Browse
Submit Data
Databases
API
Help

Dataset Information

20 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

The complete mitochondrial genome of the pallid seahorse Solegnathus hardwickii (Actinopterygii; Syngnathiformes; Syngnathidae) obtained using next-generation sequencing.

ABSTRACT: The complete mitochondrial genome of Solegnathus hardwickii was determined to be 16,519 bp long circular molecule with a typical gene arrangement of vertebrate mitochondrial. The complete mitochondrial genomes were obtained by conventional and long PCR. Tree constructed using maximum likelihood based on protein-coding genes and ribosomal RNAs showed close relationship of S. hardwickii with Hippocampus spp.

SUBMITTER: Asem A

PROVIDER: S-EPMC7800819 | biostudies-literature |

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Similar Datasets

The complete mitochondrial genome of the Asian river pipefish Doryichthys boaja (Actinopterygii; Syngnathiformes; Syngnathidae) obtained using next-generation sequencing.

Project description:The complete mitochondrial genome of the Asian river pipefish Doryichthys boaja was sequenced. The mitochondrial genome is a circular molecule of 16,439 bp in length, containing 37 mitochondrial genes and a control region. The base composition is 31.03% A, 24.22% C, 14.44% G, and 30.32% T, with an A + T content of 61.35%. All PCGs were initiated by ATG start codon expecting COX1 by GTG. A phylogenetic tree showed that Doryichthys boaja clustered with Microphis brachyurus.

| S-EPMC7800418 | biostudies-literature

Complete mitochondrial genomes of eight seahorses and pipefishes (Syngnathiformes: Syngnathidae): insight into the adaptive radiation of syngnathid fishes.

Project description:BackgroundThe evolution of male pregnancy is the most distinctive characteristic of syngnathids, and their specialized life history traits make syngnathid species excellent model species for many issues in biological evolution. However, the origin of syngnathids and the evolutionary divergence time of different syngnathid species remain poorly resolved. Comprehensive phylogenetic studies of the Syngnathidae will provide critical evidence to elucidate their origin, evolution, and dispersal patterns.ResultsWe sequenced the mitochondrial genomes of eight syngnathid species in this study, and the estimated divergence times suggested that syngnathids diverged from other teleosts approximately 48.8 Mya during the Eocene period. Selection analysis showed that many mitochondrial genes of syngnathids exhibited significantly lower Ka/Ks values than those of other teleosts. The two most frequently used codons in syngnathid fishes were different from those in other teleosts, and a greater proportion of the mitochondrial simple sequence repeats (SSRs) were distributed in non-coding sequences in syngnathids compared with other teleosts.ConclusionsOur study indicated that syngnathid fishes experienced an adaptive radiation process during the early explosion of species. Syngnathid mitochondrial OXPHOS genes appear to exhibit depressed Ka/Ks ratios compared with those of other teleosts, and this may suggest that their mitogenomes have experienced strong selective constraints to eliminate deleterious mutations.

| S-EPMC6560779 | biostudies-literature

Complete mitochondrial genome sequence of the Jayakar's seahorse Hippocampus jayakari Boulenger, 1900 (Gasterosteiformes: Syngnathidae).

Project description:In the present study, we report the complete mitochondrial genome of Jayakar's seahorse, Hippocampus jayakari Boulenger, 1900. The genome of H. jayakari is found to be 16,520 bp in length and has a base composition of A (32.82%), C (23.28%), G (14.13%), and T (29.67%). Similar to other Hippocampus species, it contains a typically conserved structure including 13 protein-coding genes, 2 rRNA genes, 1 control region (D-loop), and 22 tRNA genes. The protein-coding genes had ATG or GTG as the initiation codon and only 6 genes (COX1, ATP8, ATP6, ND4L, ND5 and ND6) terminated by the complete typical stop codon TAA. The lengths of 12S rRNA and 16S rRNA are 939 bp and 1686 bp, respectively. All tRNA genes typically formed a cloverleaf secondary structure, except for tRNA-Ser containing a dihydrouridine arm replacement loop. Hippocampus jayakari exhibited a relatively distant genetic relationship with other 13 Hippocamupus species according to the phylogenetic analysis. The complete mitochondrial genome sequence provided here would be useful for further understanding the evolution of Hippocamupus and conservation genetics of H. jayakari.

| S-EPMC7800713 | biostudies-literature

The complete mitochondrial DNA genome of the Queensland seahorse Hippocampus queenslandicus Horne, 2001 (Gasterosteiformes: Syngnathidae).

Project description:The complete mitochondrial genome of the Queensland seahorse Hippocampus queenslandicus Horne, 2001 (Gasterosteiformes: Syngnathidae) has been amplified and sequenced in this study. The mitogenome was 16,527?bp long with protein-coding genes, 2 ribosomal RNA genes, 22 transfer RNA genes and a non-coding control region. The overall base composition of the genomes was 32.2% for A, 30.1% for T, 14.9% for G, and 22.8% for C with an A?+?T-rich characteristic (62.3%). According to the phylogenetic analysis, H. queenslandicus showed a closer genetic relationship with H. spinosissimus.

| S-EPMC7800332 | biostudies-literature

Next-generation sequencing yields the first complete mitochondrial genome of the ruby dragonet Synchiropus sycorax (Syngnathiformes, Callionymidae).

