Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Complete mitochondrial genome of the Sakhalin sculpin Cottus amblystomopsis (Cottoidei: Cottidae).

ABSTRACT: The complete mitochondrial genome was sequenced in two individuals of the Sakhalin sculpin Cottus amblystomopsis. The genome sequences are 16,526 and 16,527?bp in size, and the gene arrangement, composition, and size are very similar to the other sculpin mitochondrial genomes published previously. The difference between the two genomes studied is low, 0.28%, in spite of the relatively long distance separating the localities. The data are consistent with the amphidromous life history of C. amblystomopsis, promoting gene flow even between distantly located rivers.

SUBMITTER: Balakirev ES

PROVIDER: S-EPMC7799524 | biostudies-literature | 2017 Apr

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

Complete mitochondrial genome of the Sakhalin sculpin Cottus amblystomopsis (Cottoidei: Cottidae).

Balakirev Evgeniy S ES Saveliev Pavel A PA Ayala Francisco J FJ

Mitochondrial DNA. Part B, Resources 20170424 1

The complete mitochondrial genome was sequenced in two individuals of the Sakhalin sculpin Cottus amblystomopsis. The genome sequences are 16,526 and 16,527 bp in size, and the gene arrangement, composition, and size are very similar to the other sculpin mitochondrial genomes published previously. The difference between the two genomes studied is low, 0.28%, in spite of the relatively long distance separating the localities. The data are consistent with the amphidromous life history of <i ...[more]

PMID: 33473786

Similar Datasets

Complete mitochondrial genome of the Volk's sculpin Cottus volki (Cottoidei: Cottidae).

Project description:The complete mitochondrial genome was sequenced in two individuals of the Volk's sculpin Cottus volki. The genome sequences are 16,519 and 16,536?bp in size, and the gene arrangement, composition, and size are very similar to the other sculpin mitochondrial genomes published previously. The difference between the two genomes studied is relatively high, 3.42%, which is 30% of the average interspecific divergence (8.76%) detected between seven Cottus species from the GenBank database. The data are consistent with the sedentary lifestyle in C. volki, limiting gene flow even between neighbouring rivers.

| S-EPMC7800785 | biostudies-literature

Complete mitochondrial genome of the Amur sculpin Cottus szanaga (Cottoidei: Cottidae).

Project description:The complete mitochondrial genome was sequenced in two individuals of the Amur sculpin Cottus szanaga. The genome sequences are 16,518?bp in size, and the gene arrangement, composition, and size are very similar to the other sculpin genomes published previously. The low level of sequence divergence detected between the genome of C. szanaga and the GenBank complete mitochondrial genome of the Cherskii's sculpin Cottus czerskii (KJ956027) may likely be due to recent divergence, historical hybridization, or presence of a new unrecognized taxonomic unit close to C. szanaga but erroneously identified as C. czerskii.

| S-EPMC7871824 | biostudies-literature

Complete mitochondrial genome of the Belligerent sculpin Megalocottus platycephalus (Cottoidei: Cottidae).

Project description:The complete mitochondrial (mt) genome was sequenced in two specimens of the Belligerent sculpin Megalocottus platycephalus by high-throughput sequencing technology (Ion S5 platform). The sequences are 16,673 bp in size, and the gene arrangement, composition, and size are very similar to the other sculpin mt genomes published previously. Comparison of the two M. platycephalus mt genomes now obtained with other complete mt genomes available in GenBank reveals an affinity to the sculpin fishes from the genus Myoxocephalus. The intergeneric difference between the Megalocottus and Myoxocephalus is 0.0757 ± 0.0019, which is significantly less than the corresponding value, 0.1240 ± 0.0120, obtained previously for the sculpin fishes based on the COI barcoding marker.

| S-EPMC7706993 | biostudies-literature

Complete mitochondrial genome of the great sculpin Myoxocephalus polyacanthocephalus (Cottoidei: Cottidae).

Project description:The complete mitochondrial genome was sequenced in two specimens of the great sculpin Myoxocephalus polyacanthocephalus by high-throughput sequencing technology (Ion S5 platform). The genome sequences are 16,651 and 16,652 bp in size, and the gene arrangement, composition, and size are similar to the other sculpin mitochondrial genomes published previously. Overall base composition of the complete mitochondrial DNA is A (26.9%), G (17.0%), C (29.5%), and T (26.6.0%), the percentage of A and T (53.5%) is higher than G and C (46.5%). The difference between the two genomes studied is low, 0.15%. A relatively low level of divergence (3.48%) is detected between M. polyacanthocephalus and M. scorpius, which however is high enough to consider them as separate biological species.

| S-EPMC7687637 | biostudies-literature

Complete mitochondrial genomes for Cottus asper, Cottus perifretum, and Cottus rhenanus (Perciformes, Cottidae).

Project description:Freshwater sculpins represent a diverse but poorly-understood constituent of the Holarctic ichthyofauna. Sculpins are considered sensitive to pollution and habitat change, serving as aquatic bioindicators in ecotoxicology. Many species are protected by conservation agencies, due to anthropogenic activity within restricted geographic distributions. Here, we provide the first complete mitochondrial DNA sequences for three freshwater sculpins (Cottus asper, C. perifretum, C. rhenanus). These data are used to infer an updated mtDNA phylogeny for the genus Cottus, which supports results of previous research. These data are likely to be useful for future studies in biogeography, conservation, and functional genomics.

| S-EPMC7800474 | biostudies-literature

The characteristics and phylogenetic relationship of two complete mitochondrial genomes of Cottus pollux (scorpaeniformes: cottidae).

