cox3
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cox3 -cytochrome c oxidase subunit 3
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The complete mitochondrial genome of the sandbar shark Carcharhinus plumbeus.
Journal: Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis
September/25/2016
Description

The sandbar shark, Carcharhinus plumbeus, a major representative species in shark fisheries worldwide is now considered vulnerable to overfishing. A pool of 774,234 Roche 454 shotgun sequences from one individual were assembled into a 16,706 bp mitogenome with 33× average coverage depth. It comprised 13 protein coding genes, 22 transfer RNA's, 2 ribosomal genes and 2 non-coding regions, typical of a vertebrate mitogenome. As expected for sharks, an A-T nucleotide bias was evident. This adds to rapidly growing number of mitogenome assemblies for the economically important Carcharhinidae family. The C. plumbeus mitogenome will assist researchers, fisheries and conservation managers interested in shark molecular systematics, phylogeography, conservation genetics, population and stock structure.

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Pubmed
Complete mitochondrial genome of the brown alga Sargassum vachellianum (Sargassaceae, Phaeophyceae).
Journal: Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis
October/15/2017
Description

Sargassum vachellianum C. Agardh is endemic to China. It inhabits in rocky intertidal zones and plays an important role in maintaining the structure and function of littoral ecosystems. In this study, we present the complete mitochondrial genome of S. vachellianum. The circular S. vachellianum mitogenome is 34,877 bp in size and contains the same set of 65 genes as the reported Sargassum mtDNAs. The overall AT content of the genome is 63.79%, and the inter-genic spacers constitute only 4.67%. The genome organization including the gene order, overlapping regions between genes, and the total length of inter-genic spacers is conserved among the known Sargassum mitogenomes. High divergence is in inter-genic spacer regions. Phylogenetic analyses indicated that S. vachellianum combined tightly with Sargassum species with strong support values (NJ/ML, 100%).

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The complete mitochondrial DNA of three monozoic tapeworms in the Caryophyllidea: a mitogenomic perspective on the phylogeny of eucestodes.
Journal: Parasites & vectors
July/13/2017
Description

BACKGROUND

External segmentation and internal proglottization are important evolutionary characters of the Eucestoda. The monozoic caryophyllideans are considered the earliest diverging eucestodes based on partial mitochondrial genes and nuclear rDNA sequences, yet, there are currently no complete mitogenomes available. We have therefore sequenced the complete mitogenomes of three caryophyllideans, as well as the polyzoic Schyzocotyle acheilognathi, explored the phylogenetic relationships of eucestodes and compared the gene arrangements between unsegmented and segmented cestodes.

RESULTS

The circular mitogenome of Atractolytocestus huronensis was 15,130 bp, the longest sequence of all the available cestodes, 14,620 bp for Khawia sinensis, 14,011 bp for Breviscolex orientalis and 14,046 bp for Schyzocotyle acheilognathi. The A-T content of the three caryophyllideans was found to be lower than any other published mitogenome. Highly repetitive regions were detected among the non-coding regions (NCRs) of the four cestode species. The evolutionary relationship determined between the five orders (Caryophyllidea, Diphyllobothriidea, Bothriocephalidea, Proteocephalidea and Cyclophyllidea) is consistent with that expected from morphology and the large fragments of mtDNA when reconstructed using all 36 genes. Examination of the 54 mitogenomes from these five orders, revealed a unique arrangement for each order except for the Cyclophyllidea which had two types that were identical to that of the Diphyllobothriidea and the Proteocephalidea. When comparing gene order between the unsegmented and segmented cestodes, the segmented cestodes were found to have the lower similarities due to a long distance transposition event. All rearrangement events between the four arrangement categories took place at the junction of rrnS-tRNA Arg (P1) where NCRs are common.

CONCLUSIONS

Highly repetitive regions are detected among NCRs of the four cestode species. A long distance transposition event is inferred between the unsegmented and segmented cestodes. Gene arrangements of Taeniidae and the rest of the families in the Cyclophyllidea are found be identical to those of the sister order Proteocephalidea and the relatively basal order Diphyllobothriidea, respectively.

