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 Holothuria fuscocinerea (Jaeger,1833).

ABSTRACT: In this study, the complete mitochondrial genome of Holothuria fuscocinerea was sequenced on an Illumina platform and assembled using NovoPlasty v. 2.7.1. It was submitted to NCBI GenBank and is available with accession number MN542416. The genome was 15,827 bp in size and contains 22 tRNA genes, 12 protein-coding genes, and 2 rRNA genes. The composition of A + T in Holothura spinifera mtDNA was 60.30%. Except ND6 and 5 tRNAs, the others are not on the H-strand. The phylogenetic relationship of 13 species of sea cucumber were analyzed using the neighbor-joining method by software MEGA5.0. Holothuria fuscocinerea was most closely related to Holothuria polii.

SUBMITTER: Sun Y

PROVIDER: S-EPMC7720973 | biostudies-literature | 2019 Dec

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

The complete mitochondrial genome of Holothuria fuscocinerea (Jaeger,1833).

Sun Yi Y Ding Beichen B Guo Chao C Han Rui R Li Junhao J Rong Feixiang F Ding Jun J

Mitochondrial DNA. Part B, Resources 20191209 1

In this study, the complete mitochondrial genome of Holothuria fuscocinerea was sequenced on an Illumina platform and assembled using NovoPlasty v. 2.7.1. It was submitted to NCBI GenBank and is available with accession number MN542416. The genome was 15,827 bp in size and contains 22 tRNA genes, 12 protein-coding genes, and 2 rRNA genes. The composition of A + T in Holothura spinifera mtDNA was 60.30%. Except ND6 and 5 tRNAs, the others are not on the H-strand. The phylogenetic re ...[more]

PMID: 33366409

Similar Datasets

Analysis of Complete Mitochondrial Genome of Bohadschia argus (Jaeger, 1833) (Aspidochirotida, Holothuriidae).

Project description:Bohadschia argu is a kind of sea cucumber with high economic value; it is the only undisputed species in the genus Bohadschia. In this study, the complete mitochondrial genome (mitogenome) of B. argus was acquired through high-throughput sequencing. The mitochondrial genome of B. argus was 15,656 bp in total length and contained a putative control region (CR) and 37 typical genes of animal mitochondrial genomes, including 13 protein-coding genes (PCGs), 2 ribosomal RNA genes (rrnS and rrnL) and 22 transfer RNA genes (tRNA). The sizes of the PCGs ranged from 168 bp to 1833 bp, and all PCGs except nad6 were encoded on the heavy chain (H). Both rrnS and rrnL were also encoded on the H chain. Twenty-two tRNA genes had positive AT skew and GC skew. All tRNAs had a typical cloverleaf secondary structure except for trnI, in which an arm of dihydrouridine was missing. B. argus shared the same gene arrangement order (the echinoderm ground pattern) as other species in Aspidochirotida. Phylogenetic analysis clearly revealed that B. argus belongs as a member of the Holothuriidae, and it is closely related to members of Actinopyga and Holothuria.

| S-EPMC9179316 | biostudies-literature

Holothuria scabra isolate:Jaeger 1833

Project description:Holothuria scabra isolate:Jaeger 1833 Genome sequencing and assembly

| PRJNA542245 | ENA

Characterization and phylogenetic analysis of the complete mitochondrial genome of Actinopyga lecanora (Jaeger, 1833) (Holothuriida: Holothuriidae).

Project description:The white-bottomed sea cucumber, Actinopyga lecanora, is a valuable inshore fisheries resource which is famous for its high nutrition and pharmacological compounds. However, due to morphological plasticity and limited molecular phylogenetic studies, the taxonomic histories in the genus Actinopyga have not been completely resolved yet. Moreover, there remains a complex of cryptic species within Actinopyga, many of which are incorrectly assigned within the family Holothuriidae. In this study, we report the complete mitochondrial genome of A. lecanora. The mitogenome has 15,568 base pairs (63.40% A + T content) and is made up of a total of 37 genes (13 protein-coding, 22 transfer RNAs and 2 ribosomal RNAs), plus a putative control region. This study offers useful mitogenome data for future phylogenetic and taxonomic classification of Holothuriidae.

| S-EPMC8425705 | biostudies-literature

Characterization and phylogenetic analysis of the complete mitochondrial genome of prickly redfish Thelenota ananas (Jaeger, 1833).

Project description:In this study, the complete mitochondrial genome (mitogenome) of prickly redfish Thelenota ananas (Jaeger, 1833) was determined and characterized from the South China Sea using next-generation sequencing. Our results showed that the length of the whole mitogenome in prickly redfish was 15,858 bp and the mitogenome was consist of 22 tRNA genes, two rRNA genes, 13 protein-coding genes (PCGs), and one control region. Furthermore, the nucleotide composition was significantly biased (composition of A, G, T, and C was 28.20%, 22.64%, 33.53%, and 15.63%, respectively) with AT contents of 61.73%. All the PCGs shared a standard initiation codon ATG or GTG. CYTB and ND6 genes terminated with an incomplete stop codon T, while others ended with TAA or TAG. Our phylogenetic analysis showed that Thelenota ananas was clustered with the species of genus Stichopus, and formed sister branches with species of other genera within the family Stichopodidae clade.

| S-EPMC8266223 | biostudies-literature

First record of Holothuria (Metriatyla) scabra Jaeger, 1833 (Echinodermata: Holothuroidea) from the coastal waters of the United Arab Emirates.

