Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Characterization of the complete mitochondrial genome of Golden cusk, Sirembo imberbis (Ophidiiformes:Ophidiidae).

ABSTRACT: The complete mitochondrial genome of Sirembo imberbis was determined by the bioinformatic assembly of the next generation sequencing (NGS) reads. Total length of the mitogenome was 16,717 bp, which harbors the conserved 13 protein-coding genes (PCGs), 2 ribosomal RNAs (12S and 16S), 22 tRNAs, and two non-coding region (the control region and the origin of light-strand replication). Among 13 protein-coding genes, unusual start codon (GTG) was exclusively identified in COX1, while the incomplete stop codons (TA- or T-) were detected in COX2, COX3, ND2, ND3, ND4 and CytB. As a result of phylogenetic tree, S. imberbis formed a cluster of the family Ophidiidae together with Bassozetus zenkevitchi and Lamprogrammus niger.

SUBMITTER: Tabassum N

PROVIDER: S-EPMC7759297 | biostudies-literature | 2020 Dec

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

Characterization of the complete mitochondrial genome of Golden cusk, Sirembo imberbis (Ophidiiformes:Ophidiidae).

Tabassum Nazia N Kim Yeonghye Y Kim Hyun-Woo HW

Mitochondrial DNA. Part B, Resources 20201224 4

The complete mitochondrial genome of Sirembo imberbis was determined by the bioinformatic assembly of the next generation sequencing (NGS) reads. Total length of the mitogenome was 16,717 bp, which harbors the conserved 13 protein-coding genes (PCGs), 2 ribosomal RNAs (12S and 16S), 22 tRNAs, and two non-coding region (the control region and the origin of light-strand replication). Among 13 protein-coding genes, unusual start codon (GTG) was exclusively identified in COX1, while the incom ...[more]

PMID: 33426287

Similar Datasets

A new mitochondrial gene order in the banded cusk-eel Raneya brasiliensis (Actinopterygii, Ophidiiformes).

Project description:The complete mitochondrial genome of the banded cusk-eel, Raneya brasilensis (Kaup, 1856), was obtained using next-generation sequencing approaches. The genome sequence was 16,881 bp and exhibited a novel gene order for a vertebrate. Specifically, the WANCY and the nd6 - D-loop regions were re-ordered, supporting the hypothesis that these two regions are hotspots for gene rearrangements in Actinopterygii. Phylogenetic reconstructions confirmed that R. brasiliensis is nested within Ophidiiformes. Mitochondrial genomes are required from additional ophidiins to determine whether the gene rearrangements that we observed are specific to the genus Raneya or to the subfamily Ophidiinae.

| S-EPMC7510595 | biostudies-literature

Complete mitochondrial genome of golden conure (Guaruba guarouba).

Project description:Arini tribe with 19 genera is the most diversified tribe of neotropical parrots. Six of them are classified as macaws and nine as conures. The presence of bare facial area distinguishes macaws from conures and other members of this tribe. However, such morphological division seems to be disputable as the smallest macaw (monotypic Diopsittaca genus) turned out to be more closely related to three monotypic conures genera (Guaruba, Leptosittaca, Thectocercus) than to other macaws. We sequenced the complete mitochondrial genome of Guaruba guarouba to enrich the resource of molecular markers for examination of phylogenetic relationships between macaws and conures.

| S-EPMC7800242 | biostudies-literature

Mitogenome Announcement Characterization of the complete mitochondrial genome of golden tank goby, Glossogobius aureus (Perciformes: Gobiidae).

Project description:We applied next-generation sequencing (NGS) method to construct the complete mitochondrial genome of Glossogobius aureus. The obtained mitogenome of G. aureus (16,590 bp) exhibited a typical structure harboring 13 protein-coding genes (PCGs), 22 transfer RNAs (tRNAs), two ribosomal RNAs (rRNAs), and one control regions (D-loop). Most of mitochondrial genes are encoded on the heavy (H) strand, except for eight tRNAs and ND6. Unusual start codons were identified in COX1 (GTG) and ATP6 (TTG). Six genes (ND2, COX2, COX3, ND3, ND4, and CytB) were terminated by an incomplete stop codon (TA-/T-). A phylogenetic study showed that Glossogobius formed a clade distinct from other species in the subfamily Gobiinae. G. aureus was most closely related to G. giuris with 87.04% sequence identity among the four species in the genus Glossogobius.

| S-EPMC7759244 | biostudies-literature

Complete mitochondrial genome of the golden takin (Budorcas taxicolor bedfordi).

Project description:The complete mitochondrial genome sequence of Budorcas taxicolor bedfordi was 16 662-bp long, containing 13 protein-coding genes (PCGs), 22 tRNA genes, 2 rRNA genes and a control region. All of the PCGs begin with the typical ATN start codon. Stop codons TAA and AGA are present in the PCGs; exceptions are ND2, COIII, ND3 and ND4, which possess incomplete termination codon (T--). Secondary structure prediction of the 22 tRNA genes revealed the absence of the DHU arm in tRNASer(AGN).

| S-EPMC7871817 | biostudies-literature

The complete mitochondrial genome of golden yellow snakehead fish, Channa argus.

Project description:We sequenced and characterized the complete mitochondrial genome of golden yellow snakehead fish, Channa argus. The mitogenomes contained the typical complement of 13 protein-coding genes, 22 transfer RNAs (tRNAs), 2 ribosomal RNAs (rRNAs), and a non-coding control region. They share the same gene arrangement pattern that was identical with most vertebrates. The entire mitochondrial DNA molecule of golden yellow snakehead fish was 16,558 bp long. All information reported in this article will be a useful source of sequence information for general molecular and evolutionary studies of the family Channidae.

| S-EPMC7800385 | biostudies-literature

The complete mitochondrial genome of Pacific golden plover Pluvialis fulva (Charadriiformes, charadriidae).

