondrial sequences are 24 565 and 24 951 bp in length. The circular molecule encodes all genes typical for fungal mitochondrial genomes: 15 protein-coding genes, 28 tRNAs, and large and small subunits of RNA. All structural genes are located on one strand and transcribed in one direction. Mitogenomes of species have 99% identity in protein-coding genes, but differ in some structural features: one of them has additional ORF with a similarity to cox1 gene, and another one has an intron in nad5 gene.
Publication
Journal: Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis
October/15/2017
Abstract
Blackfin tuna, Thunnus atlanticus is a widespread epipelagic oceanic species in the western Atlantic. So far the mitochondrial genome of this species remained unknown, although the mitogenomes of all congeners are known. The mitochondrial genome encodes for 13 proteins, 21 tRNAs, 2 ribosomal RNAs and the gene synteny is conserved with other previously reported mitogenomes of tunas.
Publication
Journal: Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis
October/15/2017
Abstract
In this study, the complete mitogenome sequence of the Blue-face angelfish, Pomacanthus xanthometapon (Perciformes: Pomacanthidae) has been sequenced by the next-generation sequencing method. The assembled mitogenome consisting of 16,533 bp includes 13 protein coding genes, 22 transfer RNAs, and two ribosomal RNAs genes. The overall base composition of Blue-face angelfish is 28.7% for A, 28.9% for C, 15.9% for G, 26.6% for T and show 84% identities to flame angelfish Centropyge loriculus. The complete mitogenome of the Blue-face angelfish provides essential and important DNA molecular data for further phylogeography and evolutionary analysis for marine angelfish phylogeny.
Publication
Journal: Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis
October/15/2017
Abstract
In this study, the complete mitogenome sequence of the palette surgeonfish, Paracanthurus hepatus (Perciformes: Acanthuridae), has been sequenced by next-generation sequencing method. The assembled mitogenome was 16 498 bp in length, consisted of 13 protein-coding genes, 22 transfer RNAs, 2 ribosomal RNAs genes. The overall base composition of palette surgeonfish was 28.6% for A, 28.6% for C, 16.3% for G, 26.4% for T and showed 87% identities to somber surgeonfish Zebrasoma flavescens. The complete mitogenome of the palette surgeonfish provides essential and important DNA molecular data for further phylogeography and evolutionary analysis for surgeonfish's phylogeny.
Publication
Journal: Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis
October/15/2017
Abstract
The Beaufortia szechuanensis is endemic to the upper reaches of Yangtze River in China. In this study, we successfully sequenced the mitochondrial genome of the B. szechuanensis, collected from the Qingyi River. The complete mitochondrial genome of B. szechuanensis was a circular molecule of 16,559 bp in length, containing 2 ribosomal RNA (rRNA) genes, 13 protein-coding genes, 22 transfer RNA (tRNA) genes, an origin of light-strand replication (OL) and a control region (D-loop). It is the first complete mitochondrial DNA data in the genus Beaufortia. The cytochrome c oxidase subunit I (COI) sequence of 14 species in Balitoridae was used for phylogenetic analysis. The topology demonstrated that the Balitoridae can be classified into two subfamilies, and the B. szechuanensis belongs to the subfamily Gastromyzoninae.
Publication
Journal: Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis
October/15/2017
Abstract
The Galápagos iguanas are among the oldest vertebrate lineages on the Galápagos archipelago, and the evolutionary history of this clade is of great interest to biologists. We describe here the complete mitochondrial genomes of the marine iguana, Amblyrhynchus cristatus (Genbank accession number: KT277937) and the land iguana Conolophus subcristatus (Genbank accession number: KT277936). The genomes contain 13 protein-coding genes, 22 transfer RNAs, and two ribosomal RNAs genes, as well as a control region (CR). Both species have an identical gene order, which matches that of Iguana iguana. The CR of both Galápagos iguanas features similar tandem repeats units, which are absent in I. iguana. We present a phylogeny of the Iguanidae based on complete mitochondrial genomes, which confirms the sister-group relationship of Galápagos iguanas. These new mitochondrial genomes constitute an important data source for future exploration of the phylogenetic relationships and evolutionary history of the Galápagos iguanas.
Publication
Journal: Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis
October/15/2017
Abstract
In this study, the complete mitogenome sequence of the Royal dottyback, Pictichromis paccagnellae (Perciformes: Pseudochromidae), has been sequenced by the next-generation sequencing method. The assembled mitogenome was of 16 976 bp in length, consisting of 13 protein-coding genes, 22 transfer RNAs, and two ribosomal RNAs genes. The overall base composition was 27.4% for A, 28.1% for C, 17.3% for G, and 27.2% for T and showed 76% identities to Fire-tail devil Labracinus cyclophthalmus in the same family. The complete mitogenome of P. paccagnellae provides essential and important DNA molecular data for further phylogeography and evolutionary analysis for Pseudochromidae.