Project description:The presence of an endangered and economically valuable species of sea cucumber, Holothuria (Metriatyla) scabra Jaeger, 1833, was investigated in the Alqurm Wa Lehhfaiiah Protected Area near the city of Kalba in the Emirate of Sharjah. Sea cucumber specimens were collected, and identification was first conducted using morphological keys. H. scabra identification was confirmed through microscopic observation of ossicles. Though this species is known to occur in other regions along the Gulf of Oman, this paper represents the first published record of H. scabra, in the coastal waters of the United Arab Emirates.

| S-EPMC6166627 | biostudies-literature

The complete mitochondrial genome of black sea cucumber Holothuria leucospilota (Aspidochirotida holothuriidae).

Project description:The black sea cucumber, Holothuria leucospilota, is an ecologically and economically important holothuroid in China due to broader environmental adaptation and valuable pharmacological compounds. However, the wild stocks of H. leucospilota, have been declining steadily due to overexploitation in recent years. The stock enhancement programme has become an increasingly important priority. In this study, we report the complete mitochondrial genome of H. leucospilota. The mitogenome has 15,839 base pairs (57.6% A + T content) and made up of total of 37 genes (13 protein-coding, 22 transfer RNAs and 2 ribosomal RNAs), and a putative control region. The complete mitogenomes of H. leucospilota will provide useful genetic information for future conservation and management of this valuable and vulnerable species.

| S-EPMC7707278 | biostudies-literature

The complete mitochondrial genome of rockfish Sebastes oculatus Valenciennes, 1833 from southwest Atlantic ocean.

Project description:The mitogenome of rockfish, Sebastes oculatus, has been determined for the first time. Assembled mitogenome was 16,767 bp in length, including 13 protein-coding genes, 22 transfer RNA and two ribosomal RNA genes as well as the non-coding region. The order and structure are the same as those of other Sebastes species. S. oculatus was sister to S. nigrocinctus and this clade is closely related with S. rubrivinctus, as well as support for previously published complete mitochondrial genome trees (Sandel et al. 2018). The mitogenome of S. oculatus provides significant DNA molecular data for further identification and phylogenetic analysis within Scorpaenid.

| S-EPMC7707287 | biostudies-literature

Characterization of the complete mitochondrial genome of a holothurians species: Holothuria hilla (Holothuroidea: Holothuriidae).

Project description:Mitochondrial genome sequence is a great potential method to both resolve disputed taxonomic issues and to infer phylogenetic relationships among holothurians. In this study, we present the complete mitochondrial genome of Holothuria hilla which was 15,744 bp in length, containing 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes, and a putative control region. The gene content and arrangement were typical for Holothuroidea ground pattern. The overall base composition was 32.43% A, 27.20% T, 24.35% C and 16.02% G, showing a bias toward A + T (59.63%). The maximum-likelihood tree based on the concatenated 13 protein-coding genes revealed the phylogenetic relationships among the Holothuroidea species.

| S-EPMC7706501 | biostudies-literature

The complete chloroplast genome and phylogenetic analysis of Astragalus scaberrimus Bunge 1833.

Project description:Astragalus scaberrimus Bunge 1833 is a widespread perennial herb in northern China. The plant has white flowers and white hairs on the leaves and stems. To determine the chloroplast genome, total DNA was extracted from a sample and sequenced on the Illumina HiSeq4000 platform. After sequencing, the reads of chloroplast DNA were assembled and annotated via NOVOPlasty and PGA respectively. The chloroplast genome of this plant has a circular form with a length of 123,492 bp, a 34% GC content and IR loss. After annotation, a total of 113 genes were predicted for this cp genome, comprising 79 encoded proteins, 4 rRNAs and 30 tRNAs. The evolutionary history indicates that A. scaberrimus was grouped within Astragalus and formed a clade with Astragalus laxmannii with a 100% BS support value. The complete chloroplast genome can serve as a reference for future studies on molecular biology, evolution, population genetics, taxonomy and resource protection.

| S-EPMC8594883 | biostudies-literature

Sequencing and analysis of the complete mitochondrial genome of the surgeon fish Acanthurus leucosternon BENNETT 1833 (Perciformes: acanthuridae) with phylogenetic consideration.

Project description:In this study, the complete mitochondrial genome of Acanthurus leucosternon was determined. The genome is circular, double-stranded DNA molecule with 16,434 bp in length (EU 136032). The structure, gene organization, and gene order is similar as in other vertebrates. The overall base composition is A (29.29%), C (28.53%), T (26.37%), G (15.81%), and with 44.33% G + C content. Overlapping observed between contiguous genes is encoded in the opposite strands. The two 12S and 16S rRNA genes consist of 949 and 1690 nucleotides, respectively. Non-coding control region is 754 bp long and origin of replication is located in the WANCY cluster. Conserved domains in the control regions and secondary structures for the OL regions are also predicted. Molecular phylogenetic analysis using Maximum-Likelihood method of A. leucosternon based on the protein-coding gene sequence was also studied.

| S-EPMC7799982 | biostudies-literature