Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

The complete mitochondrial genome of the plumed worm Diopatra cuprea (Annelida: Onuphidae).

ABSTRACT: In this study, we describe the complete mitochondrial genome of Diopatra cuprea (Bosc, 1802). The mitogenome was found to contain 14,990 base pairs (67.53% A + T content), with a total of 37 genes (13 protein coding, 22 transfer RNAs, and 2 ribosomal RNAs). This study also examined mitogenome phylogenetics relationships of closely related species and recovered that D. cuprea is closely related to eunicids. This work has added to the genetic resources for furthering evolutionary studies of Annelida.

SUBMITTER: Hamilton LE

PROVIDER: S-EPMC8667876 | biostudies-literature | 2022

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

The complete mitochondrial genome of the plumed worm Diopatra cuprea (Annelida: Onuphidae).

Hamilton Lauren E LE Preston Gabriel C GC Wheeler Jade B JB Janosik Alexis M AM Bogantes Viktoria E VE

Mitochondrial DNA. Part B, Resources 20211210 1

In this study, we describe the complete mitochondrial genome of Diopatra cuprea (Bosc, 1802). The mitogenome was found to contain 14,990 base pairs (67.53% A + T content), with a total of 37 genes (13 protein coding, 22 transfer RNAs, and 2 ribosomal RNAs). This study also examined mitogenome phylogenetics relationships of closely related species and recovered that D. cuprea is closely related to eunicids. This work has added to the genetic resources for furthering evolutionary stu ...[more]

PMID: 34912967

Similar Datasets

Cryptic mtDNA Diversity of Diopatra cuprea (Onuphidae, Annelida) in the Northwestern Atlantic Ocean.

Project description:Marine annelid taxonomy is experiencing a period of rapid revision, with many previously "cosmopolitan" species being split into species with more limited geographic ranges. This is exemplified by the Diopatra genus, which has recently witnessed dozens of new species descriptions rooted in genetic analyses. In the northwestern Atlantic, the name D. cuprea (Bosc 1802) has been applied to populations from Cape Cod through the Gulf of Mexico, Central America, and Brazil. Here, we sequenced mitochondrial cytochrome oxidase I (COI) in D. cuprea populations from the Gulf of Mexico to Massachusetts. We find evidence for several deep mitochondrial lineages, suggesting that cryptic diversity is present in the D. cuprea complex from this coastline.

| S-EPMC10136041 | biostudies-literature

Phylogeny and Cryptic Diversity of Diopatra (Onuphidae, Annelida) in the East Atlantic.

Project description:Diopatra Audouin & Milne-Edwards, 1833 is a species rich genus that is common in tropical and subtropical regions. The genus is readily identified by its striking, spiral branchiae, but species identification has historically been challenging due to a high variation in diagnostic characters used. This study aims to reconstruct the phylogeny of Diopatra with molecular markers and assess the species diversity of West African Diopatra with the species delimitation programs bPTP and BPP. Specimens were collected from Morocco to Angola, and the markers COI, 16S and 28S were sequenced from 76 specimens. The constructed phylogeny retrieved Diopatra as monophyletic, as well as five well supported clades within the genus. All clades were defined by morphological characters, some of which have previously not been considered to have high phylogenetic or taxonomical value. Species delimitation analyses recovered 17 new species, several of which were not readily identified morphologically. One species complex comprising between one and 12 species was left unresolved due to incongruence between the species delimitation methods and challenging morphology. Our results indicate that the diversity of Diopatra is significantly underestimated, where this regional study near to doubled the number ofknown species from the East Atlantic.

| S-EPMC8869602 | biostudies-literature

The mitochondrial genome of the bone-eating worm Osedaxrubiplumus(Annelida, Siboglinidae).

