Browse
Submit Data
Databases
API
Help

Dataset Information

10 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Characterization of the complete mitochondrial genome sequence of Nibea diacanthus and its phylogenetic implication.

ABSTRACT: The blackspotted croaker (Nibea diacanthus) is an important food fish of Indo-West Pacific and China. To study the phylogenetic status, we sequenced the complete mitochondrial genome of N. diacanthus. The mitogenome is 16,532 bp in length and composed of 13 protein-coding genes, two rRNAs, 22 tRNAs, and a control region. The gene composition and the structural arrangement of N. diacanthus complete mtDNA were identical to most of other vertebrates. The phylogenetic analysis using the complete mitochondrial genome revealed that the N. diacanthus might be separated from Nibea genera of Argyrosominae, which was inconsistent with that based on morphology. The complete mitogenome data would be useful for the evolution and conservation genetic studies of Sciaenidae.

SUBMITTER: Hu Z

PROVIDER: S-EPMC7748784 | biostudies-literature |

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Similar Datasets

Characterization of complete mitochondrial genome of Hylarana guentheri (Anura: Ranidae) and its phylogenetic implication.

Project description:The Günther's frog (Hylarana guentheri) belongs to a member of the family Ranidae. We provide a complete mitogenome of H. guentheri and examine its phylogenetic position with other related species. Its mitogenome is a closed circular molecule 18,698 bp in length including 13 protein coding genes, 22 tRNA coding genes, two rRNA-coding genes, and a control region (CR) that are conserved in most Ranidae mitogenomes. The overall base composition of the H. guentheri mitogenome is 29.27% A, 30.45% T, 26.14% C, and 14.15% G, which is typical for Amphibious animals' mitochondrial genomes. The alignment of the Ranidae species control regions showed high levels of genetic variation and abundant AT content. Seven tandem repeats were found in the control region. Phylogenetic analysis with Bayesian inference and maximum likelihood based on 13 protein-coding genes indicated that H. guentheri is more closely related to Nidirana okinavana than to Babina subaspera and B. holsti. The complete mitogenome of H. guentheri provides a potentially useful resource for further exploration of the taxonomic status and phylogenetic relationships of Hylarana and related species.

| S-EPMC7748803 | biostudies-literature

Characterization of the complete mitochondrial genome of Myrmuslateralis (Heteroptera, Rhopalidae) and its implication for phylogenetic analyses

Project description:Abstract Mitochondrial genomes (mitogenomes) are widely used in research studies on phylogenetic relationships and evolutionary history. Here, we sequenced and analyzed the mitogenome of the scentless plant bug Myrmuslateralis Hsiao, 1964 (Heteroptera, Rhopalidae). The complete 17,309 bp genome encoded 37 genes, including 13 protein-coding genes (PCGs), 22 transfer RNA (tRNA) genes, two ribosomal RNA (rRNA) genes, and a control region. The mitogenome revealed a high A+T content (75.8%), a positive AT-skew (0.092), and a negative GC-skew (–0.165). All 13 PCGs were found to start with ATN codons, except for cox1, in which TTG was the start codon. The Ka/Ks ratios of 13 PCGs were all lower than 1, indicating that purifying selection evolved in these genes. All tRNAs could be folded into the typical cloverleaf secondary structure, except for trnS1 and trnV, which lack dihydrouridine arms. Phylogenetic trees were constructed and analyzed based on the PCG+rRNA from 38 mitogenomes, using maximum likelihood and Bayesian inference methods, showed that M.lateralis and Chorosomamacilentum Stål, 1858 grouped together in the tribe Chorosomatini. In addition, Coreoidea and Pyrrhocoroidea were sister groups among the superfamilies of Trichophora, and Rhopalidae was a sister group to Alydidae + Coreidae.

| S-EPMC8599289 | biostudies-literature

Complete mitochondrial genome sequence for the cuneate drum Nibea miichthioides (Perciformes, Sciaenidae) and its phylogeny.