Project description:Pacific golden plover Pluvialis fulva (Charadriiformes, Scolopacidae) is obligate long-distance migrant bird breeding from northernmost Asia into western Alaska, and wintering on islands in the Pacific Ocean and Australia. In this study, we report the complete mitochondrial genome of P. fulva, which is a circular molecule of 16,854 bp in size and consists of 13 protein-coding genes, 2 ribosomal RNAs, 22 transfer RNAs, and a control region. The A + T content of the overall base of the composition of H-strand is 54.88% (A: 31.48%, T: 23.40%, C: 31.48%, and G: 13.65%). It is very interesting that there are some insertions/deletions in the cytb gene sequence (total of 10bp deletions and 5bp insertions in four positions), which may result in reading frame shift and/or internal stops. Some short microsatellite-like repeat regions (ACCACCC) are scatter in the control region. The phylogenetic analysis resolved a well-supported clade of Charadriiformes in which Pluvialis appears to be sister group of Vanellus. This mitogenome provides a valuable resource for further study of molecular systematics, species identification, population genetics, phylogeography, and conservation genetics of Charadriiformes.

| S-EPMC7800346 | biostudies-literature

The complete mitochondrial genome of the golden apple snail Pomacea canaliculata (Gastropoda: Ampullariidae).

Project description:We present the complete mitochondrial genome of Cipangopaludina cathayensis in this study. The mitochondrial genome is 15 706 bp in length, containing 13 protein-coding genes, two rRNA genes and 22 tRNA genes. Overall nucleotide compositions of the light strand are 40.97% of A, 30.78% of T, 20.48% of C and 12.60% of G. Its gene arrangement and distribution are different from the typical vertebrates. The absence of D-loop is consistent with the Gastropoda, but, at least, one lengthy non-coding region is an essential regulatory element for the initiation of transcription and replication. A phylogenetic tree is constructed using the maximum-likelihood method based on the complete mitogenomes of the closely related 21 Gastropoda species to assess their actual phylogenetic relationship and evolution. The result provides fundamental data for resolving phylogenetic and genetic problems related to effective management strategies.

| S-EPMC7800459 | biostudies-literature

Aporocotyle mariachristinae n. sp., and A. ymakara Villalba & Fernandez, 1986 (Digenea: Aporocotylidae) of the pink cusk-eel, Genypterus blacodes (Ophidiiformes: Ophidiidae) from Patagonia, Argentina.

Project description:Aporocotyle mariachristinae n. sp. and A. ymakara Villalba & Fernández, 1986 were collected from the bulbus arteriosus and ventral aorta of pink cusk-eels, Genypterus blacodes (Forster, 1801) from Patagonia, Argentina. A. mariachristinae n. sp. can be distinguished from all the species of Aporocotyle by the asymmetrical extension of posterior caeca (right posterior caecum longer, terminating at the area between mid-level of ovary and posterior body end; left posterior caecum shorter, terminating at the area between mid-level of cirrus sac and posterior to reproductive organs), the distribution of spines along the ventro-lateral body margins and the number of testes. The new species clearly differs from A. ymakara, from the same host species, in the esophagus / body length ratio, the absence of distal loops at caeca, the anterior caeca / posterior caeca length ratio, and the number of testes. Additionally, in A. ymakara the left posterior caecum may be longer than right posterior caecum, while in the new species left posterior caecum is always shorter. The specimen of A. ymakara collected from Argentina is also described. We also provide observations of the distribution of spines in different species of Aporocotyle, including new specimens of A. argentinensis Smith, 1969 from Merluccius hubbsi Marini, 1933. Molecular sequence data obtained from partial 18S and 28S rDNA regions were compared between the new species and other two species of Aporocotyle (A. argentinensis and A. spinosicanalis Williams, 1958). This is a new locality record for A. ymakara, extending the known geographical distribution for this species from Chile to Argentina, and the first report of two species of Aporocotyle in the same host species and locality.

| S-EPMC3671458 | biostudies-literature

Complete mitochondrial genome of golden variant of freshwater fish Labeo rajasthanicus (Cypriniformes: Cyprinidae): endemic to India.

Project description:The complete mitochondrial genome of the freshwater fish species Labeo rajasthanicus was obtained, using Illumina NovaSeq 6000 with 2 × 150 bp paired-end sequencing. The mitogenome of L. rajasthanicus is 16,738 bp in length (GenBank accession no.: OQ834146), comprised of 13 protein-coding genes, 22 tRNA genes, two rRNA genes, and a control region, i.e. D-loop. The arrangement of genes was found to be identical to other Cypriniformes fish mitogenome, available in the NCBI database. The taxonomic status of L. rajasthanicus as a valid species was debated by some researchers and it was considered a synonym of L. boggut. However, phylogenetic analysis in the present study supports the species validity of L. rajasthanicus, as it showed a distinct node well separated from L. boggut and supported by a high bootstrap value. Furtherly, the pairwise genetic divergence among studied species showed the divergence between L. rajasthanicus and L. boggut as 1.6% whereas the minimum divergence was found to be 0.13% with L. dussumieri followed by L. fimbriatus (0.58%) and L. gonius (0.63%). The complete mitogenome of L. rajasthanicus will also be useful as a baseline reference genome for the reconstruction and annotation of the mitogenome of other Labeo species.

| S-EPMC10776062 | biostudies-literature

Characterization of the complete mitochondrial genome of Conus tribblei Walls, 1977.

Project 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.

| S-EPMC5556944 | biostudies-literature