Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Sequencing and analysis of the complete mitochondrial genome of Gymnogobius laevis.

ABSTRACT: Gymnogobius laevis (Steindachner, 1879) is a small, benthic freshwater fish. In a previous study, it was reported as a rare resident in Heilongjiang Province. In this study, the mitochondrial genome of G. laevis was sequenced. It is 16,519 base pairs (bp) in length and contains 13 protein-coding genes, two ribosomal RNA genes (12S rRNA and 16S rRNA), 22 transfer RNA genes (tRNA), and two non-coding control regions. The A + T content is 55.71% in the G. laevis mitochondrial genome. A phylogenetic tree shows that G. laevis is closely related to the family Gobiinae based on complete mitogenome sequences.

SUBMITTER: Peng L

PROVIDER: S-EPMC9176352 | biostudies-literature | 2022

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

Sequencing and analysis of the complete mitochondrial genome of Gymnogobius laevis.

Peng Lina L Li Peilun P Li Hui H Zhao Wenyan W Wang Hongkun H Li Zheng Z Sun Lili L

Mitochondrial DNA. Part B, Resources 20220526 5

Gymnogobius laevis (Steindachner, 1879) is a small, benthic freshwater fish. In a previous study, it was reported as a rare resident in Heilongjiang Province. In this study, the mitochondrial genome of G. laevis was sequenced. It is 16,519 base pairs (bp) in length and contains 13 protein-coding genes, two ribosomal RNA genes (12S rRNA and 16S rRNA), 22 transfer RNA genes (tRNA), and two non-coding control regions. The A + T content is 55.71% in the G. laevis mitochondrial g ...[more]

PMID: 35692706

Similar Datasets

The complete mitochondrial genome of Gymnogobius heptacanthus (Perciformes, gobiidae).

Project description:Gymnogobius heptacanthus is a small intertidal species belonging to the family Gobiidae. Herein, we report the first sequencing and assembly of the complete mitochondrial genome of G. heptacanthus. The complete mitochondrial genome is 16,529 bp long and has the typical vertebrate mitochondrial gene arrangement, consisting of 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes, and a control region. Phylogenetic analysis using mitochondrial genomes of 12 species showed that G. heptacanthus is clustered with G. urotaenia and G. petschiliensis and rooted with other Gobiidae species. This mitochondrial genome provides potentially important resources for addressing taxonomic issues and studying molecular evolution.

| S-EPMC7800937 | biostudies-literature

The complete mitochondrial genome of a Biwa goby, Gymnogobius isaza (Tanaka, 1916).

Project description:We determined the complete mitochondrial DNA sequence of a Biwa goby, Gymnogobius isaza (Tanaka, 1916) using next-generation sequencing methods. The composition of its mitogenome is the same as that observed in most other vertebrates, comprising of 13 protein-coding genes, 22 tRNA genes, two rRNA genes, and two control regions. Our molecular phylogenetic analysis confirmed the close phylogenetic relationship between G. isaza and G. petschiliensis. This mitogenome information will be useful for distribution surveys using environmental DNA and the development of conservation strategies for this species.

| S-EPMC11198123 | biostudies-literature

The complete mitochondrial genome of Gymnogobius Petschiliensis (Gobiiformes; Gobiidae; Gobionellinae) and its phylogenetic implications.

Project description:Of the goby fishes, many Gymnogobius species have been poor recognized mainly because of the absence of enough molecular information and clear phylogenetic framework. In this study, the complete mitochondrial genome of Gymnogobius petschiliensis was determined and described. The mitogenome is 16,422 bp in length and consists of 22 tRNAs, 13 protein-coding genes, two rRNAs, one control region and a light strand replication origin (OL). The arrangement of this mitogenome is identical to that of the typical teleost. The overall base composition is 27.5%, 29.5%, 26.1%, and 16.9%, for A, T, C, and G, respectively, with a slight bias on A + T content (57.0%). The 13 protein-coding genes use the initiation codon ATG except COI, which uses GTG. Most of them use TAA or TAG as the stop codon, while COII, COIII, and Cyt b use an incomplete T or TA and ND4 uses an unusual AGA. The maximum-likelihood phylogeny tree of 19 Gobionellinae species demonstrated that G. petschiliensis had a very closely relationship with the same genus G. urotaenia. This study is expected to contributing to the phylogenetic evolution of G. petschiliensis and further phylogenetic relationship of Gobionellinae and Gobiiformes.

| S-EPMC7799598 | biostudies-literature

Gymnogobius laevis

Project description:Gymnogobius laevis Raw sequence reads

| PRJNA798544 | ENA

Characterization of the complete mitochondrial genome of Amphioplus laevis (Ophiuroidea, Amphiuridae) with phylogenetic analysis.

Project description:The complete mitochondrial genome of Amphioplus laevis was 16,084 bp in length (Genbank accession: MN276320). It contained 13 protein-coding genes, 2 ribosomal RNA and 22 transfer RNA. The GC contents of A. laevis was 37.59%. The gene order was similar with species in the same family. Phylogenetic relationships within known ophiuroids reconstructed by 13 protein-coding mitochondrial genes, which showed that it was mostly related to Amphiopholis squamata, corresponding to the gene order. These results could provide a novel insight to the phylogeny of Ophiuroidea.

| S-EPMC7706814 | biostudies-literature

Complete mitochondrial genome of Andrias davidianus (Caudata: cryptobrachidae): sequencing and analysis.

