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 cryptic species in peanut worm Sipunculus nudus (Sipuncula, Sipunculidae) from Beibu Bay.

ABSTRACT: The peanut worm Sipunculus nudus is an economic important species in the fishery and aquaculture in Indo-West Pacific. However, it is a species complex consisting of cryptic species, which can be difficult to identify based on morphology. Here, we report the complete mitochondrial genome sequence of S. nudus from Beibu Bay. The mitogenome has 15,375 base pairs and made up of total of 38 genes (13 protein-coding, 23 transfer RNAs, and two ribosomal RNAs), and a putative control region. There were 5948 mutations sites between Chinese and French populations. This study adds a distinct mitogenome of S. nudus, and will provide useful genetic information for future genetic variation identification and genetic diversity evaluation of this economic valuable marine benthic invertebrate.

SUBMITTER: Zhong S

PROVIDER: S-EPMC7800096 | biostudies-literature | 2018 Apr

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

The complete mitochondrial genome of the cryptic species in peanut worm Sipunculus nudus (Sipuncula, Sipunculidae) from Beibu Bay.

Zhong Shengping S Zhao Yanfei Y Zhang Qin Q Chen Xiuli X

Mitochondrial DNA. Part B, Resources 20180423 2

The peanut worm Sipunculus nudus is an economic important species in the fishery and aquaculture in Indo-West Pacific. However, it is a species complex consisting of cryptic species, which can be difficult to identify based on morphology. Here, we report the complete mitochondrial genome sequence of S. nudus from Beibu Bay. The mitogenome has 15,375 base pairs and made up of total of 38 genes (13 protein-coding, 23 transfer RNAs, and two ribosomal RNAs), and a putative control regi ...[more]

PMID: 33474213

Similar Datasets

Transcriptome Responses to Different Environments in Intertidal Zones in the Peanut Worm Sipunculus nudus.

Project description:The peanut worm (Sipunculus nudus) is an important intertidal species worldwide. Species living in the same aquaculture area might suffer different environmental impacts. To increase knowledge of the molecular mechanisms underlying the response to environmental fluctuations, we performed a transcriptome analysis of S. nudus from different intertidal zones using a combination of the SMRT platform and the Illumina sequencing platform. (1) A total of 105,259 unigenes were assembled, and 23,063 unigenes were perfectly annotated. The results of the PacBio Iso-Seq and IIIumina RNA-Seq enriched the genetic database of S. nudus. (2) A total of 830 DEGs were detected in S. nudus from the different groups. In particular, 33 DEGs had differential expression in the top nine KEGG pathways related to pathogens, protein synthesis, and cellular immune response and signaling. The results indicate that S. nudus from different zones experience different environmental stresses. (3) Several DEGs (HSPA1, NFKBIA, eEF1A, etc.) in pathways related to pathogens (influenza A, legionellosis, measles, and toxoplasmosis) had higher expression in groups M and L. HSPA1 was clearly enriched in most of the pathways, followed by NFKBIA. The results show that the peanut worms from the M and L tidal flats might have suffered more severe environmental conditions. (4) Some DEGs (MKP, MRAS, and HSPB1) were upregulated in peanut worms from the H tidal flat, and these DEGs were mainly involved in the MAPK signaling pathway. These results indicate that the MAPK pathway may play a vital role in the immune response of the peanut worm to the effects of different intertidal flats. This study provides a valuable starting point for further studies to elucidate the molecular basis of the response to different environmental stresses in S. nudus.

| S-EPMC10525638 | biostudies-literature

A Novel Antithrombotic Protease from Marine Worm Sipunculus Nudus.

Project description:Sipunculus nudus, an old marine species, has great potential for use as functional seafood due to its various bioactivities. Its potential antithrombotic activity pushed us to isolate the bio-active components bio-guided by tracking fibrinolytic activity. As a result, a novel protease named as SK (the kinase obtained from S. nudus) was obtained, which possessed a molecular weight of 28,003.67 Da and 15 N-terminal amino acid sequences of PFPVPDPFVWDTSFQ. SK exerted inhibitory effects on thrombus formation through improving the coagulation system with dose-effect relationship within a certain range. Furthermore, in most cases SK got obviously better effect than that of urokinase. With the help of untargeted mass spectrometry-based metabolomics profiling, arachidonic acid, sphingolipid, and nicotinate and nicotinamide mechanism pathways were found to be important pathways. They revealed that the effect mechanism of SK on common carotid arterial thrombosis induced by FeCl₃ was achieved by inhibiting vessel contraction, platelet aggregation, adhesion, and release, correcting endothelial cell dysfunction and retarding process of thrombus formation. This study demonstrated SK was a promising thrombolytic agent on the basis of its comprehensive activities on thrombosis, and it should get further exploitation and utilization.

| S-EPMC6213608 | biostudies-literature

Mitochondrial genome sequence and gene order of Sipunculus nudus give additional support for an inclusion of Sipuncula into Annelida.