Project description:The cuneate drum, Nibea miichthioides, is a native sciaenid species with relevant commercial importance in China. However, the wild resource represented by this species has been severely damaged owing to overfishing and water pollution. For conserving and recovering the species through appropriate measures, genetic studies on the population are necessary. The complete mitochondrial genome of N. miichthioides is a supplement to the mitogenome database for giant croakers and can be used to address taxonomic problems and phylogenetic relationships in Sciaenidae. In this study, we sequenced and characterized the complete mitochondrial genome of N. miichthioides. The full length of the complete mitochondrial DNA was 16,490?bp. It contained 13 protein-coding genes, 22 tRNA genes, two rRNA genes and a control region. All 21 tRNA genes can fold into a typical cloverleaf structure except for tRNASer (AGY), which lacks a dihydrouridine arm. The phylogenetic analysis using the complete mitochondrial genome revealed that N. miichthioides, A. amoyensis, N. japonica and A. japonicus might be grouped in Argyrosomus, but not belonged to Nibea of Argyrosominae, which was highly consistent with the proposal of Talwar. This investigation provides an effective molecular tool for genetic research on and protection of this endangered species.

| S-EPMC7800342 | biostudies-literature

The complete mitochondrial genome of Helice Sheni and its phylogenetic implication.

Project description:In this study, the complete mitochondrial genome (mitogenome) of Helice sheni was amplified and analyzed. The mitogenome is 16,062 bp in length, encoding the standard set of 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes, and one control region. The nucleotide frequency of the mitogenome is as follows: A, 34.81%; C, 23.24%; G, 12.68%; and T, 29.25%. Eight overlapping areas and 22 intergenic spacers were found in the complete mitogenome. The typical initiation codon (ATT) and stop codon (TAA) were observed in eight genes, respectively. The phylogenetic tree indicates that Helicana wuana is closely related to H. sheni.

| S-EPMC7800991 | biostudies-literature

Characterization of the complete mitochondrial genome of Spirocerca lupi: sequence, gene organization and phylogenetic implications.

Project description:BACKGROUND: Spirocerca lupi is a life-threating parasitic nematode of dogs that has a cosmopolitan distribution but is most prevalent in tropical and subtropical countries. Despite its veterinary importance in canids, the epidemiology, molecular ecology and population genetics of this parasite still remain unexplored. METHODS: The complete mitochondrial (mt) genome of S. lupi was amplified in four overlapping long fragments using primers designed based on partial cox1, rrnS, cox2 and nad2 sequences. Phylogenetic re-construction of 13 spirurid species (including S. lupi) was carried out using Bayesian inference (BI) based on concatenated amino acid sequence datasets. RESULTS: The complete mt genome sequence of S. lupi is 13,780 bp in length, including 12 protein-coding genes, 22 transfer RNA genes and two ribosomal RNA genes, but lacks the atp8 gene. The gene arrangement is identical to that of Thelazia callipaeda (Thelaziidae) and Setaria digitata (Onchocercidae), but distinct from that of Dracunculus medinensis (Dracunculidae) and Heliconema longissimum (Physalopteridae). All genes are transcribed in the same direction and have a nucleotide composition high in A and T. The content of A?+?T is 73.73% for S. lupi, in accordance with mt genomes of other spirurid nematodes sequenced to date. Phylogenetic analyses using concatenated amino acid sequences of the 12 protein-coding genes by BI showed that the S. lupi (Thelaziidae) is closely related to the families Setariidae and Onchocercidae. CONCLUSIONS: The present study determined the complete mt genome sequence of S. lupi. These new mt genome dataset should provide novel mtDNA markers for studying the molecular epidemiology and population genetics of this parasite, and should have implications for the molecular diagnosis, prevention and control of spirocercosis in dogs and other canids.

| S-EPMC3606334 | biostudies-literature

Characterization of the complete mitochondrial genome sequence of Charybdis bimaculata and phylogenetic analysis.

Project description:In this study, the complete mitogenome of Charybdis bimaculata was sequenced and annotated. The mitogenome is 15,441?bp in length, containing 37 classical eukaryotic mitochondrial regions (13 typical protein-coding genes (PCGs), 22 tRNA genes, two rRNA genes) and a non-coding control region. Most of the genes are initiated with ATA, ATG, and ATT, though GTG is also used as an initiation codon. Twelve PCGs stop with complete termination codon TAA and TAG, while Cob uses incomplete codon (T-). The phylogenetic relationships based on 13 PCGs show that C. bimaculata clusters closest to C. fariata and C. natator.

| S-EPMC7799625 | biostudies-literature

The Complete Mitochondrial Genome of Ctenoptilum vasava (Lepidoptera: Hesperiidae: Pyrginae) and Its Phylogenetic Implication.