Project description:In this study, the total mitochondrial genome sequence of Andrias davidianus (Caudata: Cryptobrachidae) was determined. The genome is 16,519 bases in length. It consists of 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes and 2 non-coding regions. These results will contribute to the natural resources conservation and species identification Of A. davidianus.

| S-EPMC7799949 | biostudies-literature

Sequencing and phylogenetic analysis of the Pyrgilauda ruficollis (Aves, Passeridae) complete mitochondrial genome.

Project description:In this study, both long PCR and conserved primers walking sequencing methods were used to determine the complete sequence of the of Pyrgilauda ruficollis mitochondrial genome (KC836121). The results showed that the complete mitochondrial genome of P. ruficollis is 1 6909 bp in length with 55.0% A+T content, harboring the typical 37 genes. The mitogenome had the same gene order with that of Podoces hendersoni. All protein coding genes started with ATG codon, except ND3 with GTG. For the stop codon usage, most genes terminate with codons TAA or TAG, but ND5 terminated with AGA, while ND1 and COI genes with AGG, and both the genes COⅢ and ND4 have an incomplete termination codon (T). The secondary structures of 22 tRNA genes were also predicted, showing that all tRNAs can form typical clover-leaf secondary structures, except for the tRNA(Ser) (AGN) which loses the DHU arm, while tRNA(Phe) harbor an extra nucleotide inserted in the TψC arm. The predicted secondary structures of 12S rRNA and 16S rRNA exhibit 47 helices in 4 domains and 60 helices in 6 domains respectively. The control region of P. ruficollis with the length of 1 305 bp was located between tRNA(Glu) and tRNA(Phe), and typical domains of which could be found as other bird groups. Using the data from 13 mitochondrial protein-coding genes, results of a final phylogenetic analysis strongly supports the traditional view that P. ruficollis is closely related with Passeridae and Fringillidae.

| S-EPMC5042932 | biostudies-literature

Sequencing and analysis of the complete mitochondrial genome of Hippopus porcellanus.

Project description:In this study, the complete mitochondrial genome of Hippopus porcellanus was reported. The whole mitochondrial genome was 21,565bp in length with a typical mitochondrial genomic structure including 13 protein-coding genes, 23 transfer RNA genes, 2 ribosomal RNA genes and 1 control region (D-loop). Mitogenome base composition was biased toward A + T content, at 60.3%. A phylogenetic tree based on complete mitogenome sequences revealed that, H. porcellanus is closely related to H. hippopus, both of which belong to the genus Hippopus.

| S-EPMC8317960 | biostudies-literature

Sequencing and analysis of the complete mitochondrial genome in Anopheles sinensis (Diptera: Culicidae).

Project description:BackgroundAnopheles sinensis (Diptera: Culicidae) is a primary vector of Plasmodium vivax and Brugia malayi in most regions of China. In addition, its phylogenetic relationship with the cryptic species of the Hyrcanus Group is complex and remains unresolved. Mitochondrial genome sequences are widely used as molecular markers for phylogenetic studies of mosquito species complexes, of which mitochondrial genome data of An. sinensis is not available.MethodsAn. sinensis samples was collected from Shandong, China, and identified by molecular marker. Genomic DNA was extracted, followed by the Illumina sequencing. Two complete mitochondrial genomes were assembled and annotated using the mitochondrial genome of An. gambiae as reference. The mitochondrial genomes sequences of the 28 known Anopheles species were aligned and reconstructed phylogenetic tree by Maximum Likelihood (ML) method.FindingsThe length of complete mitochondrial genomes of An. sinensis was 15,076 bp and 15,138 bp, consisting of 13 protein-coding genes, 22 transfer RNA (tRNA) genes, 2 ribosomal RNA (rRNA) genes, and an AT-rich control region. As in other insects, most mitochondrial genes are encoded on the J strand, except for ND5, ND4, ND4L, ND1, two rRNA and eight tRNA genes, which are encoded on the N strand. The bootstrap value was set as 1000 in ML analyses. The topologies restored phylogenetic affinity within subfamily Anophelinae. The ML tree showed four major clades, corresponding to the subgenera Cellia, Anopheles, Nyssorhynchus and Kerteszia of the genus Anopheles.ConclusionsThe complete mitochondrial genomes of An. sinensis were obtained. The number, order and transcription direction of An. sinensis mitochondrial genes were the same as in other species of family Culicidae.

| S-EPMC5625653 | biostudies-literature

Sequencing and Analysis of the Complete Mitochondrial Genome of Lentipes ikeae.

Project description:We sequenced and analyzed the complete mitochondrial genome of Lentipes ikeae and explored the phylogenetic relationships among Sicydiinae based on mitochondrial genome sequences. The complete mitochondrial genome sequence of L. ikeae was determined using the Illumina HiSeq X Ten sequencing platform, and the gene structural characteristics and base composition were analyzed. Based on the mitochondrial genome sequences of 28 Sicydiinae species published in GenBank and mitochondrial protein-coding genes (PCGs), Acanthogobius flavimanus (Gobionellinae) was selected as an outgroup to construct phylogenetic trees of Sicydiinae using the maximum likelihood and Bayesian inference methods. The mitochondrial genome of L. ikeae (GenBank number: OP764680) has a total length of 16,498 bp and encodes 13 PCGs, 22 transfer RNA genes, two ribosomal RNA genes, and a D-loop (control) region. Gene rearrangement is not observed. The mitochondrial genome of L. ikeae exhibits an AT preference, with AT skew > 0 and GC skew < 0 across the entire genome. The phylogenetic relationships of Sicydiinae based on 13 mitochondrial PCG sequences are Sicydium + (Stiphodon + (Sicyopus + Lentipes)) + Sicyopterus, indicating that Sicydium, Sicyopterus, Lentipes, and Stiphodon are all monophyletic groups.

| S-EPMC10967545 | biostudies-literature