Project description:Osedaxrubiplumus(Annelida, Siboglinidae)uses heterotrophic bacteria to feed onvertebrate carcasses and is currently found in the Pacific, Antarctic and Indian Ocean.Here, we report its nearly complete mitochondrial genomes assembled for 2 individuals, one from the East Pacific and the other from the Southwest Indian Ocean. Recoveredmitogenomes were 15591 and 15972 bp in length, with both consisting of 37 typical metazoan mitochondrial genes. All genes were transcribed from the same strand, and arranged in the same order as the other siboglinids, revealing conserved gene arrangement withinSiboglinidae. Phylogeneticanalysis of 13 protein coding genes confirms the placement of Osedaxsister to the Vestimentifera+Sclerolinum clade.

| S-EPMC7510606 | biostudies-literature

Live to Die Another Day: Regeneration in Diopatra aciculata Knox and Cameron, 1971 (Annelida: Onuphidae) Collected as Bait in Knysna Estuary, South Africa.

Project description:Regeneration is critical for survivorship after injury, sublethal predation, and asexual reproduction; it allows individuals to recover, potentially enabling populations of bait species to overcome the effects of bait collection through incidental asexual reproduction. Opportunities for regeneration are created when worms break during collection (which happens more often than not) and are thrown back into the estuary. Additionally, the trade and movement of bait could result in the range expansion of invasive species. This study investigated bait collection habits of local fishermen and the in situ incidence of regeneration in the estuarine moonshine worm, Diopatra aciculata. The evidence shows that this species is capable of anterior and posterior regeneration. The disproportionately small percentage of worms that seem to be recovering from the degree of damage that may be inflicted during bait collection suggests that regeneration may not help worms to withstand the effects of bait collection. However, the continuous movement and discarding of even small numbers of bait in other estuaries can lead to range expansion through incremental build-up, forming new populations, if these fragments are large enough to regenerate.

| S-EPMC10045322 | biostudies-literature

Sulfate-reducing bacteria in tubes constructed by the marine infaunal polychaete Diopatra cuprea.

Project description:Marine infaunal burrows and tubes greatly enhance solute transport between sediments and the overlying water column and are sites of elevated microbial activity. Biotic and abiotic controls of the compositions and activities of burrow and tube microbial communities are poorly understood. The microbial communities in tubes of the marine infaunal polychaete Diopatria cuprea collected from two different sediment habitats were examined. The bacterial communities in the tubes from a sandy sediment differed from those in the tubes from a muddy sediment. The difference in community structure also extended to the sulfate-reducing bacterial (SRB) assemblage, although it was not as pronounced for this functional group of species. PCR-amplified 16S rRNA gene sequences recovered from Diopatra tube SRB by clonal library construction and screening were all related to the family Desulfobacteriaceae. This finding was supported by phospholipid fatty acid analysis and by hybridization of 16S rRNA probes specific for members of the genera Desulfosarcina, Desulfobacter, Desulfobacterium, Desulfobotulus, Desulfococcus, and Desulfovibrio and some members of the genera Desulfomonas, Desulfuromonas, and Desulfomicrobium with 16S rRNA gene sequences resolved by denaturing gradient gel electrophoresis. Two of six SRB clones from the clone library were not detected in tubes from the sandy sediment. The habitat in which the D. cuprea tubes were constructed had a strong influence on the tube bacterial community as a whole, as well as on the SRB assemblage.

| S-EPMC535212 | biostudies-literature

Complete mitochondrial genome of yellow meal worm (Tenebrio molitor).

Project description:The yellow meal worm (Tenebrio molitor L.) is an important resource insect typically used as animal feed additive. It is also widely used for biological research. The first complete mitochondrial genome of T. molitor was determined for the first time by long PCR and conserved primer walking approaches. The results showed that the entire mitogenome of T. molitor was 15 785 bp long, with 72.35% A+T content [deposited in GenBank with accession number KF418153]. The gene order and orientation were the same as the most common type suggested as ancestral for insects. Two protein-coding genes used atypical start codons (CTA in ND2 and AAT in COX1), and the remaining 11 protein-coding genes started with a typical insect initiation codon ATN. All tRNAs showed standard clover-leaf structure, except for tRNA(Ser) (AGN), which lacked a dihydrouridine (DHU) arm. The newly added T. molitor mitogenome could provide information for future studies on yellow meal worm.

| S-EPMC4790282 | biostudies-literature

Occurrence of Diopatramarocensis (Annelida, Onuphidae) in the eastern Mediterranean.