Project description:We report two complete mitochondrial genomes of Cottus pollux based on specimens collected from Deokdong and Hoam Streams in the Republic of Korea. The two complete mitochondrial genomes were 16,558 and 16,557 bp long. Both contain the 37 standard genes (13 protein-coding genes, 22 transfer RNA genes, two ribosomal RNA genes, and one control region) in the same order and have similar nucleotide compositions. According to the phylogenetic tree constructed using the maximum-likelihood method, C. pollux is closely related to C. reinii. The genetic information provided by the complete mitochondrial genome of C. pollux will contribute to an understanding of the phylogenetic position, evolutionary relationships, and biogeographical patterns of this species within the genus Cottus.

| S-EPMC10776038 | biostudies-literature

Complete mitochondrial genome of Hemilepidotus gilberti (Scorpaeniformes: Cottidae).

Project description:The complete mitochondrial genome of gilbert's irish lord (Hemilepidotus gilberti), a fish belonging to family Cottidae, was sequenced for the first time. This complete mitochondrial genome was 16,907 nucleotides in length, consisting of 38 mitochondrial genes (13 protein-coding genes, 22 tRNA genes, 2 rRNA genes, and a control region). The order of these genes was similar to that of other teleosts. The overall A, C, G, and T nucleotide contents in mitogenome were 26.8%, 30.4%, 17.0%, and 25.8%, respectively. The A?+?T content (52.6%) was higher than the G?+?C content (47.4%). NJ phylogenetic analysis was performed for 10 related species within the family of Cottidae along with, two fish species belonging to another family (Sebastidae).

| S-EPMC7800366 | biostudies-literature

Complete Mitochondrial Genomes of the Cherskii's Sculpin Cottus czerskii and Siberian Taimen Hucho taimen Reveal GenBank Entry Errors: Incorrect Species Identification and Recombinant Mitochondrial Genome.

Project description:The complete mitochondrial (mt) genome is sequenced in 2 individuals of the Cherskii's sculpin Cottus czerskii. A surprisingly high level of sequence divergence (10.3%) has been detected between the 2 genomes of C czerskii studied here and the GenBank mt genome of C czerskii (KJ956027). At the same time, a surprisingly low level of divergence (1.4%) has been detected between the GenBank C czerskii (KJ956027) and the Amur sculpin Cottus szanaga (KX762049, KX762050). We argue that the observed discrepancies are due to incorrect taxonomic identification so that the GenBank accession number KJ956027 represents actually the mt genome of C szanaga erroneously identified as C czerskii. Our results are of consequence concerning the GenBank database quality, highlighting the potential negative consequences of entry errors, which once they are introduced tend to be propagated among databases and subsequent publications. We illustrate the premise with the data on recombinant mt genome of the Siberian taimen Hucho taimen (NCBI Reference Sequence Database NC_016426.1; GenBank accession number HQ897271.1), bearing 2 introgressed fragments (≈0.9 kb [kilobase]) from 2 lenok subspecies, Brachymystax lenok and Brachymystax lenok tsinlingensis, submitted to GenBank on June 12, 2011. Since the time of submission, the H taimen recombinant mt genome leading to incorrect phylogenetic inferences was propagated in multiple subsequent publications despite the fact that nonrecombinant H taimen genomes were also available (submitted to GenBank on August 2, 2014; KJ711549, KJ711550). Other examples of recombinant sequences persisting in GenBank are also considered. A GenBank Entry Error Depositary is urgently needed to monitor and avoid a progressive accumulation of wrong biological information.

| S-EPMC5574479 | biostudies-literature

The complete mitochondrial genome of Trachidermus fasciatus (Scorpaeniformes: Cottidae) and phylogenetic studies of Cottidae.

Project description:Trachidermus fasciatus is a small catadromous fish and has been listed as a second class state protected aquatic animal since 1988 in China due to the declines in its abundance. We describe the complete mitogenome of T. fasciatus in this study. The mitogenome is 16,536 nucleotides long and contains 13 protein-coding genes (PCGs), two ribosomal RNA genes, 22 transfer RNA genes, and two main non-coding regions. The overall base composition includes C (30%), A (26.3%), T (25.5%), and G (18.2%). Moreover, the 13 PCGs encode 3800 amino acids in total, all the PCGs use the initiation codon ATG except COI uses GTG. Most of them have TAA or TAG as the stop codon, except COII, ND4 and Cytb use an incomplete stop codon T. The phylogenetic tree based on the neighbour joining method was constructed to provide relationship within Cottidae, which could be a useful basis for management of this species.

| S-EPMC7799978 | biostudies-literature

Complete mitochondrial genome of the Sakhalin nine-spined stickleback Pungitius tymensis (Gasterosteiformes, Gasterosteidae).

Project description:The complete mitochondrial genome of the Sakhalin nine-spined stickleback Pungitius tymensis was determined using Illumina paired-end sequencing of genomic DNA. The genome sequence was 16?481?bp in length, consisting of 13 protein-coding genes, 22 transfer RNA genes, two ribosomal RNA genes and a control region. The content and arrangement of the genes were identical to those of other Gasterosteidae species. P. tymensis was phylogenetically positioned with other Pungitius species (P. kaibarae, P. pungitius and P. sinensis) with a clear distinction from them. Nucleotide identity in the 37 genic regions ranged from 94.7% to 94.9% between P. tymensis and the other Pungitius species.

| S-EPMC7799693 | biostudies-literature