Project description:We here report the first complete mitochondrial (mt) genome of a skipper, Ctenoptilum vasava Moore, 1865 (Lepidoptera: Hesperiidae: Pyrginae). The mt genome of the skipper is a circular molecule of 15,468?bp, containing 2 ribosomal RNA genes, 24 putative transfer RNA (tRNA), genes including an extra copy of trnS (AGN) and a tRNA-like insertion trnL (UUR), 13 protein-coding genes and an AT-rich region. All protein-coding genes (PCGs) are initiated by ATN codons and terminated by the typical stop codon TAA or TAG, except for COII which ends with a single T. The intergenic spacer sequence between trnS (AGN) and ND1 genes also contains the ATACTAA motif. The AT-rich region of 429?bp is comprised of nonrepetitive sequences, including the motif ATAGA followed by an 19?bp poly-T stretch, a microsatellite-like (AT)(3) (TA)(9) element next to the ATTTA motif, an 11?bp poly-A adjacent to tRNAs. Phylogenetic analyses (ML and BI methods) showed that Papilionoidea is not a natural group, and Hesperioidea is placed within the Papilionoidea as a sister to ((Pieridae + Lycaenidae) + Nymphalidae) while Papilionoidae is paraphyletic to Hesperioidea. This result is remarkably different from the traditional view where Papilionoidea and Hesperioidea are considered as two distinct superfamilies.

| S-EPMC3335176 | biostudies-literature

Complete mitochondrial genome of Lelecella limenitoides (Lepidoptera: Nymphalidae: Apaturinae) and phylogenetic implication.

Project description:The length of Lelecella limenitoides complete mitogenome was 15,203 bp and contained the typical gene arrangement, base composition, and codon usage found in other related species. The overall base composition exhibited obvious anti-G (7.5%) and AT bias (81.6%). The initiation codons of all PCGs were typical ATN (ATA/ATG/ATT), and the termination codons were TAA, TAG, or incomplete stop codon T-. All tRNAs could be folded into typical cloverleaf secondary structures, except tRNASer (AGN). Phylogenetic analysis showed that L. limenitoides was clustered with the clade of Sasakia, Euripus, and Apatura.

| S-EPMC7510825 | biostudies-literature

The complete mitochondrial genome of Heteropriacanthus cruentatus and implication of phylogenetic status.

Project description:The complete mitochondrial genome of Heteropriacanthus cruentatus has been obtained and annotated through Illumina next-generation sequencing. This mitogenome was found to be 16,506 bp in length, containing 13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNA), and 2 ribosomal RNA genes (rRNA). This overall base composition of the complete mitogenome for this species included 27.52% A, 24.46% T, 16.99% G and 31.04% C. The phylogenetic analysis revealed that the H. cruentatus has the closest relationship with Pristigenys niphonia. This study provides an important resource for reviewing the phylogenetic relationships and taxonomic status of this species.

| S-EPMC8291074 | biostudies-literature

Insights into molecular structure, genome evolution and phylogenetic implication through mitochondrial genome sequence of Gleditsia sinensis.

Project description:Gleditsia sinensis is an endemic species widely distributed in China with high economic and medicinal value. To explore the genomic evolution and phylogenetic relationships of G. sinensis, the complete mitochondrial (mt) genome of G. sinensis was sequenced and assembled, which was firstly reported in Gleditsia. The mt genome was circular and 594,121 bp in length, including 37 protein-coding genes (PCGs), 19 transfer RNA (tRNA) genes and 3 ribosomal RNA (rRNA) genes. The overall base composition of the G. sinensis mt genome was 27.4% for A, 27.4% for T, 22.6% for G, 22.7% for C. The comparative analysis of PCGs in Fabaceae species showed that most of the ribosomal protein genes and succinate dehydrogenase genes were lost. In addition, we found that the rps4 gene was only lost in G. sinensis, whereas it was retained in other Fabaceae species. The phylogenetic analysis based on shared PCGs of 24 species (22 Fabaceae and 2 Solanaceae) showed that G. sinensis is evolutionarily closer to Senna species. In general, this research will provide valuable information for the evolution of G. sinensis and provide insight into the phylogenetic relationships within the family Fabaceae.

| S-EPMC8295344 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data