Project description:The present study deals with the presence of Diopatramarocensis in the eastern Mediterranean. This species is small-sized and inhabited muddy bottom near the opening of rivers or lagoons [salinity range: 33-39‰] in the Aegean and Levantine Seas, and reached a maximum density of 90 ind.m(-2) in Mersin Bay. This species might be an alien species that was introduced from the East Atlantic (near Gibraltar) to the eastern Mediterranean via ballast water of ships, as it has never been reported from the western Mediterranean Sea.

| S-EPMC4205737 | biostudies-literature

The complete mitogenome of nereid worm, Neanthes glandicincta (Annelida: Nereididae).

Project description:In this study, the complete mitogenome sequence of nereid worm, Neanthes glandicincta (Annelida: Nereididae), has been decoded for the first time by PCR amplification and Sanger sequencing methods. The overall base composition of N. glandicincta mitogenome is 31.5% for A, 22.2% for C, 14.5% for G and 31.7% for T, and has GC content of 36.7%. The assembled mitogenome, consisting of 16,126 bp, has unique 13 protein-coding genes (PCGs), 22 transfer RNAs and 2 ribosomal RNAs genes. The complete mitogenome of N. glandicincta shows 65% identities to Namalycastis abiuma. All PCGs, tRNA and rRNA genes were encoded on H-strand. The potential D-loop is 1625 bp in length and located between tRNA-Gly and tRNA-Met. The complete mitogenome provides essential and important DNA molecular data for further phylogenetic and evolutionary analysis for Annelida.

| S-EPMC7799960 | biostudies-literature

Insights into Environmental Drivers on the Reproductive Cycle of Diopatra neapolitana (Polychaeta: Onuphidae).

Project description:The reproductive cycle of Diopatra neapolitana was studied over two years in Redondela (NW Spain), considering both the monthly evolution of the percentage of individuals with oocytes and the variation of the mean oocyte size. Moreover, since three other species of Diopatra have recently been documented in regions geographically close to NW Spain, we first confirmed the identity of this species by carrying out a morphological identification of a representative number of the specimens collected. Our data showed a discontinuous reproductive season, with a period of proliferation and maturation of oocytes from January to September and asynchronous spawning events between July and October. Then, a resting period in the months of November and December was observed. We also explored the influence of some relevant environmental factors (namely, water temperature, photoperiod, salinity, primary production and upwelling index) on the observed reproductive cycle. The results suggest that water temperature is one of the most important drivers of the reproductive cycle for this species. Particularly, in Ría de Vigo, the reproductive cycle seems to be influenced by upwelling events of deep cold water that occur frequently between March and September, and that could act as a spawning-inducing switch.

| S-EPMC9598824 | biostudies-literature

Complete Mitochondrial Genome of a Tongue Worm Armillifer agkistrodontis.

Project description:Armillifer agkistrodontis (Ichthyostraca: Pantastomida) is a parasitic pathogen, only reported in China, which can cause a zoonotic disease, pentastomiasis. A complete mitochondrial (mt) genome was 16,521 bp comprising 13 protein-coding genes (PCGs), 22 tRNA genes, 2 rRNA genes, and 1 non-coding region (NCR). A phylogenetic tree drawn with the concatenated amino acid sequences of the 6 conserved PCGs (atp6, cox1-3, and nad2) showed that A. agkistrodontis and Armillifer armillatus constituted a clade Pentastomida which was a sister group of the Branchiura. The complete mt genome sequence of A. agkistrodontis provides important genetic markers for both phylogenetic and epidemiological studies of pentastomids.

| S-EPMC5266366 | biostudies-literature