Project description:BACKGROUND:Mitochondrial genomes are a valuable source of data for analysing phylogenetic relationships. Besides sequence information, mitochondrial gene order may add phylogenetically useful information, too. Sipuncula are unsegmented marine worms, traditionally placed in their own phylum. Recent molecular and morphological findings suggest a close affinity to the segmented Annelida. RESULTS:The first complete mitochondrial genome of a member of Sipuncula, Sipunculus nudus, is presented. All 37 genes characteristic for metazoan mtDNA were detected and are encoded on the same strand. The mitochondrial gene order (protein-coding and ribosomal RNA genes) resembles that of annelids, but shows several derivations so far found only in Sipuncula. Sequence based phylogenetic analysis of mitochondrial protein-coding genes results in significant bootstrap support for Annelida sensu lato, combining Annelida together with Sipuncula, Echiura, Pogonophora and Myzostomida. CONCLUSION:The mitochondrial sequence data support a close relationship of Annelida and Sipuncula. Also the most parsimonious explanation of changes in gene order favours a derivation from the annelid gene order. These results complement findings from recent phylogenetic analyses of nuclear encoded genes as well as a report of a segmental neural patterning in Sipuncula.

| S-EPMC2639372 | biostudies-literature

The complete mitogenome of a peanut worm Phascolosoma pacificum (Sipuncula, Phascolosomatida, Phascolosomatidea).

Project description:Sipuncula (peanut worms) is a traditional phylum which consists of unsegmented bilateral symmetric marine worms. Although it is accepted as a phylum, the phylogenetic position of Sipuncula has been questionable. There is lack of molecular record on Sipuncula species while morphological data is not enough to distinguish the closer relationships between Annelida and Sipuncula. In order to add more data to genomic library of sipunculan species, Phascolosoma pacificum (Keferstein, 1866) was collected from seagrass area of Chuuk lagoon/Micronesia and its complete mitochondrial genome sequenced. Furthermore, phylogenetic relationship of the phylum Sipuncula and the other Trochozoan phyla investigate due to mitochondrial protein coding genes. Although there is lack of recorded data, our results support the idea that Sipuncula are nested within Annelida according to phylogenetic analyses of mitochondrial protein coding genes.

| S-EPMC7800858 | biostudies-literature

The first high-quality chromosome-level genome of the Sipuncula Sipunculus nudus using HiFi and Hi-C data.

Project description:Sipuncula is a class of exocoelomic unsegmented animals whose evolutionary relationships are unresolved. The peanut worm Sipunculus nudus is a globally distributed, economically important species belonging to the class Sipuncula. Herein, we present the first high-quality chromosome-level assembly of S. nudus based on HiFi reads and high-resolution chromosome conformation capture (Hi-C) data. The assembled genome was 1,427 Mb, with a contig N50 length of 29.46 Mb and scaffold N50 length of 80.87 Mb. Approximately 97.91% of the genome sequence was anchored to 17 chromosomes. A BUSCO assessment showed that 97.7% of the expectedly conserved genes were present in the genome assembly. The genome was composed of 47.91% repetitive sequences, and 28,749 protein-coding genes were predicted. A phylogenetic tree demonstrated that Sipuncula belongs to Annelida and diverged from the common ancestor of Polychaeta. The high-quality chromosome-level genome of S. nudus will serve as a valuable reference for studies of the genetic diversity and evolution of Lophotrochozoa.

| S-EPMC10212961 | biostudies-literature

The complete mitochondrial genome of Matuta victor (Decapoda: Matutidae) from Beibu Bay.

Project description:The true crabs (Brachyura) including Calappidea are one of the most diverse groups of Decapod crustaceans However, despite their great diversity and commercial importance, phylogenetic and classification relationships within Calappidea are still complicated and controversial. In this study, we report the first complete mitochondrial genome of Matuta victos. The mitogenome has 17,782 base pairs (70.1% A + T content) and is made up of a total of 37 genes (13 protein-coding, 22 transfer RNAs and two ribosomal RNAs), plus a putative control region. This study will provide useful molecular resources for clarifying evolutionary and phylogenetic confusion within Calappidea.

| S-EPMC7832593 | biostudies-literature

The complete mitochondrial genome of the mudskipper, Boleophthalmus pectinirostris (Gobiiformes, Oxudercidae) from Beibu Bay.

Project description:The mudskipper, Boleophthalmus pectinirostris (B. pectinirostris), is an amphibious fish that lives in the intertidal mudflats. It is a cultured economic fish with nutritional and pharmacological value. Here, we report the complete mitochondrial genome sequence of B. pectinirostris, which is 17,111 base pairs (55.3% A + T content) in length and consists of 13 protein-coding genes, 22 transfer RNAs, 2 ribosomal RNAs, and a 1453 bp D-loop region. The complete mitochondrial genome of B. pectinirostris will provide useful genetic information for future phylogenetic and taxonomic classification of B. pectinirostris.

| S-EPMC8023618 | biostudies-literature

The complete mitochondrial genome of yellowfin seabream, Acanthopagrus latus (Percoiformes, Sparidae) from Beibu Bay.

Project description:The yellowfin seabream, Acanthopagrus latus Houttuyn 1782, is a commercially and ecologically important species and a good model for studies of sexual differentiation. In this study, the complete mitochondrial genome of A. latus has been determined, which is 16,635 base pairs (54.3% A + T content) in length and consists of 13 protein-coding genes, 22 transfer RNAs, two ribosomal RNAs, and a 948 bp D-loop region. The phylogenetic analyses showed that A. latus has a close relationship with Acanthopagrus schlegelii Bleeker 1854.

| S-EPMC8018338 | biostudies-literature