Publication
Journal: Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis
October/15/2017
Abstract
The complete mitochondrial genomes of Red-billed Chough (Pyrrhocorax pyrrhocorax) and Yellow-billed Chough (Pyrrhocorax graculus) were sequenced using the Ion Torrent PGM platform. These mitogenomes contain 16,889 bp (Red-billed Chough) and 16,905 bp (Yellow-billed Chough), including 13 protein-coding genes (PCGs), two ribosomal RNA (rRNA) genes, 22 transfer RNA (tRNA) genes, and a control region (D-loop). The gene content, orientation, and structure are similar to a wide range of other vertebrate species and the nucleotide composition is very similar to other Passeriformes. All PCGs start with ATG, except for COX1 that starts with GTG, and four stop codons and one incomplete stop codon are used (TAA, TAG, AGG, AGA, and T-). The size of PCGs is the same in both mitogenomes, except for ND6 that has one codon less in the Yellow-billed Chough. All the tRNAs can fold into a typical cloverleaf secondary structure. These mitogenomic data can be of great value in complementing forthcoming approaches on molecular ecology, comparative and functional genomics.
Publication
Journal: Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis
October/15/2017
Abstract
The complete mitochondrial genome (KM507783) of the green crab spider Oxytate striatipes was determined. The mitochondrial genome of O. striatipes was 14,407 bp long with a total base composition of 35.80% A, 42.40% T, 8.60% C, and 13.20% G. Total length of 13 protein-coding genes was 10,801 bp and 9 of them were encoded on heavy strand. COX1 started with TTA, uncommon start codon in invertebrate mitogenomes. The total length of 22 tRNA genes was 1202 bp, varying from 46 bp (tRNA(Thr)) to 67 bp (tRNA(Trp) and tRNA(Gln)). The standard cloverleaf secondary structure was found in 8 tRNA genes and TV-replacement loop was not found in the other 14 tRNA genes.
Publication
Journal: Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis
October/15/2017
Abstract
Meriones libycus belongs to the genus Meriones in Gerbillinae, its complete mitochondrial genome is 16,341 bp in length. The heavy strand contains 32.8% A, 13.1% G, 25.3% C, 28.8% T, protein-coding genes approximately accounting for 69.54%. Results of phylogenetic analysis showed that M. libycus and Meriones unguiculatus were clustered together, and it was consistent with that of primary morphological taxonomy. This study verifies the evolutionary status of M. libycus in Meriones at the molecular level. The mitochondrial genome would be a significant supplement for the gene pool of Rodentia and the conclusion of phylogenetic analysis could be an important molecular evidence for the classification of Gerbillinae.
Publication
Journal: Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis
October/15/2017
Abstract
In the present study, the complete mitochondrial genome of the Terapon jarbua has been sequenced. The mitochondrial genome is 16,570 bp in length, containing 13 protein-coding genes, two ribosomal RNA genes, 22 transfer RNA genes, and one control region. The gene order and the composition of T. jarbua mitochondrial genome were similar to that of most other vertebrates. The overall nucleotides base composition of the heavy strand is A (27.36%), G (16.57%), C (29.87%), and T (26.20%). With the exception of the NADH dehydrogenase subunit 6 (ND6) and eight tRNA genes, all other mitochondrial genes are encoded on the heavy strand. The tRNA-Ser2 gene lacked DHC arm and could not fold into a typical clover-leaf secondary structure. Seen from the phylogenetic tree, T. jarbua, Bidyanus bidyanus, and Rhynchopelates oxyrhynchus from the same family (Terapontidae) clustered into one branch and were significantly divergent from the other families of closely related fish species.
Publication
Journal: Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis
October/15/2017
Abstract
We describe the complete mitochondrial genome sequence of Rasbora trilineata, which is a small cyprinid popular in aquarium trade. The circle genome (16,747 bp) has the typical vertebrate mitochondrial gene arrangement, including 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes and a non-coding control region. The overall base composition of R. trilineata is 25.35% for T, 26.43% for C, 33.57% for A, and 14.65% for G, with a slight AT bias of 58.92%.
Publication
Journal: Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis
October/15/2017
Abstract
In this paper, we report the complete mitochondrial genome of Scolopax rusticola (Charadriiformes: Scolopacidae), which is a circular DNA with 16,984 bp in length and contains 13 protein-coding genes, 2 ribosomal RNAs, 22 transfer RNAs, and a control region. The overall base composition of the complete mitochondrial DNA is 31.79% A, 25.02% T, 13.34% G and 29.85% C. The control region is 1413 bp in length which located between tRNA(Phe) and tRNA(Glu).
Publication
Journal: Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis
October/15/2017
Abstract
The Rhynchocypris oxycephalus (Cypriniformes: Cyprinidae) is an ecological important fish in East Asia. In this study, we firstly sequenced the complete mitochondrial genome of R. oxycephalus. The mitogenome is 16,606 bp in length, including 13 protein-coding genes, 22 transfer RNA genes, two ribosomal RNA genes, and two non-coding regions (origin of light-strand replication and control region). The gene content and order is in accord with the common vertebrate form. The nucleotide base composition of H-strand is 28.4% A, 27.2% T, 26.4% C and 18.0% G. The complete mitochondrial genome data would be useful for further studies of genetics, conservation biology and adaptive evolution of R. oxycephalus.
