Browse
Submit Data
Databases
API
Help

Dataset Information

16 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

The complete mitochondrial genome of the pink sea fan, Eunicella verrucosa (Pallas, 1766)

ABSTRACT: Abstract The pink sea fan, Eunicella verrucosa (Pallas, 1766), inhabits rocky substrates across the northeast Atlantic and the western Mediterranean. Across much of its range it has been detrimentally affected by fishing. DNA from 17 E. verrucosa specimens was amplified by phi29-induced rolling circle amplification. Following purification by sodium acetate-ethanol precipitation, the circular genomic DNA was sequenced on an Illumina MiSeq v2. Specimens originated from sites along the west coast of Ireland, southwest Wales, southwest/southern England, northwest France, southern Portugal, and the Mediterranean coast of northeast Spain. All samples had identical mitochondrial genome sequences of 19,267 bp and included 14 protein-coding genes (including the mutS gene), two ribosomal RNA subunits (12S and 16S) and one methionine tRNA gene. Two genes (nad2 and nad5) overlapped by 13 bp; all other genes were separated by non-coding intergenic regions. All protein-coding genes had the same start codon (ATG) and a TAA or TAG stop codon, except for cox1 that terminated with the incomplete stop codon T--. The mitochondrial genome of E. verrucosa (MW588805) showed 99.72% similarity with that of a related sea fan species, Eunicella cavolini, with six SNPs and a 49 bp deletion between nad5 and nad4 in E. verrucosa distinguishing the two.

SUBMITTER: Hooper L

PROVIDER: S-EPMC8547875 | biostudies-literature |

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Similar Datasets

The complete mitochondrial genome of Pink warty sea cucumber (Cercodemas anceps Selenka, 1867).

Project description:In this study, we sequenced the circular mitochondrial genome (mitogenome) of Cercodemas anceps. This genome was determined to measure 16,539 bp in length and contain 13 protein-coding genes (PCGs), 22 tRNA genes, and 2 rRNA genes. The longest gene was observed to be nad5, which measures 1,641 bp in length and is located at position 6,540 ∼ 8,180 of the C. anceps mitogenome. One PCG, nad6, and five tRNA genes (tRNASer(UCN) , tRNAGln , tRNAAla , tRNAVal, and tRNAAsp ) were located on the light chain, and the other genes were located on the heavy chain. A phylogenetic tree was constructed with the mitogenome sequences of 26 types of echinoderm species, and the results show that C. anceps is most closely related to C. quadrangularis.

| S-EPMC8006909 | biostudies-literature

The complete mitochondrial genome of Hemitripterus villosus (Pallas, 1814) from Zhoushan archipelago.

Project description:In this study, we used whole genome sequencing to obtain the complete mitochondrial genome of Hemitripterus villosus. This mitochondrial genome, consisting of 17,449 base pairs (bp), contains 13 protein-coding genes, 2 ribosomal RNAs, 22 transfer RNAs and 2 noncoding control regions (control region and origin of light-strand replication) as those found in other vertebrates. Control region, of 1799 bp in length, is located between tRNAPro and tRNAPhe. We identified short tandem repeat sequences in the control region, which contributed largely to the relatively long mitogenome. The complete mitogenome data provides useful genetic markers for the studies on the molecular identification, phylogenetic analysis and conservation genetics.

| S-EPMC8366612 | biostudies-literature

The complete mitochondrial genome of the Kaloula verrucosa (Anura: Microhylidae) and phylogenetic analyses.

Project description:The first complete mitochondrial genome of a Kaloula verrucosa frog was characterized in this work. The mitogenome was 17,061 base pairs (bp) in length, containing 13 protein-coding genes (PCGs), 2 rRNA genes, 22 tRNA genes, and a control region (D-loop). The overall base composition was 29.65% A, 30.77% T, 25.41% C and 14.17% G. Besides, the gene arrangement was identical to that observed in vertebrates. Five of 13 PCGs (COII, ATP6, COIII, ND3 and ND4) were ended with incomplete stop codon T. Except for ND6 gene encoded on L-strand, all other PCGs were encoded on H-strand. The non-coding region was 1665?bp in size, which was heavily biased to A?+?T (65.77%). Additionally, we found mitogenome size of all sequenced Kaloula species were bigger than that of Microhyla species, which was ascribe to the difference of D-loop size. Phylogenetic analysis showed that K. verrucosa was the sister species of Kaloula regifera. This work will provide basic molecular data for further molecular evolution and phylogenetic research of K. verrucosa and other microhylids.

| S-EPMC7800625 | biostudies-literature

Complete mitochondrial genome of the Eurasian collared lemming Dicrostonyx torquatus Pallas, 1779 (Rodentia: Arvicolinae).

Project description:The complete mitochondrial genome the Eurasian collared lemming was obtained by using PCR amplification and capillary sequencing (GenBank accession no. KX066190). The collared lemming mitochondrial genome is 16,340 base pairs long and shows the gene order, contents and gene strand asymmetry typical for mammals. The mitogenome sequence provides an important new genomic resource for the collared lemming, which is a model study species in Arctic phylogeography and biotic history.

| S-EPMC5486970 | biostudies-literature

The complete mitochondrial genome of the Pink dentex Dentex gibbosus (Perciformes: Sparidae).

