Browse
Submit Data
Databases
API
Help

Dataset Information

31 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Complete mitochondrial genome of the crinoid echinoderm, Florometra species (Echinodermata, Crinoidea).

ABSTRACT: In this study, we report the sequence of the mitochondrial genome (mitogenome) of the crinoid echinoderm, Florometra species (Echinodermata, Crinoidea). The complete mitogenome of Florometra sp. was 15,792 base pairs long and was composed of 13 protein-coding genes (PCGs), two ribosomal RNA (rRNA) genes, 22 transfer RNA (tRNA) genes, and three regions of unassigned sequence (UAS) including one putative control region. Unique nucleotide composition, a clear positive bias for T with an apparent loss of C in PCGs as observed in the Crinoidea mitogenomes, was also seen in the Florometra sp. mitogenome (45% T, 12% C). Phylogenetic analysis with the concatenated nucleotide sequences of entire PCGs of echinoderms confirmed that Florometra sp. is highly related to F. serratissima within the family Crinoidea.

SUBMITTER: Nam SE

PROVIDER: S-EPMC7748595 | biostudies-literature |

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Similar Datasets

Computational Fluid Dynamics Analysis of the Fossil Crinoid Encrinus liliiformis (Echinodermata: Crinoidea).

Project description:Crinoids, members of the phylum Echinodermata, are passive suspension feeders and catch plankton without producing an active feeding current. Today, the stalked forms are known only from deep water habitats, where flow conditions are rather constant and feeding velocities relatively low. For feeding, they form a characteristic parabolic filtration fan with their arms recurved backwards into the current. The fossil record, in contrast, provides a large number of stalked crinoids that lived in shallow water settings, with more rapidly changing flow velocities and directions compared to the deep sea habitat of extant crinoids. In addition, some of the fossil representatives were possibly not as flexible as today's crinoids and for those forms alternative feeding positions were assumed. One of these fossil crinoids is Encrinus liliiformis, which lived during the middle Triassic Muschelkalk in Central Europe. The presented project investigates different feeding postures using Computational Fluid Dynamics to analyze flow patterns forming around the crown of E. liliiformis, including experimental validation by Particle Image Velocimetry. The study comprises the analysis of different flow directions, velocities, as well as crown orientations. Results show that inflow from lateral and oral leads to direct transport of plankton particles into the crown and onto the oral surface. With current coming from the "rear" (aboral) side of the crinoid, the conical opening of the crown produces a backward oriented flow in its wake that transports particles into the crown. The results suggest that a conical feeding position may have been less dependent on stable flow conditions compared to the parabolic filtration fan. It is thus assumed that the conical feeding posture of E. liliiformis was suitable for feeding under dynamically changing flow conditions typical for the shallow marine setting of the Upper Muschelkalk.

| S-EPMC4887110 | biostudies-literature

The complete mitochondrial genome of Comaster schlegelii (Crinoidea, Comatulida).

Project description:Comaster schlegelii, belonging to the family Comatulidae, is a variable feather star distributed in the Pacific Ocean. The complete mitochondrial genome of this species was 15,887 bp in length, consisting of 13 protein-coding genes, 22 transport RNA genes, two ribosomal RNA genes and one control region. The whole mitochondrial genome of C. schlegelii had a high AT content of 72.73%. The phylogenetic relationship was reconstructed with 16 relevant echinoderms, which revealed C. schlegelii was closely clustered with Anneissia pinguis in the family Comatulidae.

| S-EPMC8820819 | biostudies-literature

The complete mitochondrial genome of Anneissia intermedia (Crinoidea: Comatulida: Comatulidae).

Project description:Anneissia intermedia (A.H. Clark, 1916) is a common crinoid found in waters along the coastlines of China, Japan, and Korea. In this study, we determined the complete mitogenome of A. intermedia. The genome was found to be 15,874 bp in length and consists of 13 protein-coding genes, 22 tRNAs, and 2 rRNAs. With the exception of Antedon mediterranea, the gene order and genetic characteristics of the A. intermedia mitogenome are identical with those of the mitogenomes of other crinoids. The complete mitogenome of A. intermedia will contribute to enhance our understanding of the phylogeny of crinoids.

| S-EPMC8168746 | biostudies-literature

The complete mitochondrial genome sequence of Stichopus variegatus (Echinodermata: Holothuroidea) and phylogenetic studies of Echinodermata.

Project description:At present, there exist some confusing issues on the species classification and phylogeny in Echinodermata. In this study, we first determined and described the complete mitochondrial genome of Stichopus variegatus. The complete mitogenome sequence had a circular mapping molecular with the total length of 16,315 bp and contained 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes, and a putative control region. To further validate the newly determined sequences, phylogenetic trees involving all the Holothuroidea and other Echinodermata species available in GenBank Database were constructed. These results would be used for the species identification and further phylogenetic studies of Echinodermata.

| S-EPMC7707333 | biostudies-literature

Complete mitochondrial genome analysis of Distolasterias nipon (Echinodermata, Asteroidea, Forcipulatida).

Project description:In this study, we determined the complete mitochondrial genome sequences of Distolasterias nipon belonging to the class Asteroidea in the phylum Echinodermata. The complete mitogenome of D. nipon was 16,193?bp in length and consisted of 13 protein-coding genes (PCGs), 22 tRNAs, and 2 rRNAs. The orders of PCGs and rRNAs were identical to those of the eight recorded mitogenomes of asteroids. The phylogenetic tree determined by the maximum likelihood method revealed that D. nipon was clearly grouped with Aphelasterias japonica and Asterias amurensis, which belong to the family Asteriidae.

| S-EPMC7800799 | biostudies-literature

Complete mitochondrial genome analysis of Aquilonastra batheri (Echinodermata, Asteroidea, Valvatida).