Project description:The complete mitogenome sequence of the ruby dragonet Synchiropus sycorax was first determined using next-generation sequencing strategy in this study. The circle genome was 16,656 bp in length and consisted of 13 protein-coding genes, 2 ribosomal RNA genes, 22 transfer RNA genes, and 1 control region. The mitochondrial gene arrangement of S. sycorax is similar to those of most other fish species. Results from neighbor-joining phylogenetic analysis showed that S. sycorax clustered with S. splendidus and other species of the family Callionymidae. This study will be valuable for phylogenetic analysis of the genus Synchiropus and the other genera of the order Syngnathiformes.

| S-EPMC7748508 | biostudies-literature

The complete mitochondrial genome of Porites harrisoni (Cnidaria: Scleractinia) obtained using next-generation sequencing.

Project description:In this study, we sequenced the complete mitochondrial genome of Porites harrisoni using ezRAD and Illumina technology. Genome length consisted of 18,630?bp, with a base composition of 25.92% A, 13.28% T, 23.06% G, and 37.73% C. Consistent with other hard corals, P. harrisoni mitogenome was arranged in 13 protein-coding genes, 2 rRNA, and 2 tRNA genes. nad5 and cox1 contained embedded Group I Introns of 11,133?bp and 965?bp, respectively.

| S-EPMC7800593 | biostudies-literature

Complete mitochondrial genome of Sinogastromyzon szechuanensis (Teleostei, Cypriniformes, Balitoridae) obtained using next-generation sequencing.

Project description:The complete mitogenome sequence of Sinogastromyzon szechuanensis was obtained using next generation sequencing and confirmed via overlap-PCR method. The genome was 16,565 bp in length and consisted of 13 protein-coding genes (PCGs), 2 ribosomal RNA genes, 23 transfer RNA genes and 1 control region. The overall nucleotide composition of heavy strand was 30.38% A (5033), 16.62% G (2753), 25.25% T (4182) and 27.75 (4597), with a slight A-T skew (55.63%), which is most obvious in the D-loop and most transfer RNA genes. Mitochondrial genome analyses based on ML analyses yielded identical phylogenetic trees.

| S-EPMC7819126 | biostudies-literature

The complete mitochondrial genome of Ternate False Fusus Brunneifusus ternatanus Gmelin, 1791 (Neogastropoda: Buccinoidea: Melongenidae) obtained using next-generation sequencing.

Project description:In this paper, the complete mitochondrial genome of Ternate False Fusus Brunneifusus ternatanus Gmelin, 1791 was determined and characterized for the first time from the South China Sea. Our results showed that the length of the whole mitogenome of B. ternatanus was 16,254 bp and the mitogenome consisted of 22 tRNA genes, 13 protein-coding genes (PCGs), and 2 rRNA genes. Furthermore, the nucleotide composition of this mitogenome is significantly biased with G + C contents of 31.85% (the base content was 30.38% A, 16.17% G, 37.77% T, and 15.68% C). All PCGs shared ATG as the initiation codon, and stop codon of TAA or TAG, with the exception of COX2 which ended with a single T. The phylogenetic tree showed that B. ternatanus was first clustered with Hemifusus tuba, and from a single distinct cluster. The new complete mitochondrial genome provides new insight into the phylogenetic of Melongenidae and its evolution.

| S-EPMC8218847 | biostudies-literature

Characterization of the complete mitochondrial genome of Dactylopterus volitans (Syngnathiformes, Dactylopteridae).

Project description:The complete mitochondrial genome was determined for the flying gurnard Dactylopterus volitans belonging to the family Dactylopteridae. The total length of the D. volitans mitochondrial genome is 16,632 bp, which consists of 13 protein-coding genes, 22 tRNA genes, two rRNA genes, and a control region. It has the typical vertebrate mitochondrial gene arrangement. Phylogenetic analysis using mitochondrial genomes of 20 species showed that D. volitans formed a well-supported monophyletic group with other Dactylopteridae species.

| S-EPMC7748829 | biostudies-literature

Hippocampusjapapigu, a new species of pygmy seahorse from Japan, with a redescription of H.pontohi (Teleostei, Syngnathidae).

Project description:The pygmy seahorse Hippocampusjapapigusp. n. is described based on three specimens, 13.9-16.3 mm SL, collected from a mixed soft coral and algae reef at 11 m depth at Hachijo-jima Island, Izu Islands, Japan. The new taxon shares morphological synapomorphies with the previously described central Indo-Pacific pygmy seahorses, H.colemani, H.pontohi, H.satomiae, and H.waleananus, including extremely small size, 12 trunk rings, strongly raised continuous cleithral ring, snout spine, large spine on the eighth lateral and fifth and 12 superior trunk ridges, respectively, and unusual wing-like-protrusions immediately posterior to the head. Hippocampusjapapigusp. n. can be distinguished from all congeners by the following combination of features in the anterodorsal area of the trunk: bilaterally paired wing-like protrusions formed by a single pair of large, truncate spines projecting dorsolaterad on the first superior trunk ridge, followed by a unique elevated dorsal ridge formed by triangular bony mounds dorsally on the second to fourth superior trunk ridges. In contrast, H.pontohi possesses a pair of large truncate spines projecting strongly laterad on both the first and second superior trunk ridges followed by flat surfaces dorsally on the third and fourth superior trunk rings. The new species can be further differentiated by genetic divergence from H.pontohi (an uncorrected p-distance of 10.1% in the mitochondrial COI gene) and a striking reticulated white and brown lattice pattern on the head, trunk, and tail. Hippocampusjapapigusp. n. represents the fifth species of pygmy seahorse recorded in Japan.

| S-EPMC6110155 | 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