Publication
Journal: Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis
October/15/2017
Abstract
The complete mitochondrial genome of Trichogaster fasciata is determined in this study. It is 16,635 bp in size and consists of 2 rRNA genes, 13 protein-coding genes, 22 tRNA genes and 1 non-coding control region (D-loop). The overall base composition of the heavy strand of the T. fasciata mitochondrial genome is A: 29.18%, T: 30.22%, C: 25.14%, and G: 15.46%. A 78 bp AT tandem repeats was identified in the control region. This present study will be helpful to bring out the fact of genetic divergence among the genus Trichogaster.
Publication
Journal: Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis
October/15/2017
Abstract
Complete mitochondrial genome sequences were determined for two Indonesian freshwater fishes, Rasbora aprotaenia and Rasbora lateristriata. These genomes are 16,541 bp and 16,539 bp in length, respectively and encode 37 genes in the typical vertebrate gene arrangement. Phylogenetic analyses supported a view that these species are very closely related to each other.
Publication
Journal: Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis
October/15/2017
Abstract
The South Polar Skua, gull-like seabirds is the most fascinating Antarctic seabirds that lay two eggs at sites free of snow and ice and predominantly hunt pelagic fish and penguins. Blood samples of the South Polar Skua Stercorarius maccormicki was collected during the summer activity near King Sejong station in Antarctica. The complete mitochondrial DNA sequence of S. maccormicki was 16,669 bp, showing conserved genome structure and orientation found in other avian species. The control region of S. maccormicki was 93- and 80 bp shorter compared to those of Chroicocephalus saundersi and Synthliboramphus antiquus respectively. Interestingly, there is a (CAACAAACAA)6 repeat sequence in the control region. Our results of S. maccormicki mt genome including the repeat sequence, may provide useful genetic information for phylogenetic and phylogeographic histories of the southern skua complex.
Publication
Journal: Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis
October/15/2017
Abstract
The Downy woodpecker (Picoides pubescens) is a species of woodpecker which is the smallest in North America. This present study firstly reported the complete mitochondrial genome of downy woodpecker. We performed assembly of mitogenome structural by SPAdes and the Picidae species Dryocopus pileatus act as a reference. The mitogenome was 16 840 bp in length, which contains 13 protein-coding genes, 22 transfer RNAs, 2 ribosomal RNAs and 1 putative misc-feature region. The overall AT content is 52.76% which is higher than GC. To approve the accuracy of new determined mitogenome sequences, a phylogenetic tree of downy woodpecker together with other nine closely species was established by 12 protein-coding genes. This first complete mitogenome of Picoides species will contribute to identify species and study the related evolution events.
Publication
Journal: Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis
October/15/2017
Abstract
We obtained the complete mitochondrial genome of the Ussuri white-toothed shrew Crocidura lasiura (Insectivora, Soricidae) at 17 362 base pairs (bp) containing 13 protein-coding genes, two ribosomal RNAs, 22 transfer RNAs, and a non-coding control region. Its gene order is identical to that of other vertebrates. Several repeat elements were identified in the non-coding control region (D-loop). Phylogenetic tree using mt protein-coding gene sequences showed that C. lasiura was closely related to C. attenuata. The reports of mt genome sequences of Crocidura were not enough to study phylogenetic relationships in genome levels. However, this report may help us to understand the phylogenetic relationships and evolutionary history of Crocidura.
Publication
Journal: Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis
October/15/2017
Abstract
In this study, the complete mitogenome sequence of great seahorse Hippocampus kelloggi (Gasterosteiformes: Syngnathidae) has been amplified and sequenced employing the polymerase chain reaction-based method. The total length of mitochondrial DNA is 16 536 bp and includes 13 protein-coding genes, two ribosomal RNA, 22 transfer RNA genes, and a control region. The mitochondrial gene arrangement of H. kelloggi was similar to that observed in most vertebrate creatures. The overall base composition of H. kelloggi is 32.19% for A, 23.68% for C, 29.30% for T, and 14.82% for G, with a slight AT bias of 61.49%. Phylogenetic analyses based on complete mitochondrial genome sequence showed that H. kelloggi has a close genetic relationship to H. reidi, H. ingens, and H. kuda.
Publication
Journal: Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis
October/15/2017
Abstract
Gonista bicolor belongs to Orthoptera, Acrididae, Gonista Bolivar, which is widely distributed in China. In this work, we first published the complete mitochondrial genome of G. bicolor. It is 15 618 bp long, and the AT content of the whole genome (J-strand) is 76.3%. The mitogenome consists of 37 typical invertebrate mitochondrial genes and a 761 bp (A + T) rich region. Of the 13 protein-coding genes (PCGs), 12 start with a standard ATN codon except for COI, whose initiation codon is ACC. Eight PCGs use TAG or TAA as complete termination codons, while others terminate with T or TA. The size of the lrRNA and srRNA genes is 1321 and 793 bp, respectively. Here, we use the 13 PCGs of G. bicolor, together with 12 other related species (two species as the outgroup) as PCGs data set, to construct the species phylogenetic tree.
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