Project description:In this study, we determined the complete mitochondrial genome sequences of Aquilonastra batheri. This is the first study on mitochondrial genome sequencing of the genus Aquilonastra belonging to the family Asterinidae, order Valvatida, and class Asteroidea. The complete mitogenome of A. batheri was 16,463 bp and consisted of 13 protein-coding genes (PCGs), 22 tRNAs, and two rRNAs. The orders of PCGs and rRNA genes were identical to those of nine recorded mitogenomes of asteroids. The phylogenetic tree determined by the maximum likelihood method revealed that A. batheri was clearly grouped with Patiria pectinifera, which belongs to the family Asterinidae.

| S-EPMC7800510 | biostudies-literature

Circumpolar dataset of sequenced specimens of Promachocrinus kerguelensis (Echinodermata, Crinoidea).

Project description:This circumpolar dataset of the comatulid (Echinodermata: Crinoidea) Promachocrinus kerguelensis (Carpenter, 1888) from the Southern Ocean, documents biodiversity associated with the specimens sequenced in Hemery et al. (2012). The aim of Hemery et al. (2012) paper was to use phylogeographic and phylogenetic tools to assess the genetic diversity, demographic history and evolutionary relationships of this very common and abundant comatulid, in the context of the glacial history of the Antarctic and Sub-Antarctic shelves (Thatje et al. 2005, 2008). Over one thousand three hundred specimens (1307) used in this study were collected during seventeen cruises from 1996 to 2010, in eight regions of the Southern Ocean: Kerguelen Plateau, Davis Sea, Dumont d'Urville Sea, Ross Sea, Amundsen Sea, West Antarctic Peninsula, East Weddell Sea and Scotia Arc including the tip of the Antarctic Peninsula and the Bransfield Strait. We give here the metadata of this dataset, which lists sampling sources (cruise ID, ship name, sampling date, sampling gear), sampling sites (station, geographic coordinates, depth) and genetic data (phylogroup, haplotype, sequence ID) for each of the 1307 specimens. The identification of the specimens was controlled by an expert taxonomist specialist of crinoids (Marc Eléaume, Muséum national d'Histoire naturelle, Paris) and all the COI sequences were matched against those available on the Barcode of Life Data System (BOLD: http://www.boldsystems.org/index.php/IDS_OpenIdEngine). This dataset can be used by studies dealing with, among other interests, Antarctic and/or crinoid diversity (species richness, distribution patterns), biogeography or habitat / ecological niche modeling. This dataset is accessible through the GBIF network at http://ipt.biodiversity.aq/resource.do?r=proke.

| S-EPMC3713352 | biostudies-literature

Complete mitochondrial genome of the feather star Cenometra bella (Hartlaub, 1890) (Crinoidea: Colobometridae).

Project description:The complete mitochondrial genome of the feather star Cenometra bella was sequenced in this study. The mitogenome is 15,872 bp in length, with 13 PCGs, 22 tRNA, and two rRNA, and nucleotide composition was as follows: 24.38% A, 47.79% T, 11.16% C, and 16.68% G. Phylogenetic analyses place C. bella as closely related to Stephanometra indica, consistent with previous inferences.

| S-EPMC9176372 | biostudies-literature

Characterization of the complete mitochondrial genome of Thyonella gemmata (Echinodermata: Cucumariidae).

Project description:Thyonella gemmata , also known as the Green sea cucumber, is a biomedically and ecologically important species. In this study, the complete mitogenome of T. gemmata (Echinodermata: Holothuroidea) collected from the Florida Panhandle, USA is reported. The mitochondrial genome of T. gemmata consisted of 15,696 base pairs, and was composed of 36.10% A, 28.27% T, 23.18% C, and 12.45% G. There were 13 protein coding genes, 22 tRNA genes, and 2 rRNA genes within the mitogenome of T. gemmata. Mapping out the complete mitochondrial genome of T. gemmata, will help aid in future evolutionary studies and can be applied to future phylogenetic research of holothurians and related species.

| S-EPMC8462864 | biostudies-literature

Uncovering the hidden diversity of Mississippian crinoids (Crinoidea, Echinodermata) from Poland.

Project description:Partial crinoid crowns and aboral cups are reported from the Mississippian of Poland for the first time. Most specimens are partially disarticulated or isolated plates, which prevent identification to genus and species, but regardless these remains indicate a rich diversity of Mississippian crinoids in Poland during the Mississippian, especially during the late Viséan. Lanecrinus? sp. is described from the late Tournaisian of the Dębnik Anticline region. A high crinoid biodiversity occurred during late Viséan of the Holy Cross Mountains, including the camerate crinoids Gilbertsocrinus? sp., Platycrinitidae Indeterminate; one flexible crinoid; and numerous eucladid crinoids, including Cyathocrinites mammillaris (Phillips), three taxa represented by partial cups left in open nomenclature, and numerous additional taxa known only from isolated radial plates, brachial plates, and columnals. To date, the youngest occurrence of Gilbertsocrinus was the early Viséan of the United States, thus the present finding in upper Viséan extends this genus range. Furthermore, the occurrence of Lanecrinus? sp. expands the Western European range of this genus into the Tournaisian. A single partially disarticulated crown, Crinoidea Indeterminate B, is described from the Serpukhovian of the Upper Silesian Coal Basin. In addition, several echinoid test plates and spines are also reported.

| S-EPMC7759130 | 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