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First confirmed human case of Diphyllobothrium stemmacephalum infection and molecular verification of the synonymy of Diphyllobothrium yonagoense with D. stemmacephalum (Cestoda: Diphyllobothriidea).
Journal: Parasitology international
March/12/2017
Description

Several tapeworm species in the genus Diphyllobothrium Cobbold, 1858 have uncertain taxonomic positions, leading to taxonomic confusion as well as misdiagnosis of infections. Taxonomic revision based on DNA sequence analysis is considered necessary to resolve the taxonomy of several cases, including that between Diphyllobothrium stemmacephalum, the type species of the genus, and Diphyllobothrium yonagoense. Diphyllobothrium yonagoense was synonymized with D. stemmacephalum based on morphological observations by Andersen (1987), however no molecular studies have been undertaken to verify the validity of this synonymization. In the present study, the first human case confirmed molecularly as D. stemmacephalum infection is reported, and the validity of the synonymization of D. yonagoense with D. stemmacephalum was assessed based on molecular phylogenetics. Diphyllobothrium stemmacephalum and D. yonagoense grouped into the same clades with high bootstrap confidence values for both cox1 and nad3. Genetic distances between the two taxa were very small (0.000-0.012 and 0.000-0.017 for cox1 and nad3, respectively) and were considered to fall within the range of intraspecific variation. Using these molecular analyses, this study verified molecularly that D. yonagoense is a junior synonym of D. stemmacephalum. Further, the closer phylogenetic relationship between D. stemmacephalum and Diplogonoporus species rather than other diphyllobothriids, including Diphyllobothrium nihonkaiense and Diphyllobothrium latum, was corroborated. The genus name for D. nihonkaiense and D. latum is also discussed.

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Mitochondrial genome of the Aix galericula (Anatidae: Aix).
Journal: Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis
October/17/2016
Description

Aix galericula has very wide geographical range in eastern Asia. Here, the complete mitochondrial genome of A. galericula (16,605 bp in length) been analyzed for building the database. Similar to the typical mtDNA of vertebrates, it contained 37 genes (13 protein-coding genes, 2 rRNA genes and 22 tRNA genes) and a non-coding region (D-loop). All the genes in A. galericula were distributed on the H-strand, except for the ND6 subunit gene and 10 tRNA genes which were encoded on the L-strand.

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Pubmed
The complete mitochondrial genome of the Babylonia lutosa.
Journal: Mitochondrial DNA
May/12/2016
Description

The complete mitochondrial genome sequence of the Babylonia lutosa was determined using the PCR-based method. The total length of the mitogenome is 15,346 bp, including 2 ribosomal RNA genes, 13 protein-coding genes and 22 transfer RNA genes. The overall composition of the mitogenome was estimated to be 29.10% for A, 37.24% for T, 16.82% for C and 16.85% for G, indicating that an A + T (66.34%)-rich feature occurs in the B. lutosa mitogenome.

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Pubmed
The complete mitochondrial genome sequence of Metzia formosae (Cypriniformes, Cyprinidae).
Journal: Mitochondrial DNA
December/16/2015
Description

We determined the complete mitochondrial genome (mitogenome) sequence of Metzia formosae, which is known as an endangered freshwater species in Taiwan and mainland China, with a long polymerase chain reaction (PCR) method. The total length of M. formosae mitogenome is 16,614 bp, consisting of 13 protein-coding genes, 22 transfer RNAs, 2 ribosomal RNAs genes and a noncoding control region. The overall base composition of M. formosae is 31.39% for A, 25.56% for T, 16.23% for G and 26.82% for C, with a slight AT bias of 56.95%. The molecular data here we presented could play a useful role not only for studying the evolutionary relationships and population genetics of Metzia species, but for practicing conservation on endangered fishes.

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Pubmed
The complete mitochondrial genome of a flea, Jellisonia amadoi (Siphonaptera: Ceratophyllidae).
Journal: Mitochondrial DNA
December/16/2015
Description

The complete mitogenome sequence of the flea, Jellisonia amadoi (Siphonaptera: Ceratophyllidae), was sequenced. The 17,031 bp long genome has the standard metazoan complement of 37 genes, in the insect ancestral genome arrangement. The very large (2338 bp) A + T rich region is marked by two macro-repeats and multiple microsatellite and homopolymer regions. The protein-coding, rRNA and tRNA genes are all highly similar to homologues in related insect orders - similar length, few indels and high proportion of invariant sites. Sequencing of a flea mitogenome provides data for one of the last three insect orders from which data were lacking and provides further proof that parasitic life histories alone do not cause aberrant mitogenomes.

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Characterization of the complete mitochondrial genome of Conus tribblei Walls, 1977.
Journal: Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis
October/31/2017
Description

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.

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Complete mitochondrial genome of yellow-browed tit (Sylviparus modestus).
Journal: Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis
October/15/2017
Description

The complete mitochondrial genome of yellow-browed tit was 17,086 bp in length, and consisted of 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes and a control region. In control region, a 117 bp long tandem repeat was identified, which was the first reported tandem repeats in tits.

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