Project description:The Pink dentex (Dentex gibbosus, Rafinesque 1810) is one of the most commercially important Sparidae species and it is often subjected to fraud. Here, we report the complete mitochondrial genome of D. gibbosus. The mitogenome is 16,771?bp in length and contained 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes and 2 non-coding regions. The overall base composition of D. gibbosus mtDNA is: 27.8% for A, 28.60% for C, 16.5% for G, 27.05% for T.

| S-EPMC7799670 | biostudies-literature

The diversity of the Baikal lineage of Hydra oligactis Pallas, 1766: molecular and morphological evidence.

Project description:In this paper, molecular analyses of Baikal hydras from the 'oligactis group', based on COI and ITS1-5.8S-ITS2, and morphological analysis of their holotrichous isorhizas, were performed. Low genetic diversity and shared haplotypes were found between Hydra oligactis Pallas, 1766 and Hydra baikalensis Swarczewsky, 1923 specimens, which is evidence of the mixing of these lineages. Genetic distances among all Baikal hydras (0.006) were less than the interspecific distances of other hydras. The size of hydras and proportions of their holotrichous isorhizas varied depending on microhabitat and environmental conditions. Our combined molecular and morphological approach proves that H. baikalensis is synonymous with H. oligactis.

| S-EPMC7040048 | biostudies-literature

Complete sequence of a sea lamprey (Petromyzon marinus) mitochondrial genome: early establishment of the vertebrate genome organization.

Project description:The complete nucleotide sequence of a sea lamprey (Petromyzon marinus) mitochondrial genome has been determined. The lamprey genome is 16,201 bp in length and contains genes for 13 proteins, two rRNAs, 22 tRNAs and two major noncoding regions. The order and transcriptional polarities of protein-coding genes are basically identical to those of other chordate mtDNAs, demonstrating that the common mitochondrial gene organization of vertebrates was established at an early stage of vertebrate evolution. The two major noncoding regions are separated by two tRNA genes. The first region probably functions as the control region because it contains distinctive conserved sequence blocks (CSB-II and III) common to other vertebrate control regions. The central conserved domain observed in other vertebrate control regions is not found in the lamprey, suggesting that it is a recently evolved functional domain in vertebrates. Noncoding segments are not found in the expected position of the origin of replication for the second strand, suggesting either that one of the tRNA genes has a dual function or that the second noncoding region may function as the second-strand origin. The base composition at the wobble positions of fourfold degenerate codon families is highly biased toward thymine (32.7%). Values of GC- and AT-skew are typical of vertebrate mitochondrial genomes.

| S-EPMC1206387 | biostudies-other

Complete mitochondrial genome of yellowback sea bream Evynnis tumifrons.

Project description:The complete mitochondrial genome of the Evynnis tumifrons was 16 616?bp in length and contained 13 protein-coding genes, 22 transfer RNA genes and 2 ribosomal RNA genes. The overall base composition of E. tumifrons was A 27.05%, T 26.42%, C 29.45% and G 17.07%. Phylogenetic tree construction indicated that Evynnis tumifrons was most closely related to Parargyrops edita and Pagrus auriga. This molecular information will contribute to better understand its evolution and population genetics.

| S-EPMC7800024 | biostudies-literature

The complete mitochondrial genome of the pink stem borer, Sesamia inferens, in comparison with four other Noctuid moths.

Project description:The complete 15,413-bp mitochondrial genome (mitogenome) of Sesamia inferens (Walker) (Lepidoptera: Noctuidae) was sequenced and compared with those of four other noctuid moths. All of the mitogenomes analyzed displayed similar characteristics with respect to gene content, genome organization, nucleotide comparison, and codon usages. Twelve-one protein-coding genes (PCGs) utilized the standard ATN, but the cox1 gene used CGA as the initiation codon; cox1, cox2, and nad4 genes had the truncated termination codon T in the S. inferens mitogenome. All of the tRNA genes had typical cloverleaf secondary structures except for trnS1(AGN), in which the dihydrouridine (DHU) arm did not form a stable stem-loop structure. Both the secondary structures of rrnL and rrnS genes inferred from the S. inferens mitogenome closely resembled those of other noctuid moths. In the A+T-rich region, the conserved motif "ATAGA" followed by a long T-stretch was observed in all noctuid moths, but other specific tandem-repeat elements were more variable. Additionally, the S. inferens mitogenome contained a potential stem-loop structure, a duplicated 17-bp repeat element, a decuplicated segment, and a microsatellite "(AT)(7)", without a poly-A element upstream of the trnM in the A+T-rich region. Finally, the phylogenetic relationships were reconstructed based on amino acid sequences of mitochondrial 13 PCGs, which support the traditional morphologically based view of relationships within the Noctuidae.

| S-EPMC3431856 | biostudies-literature

The complete chloroplast genome of Narcissus 'Pink Charm'.

Project description:The first complete chloroplast (cp) genome of Narcissus 'Pink Charm' was sequenced and characterized using Illumina paired-end data. The assembled cp genome was 159,988 in length with a GC content of 37.82%. A total of 137 genes were annotated, consisting of 91 protein-coding genes, eight ribosomal RNA genes, and 38 transfer RNA genes. The phylogenetic position based on the cp genome data revealed that Narcissus 'Pink Charm' is more closely related to Narcissus poeticus than other relative species.

| S-EPMC8477918 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

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