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 sequence of the sakura shrimp, Sergia lucens (Crustacea, Decapoda, Sergestidae).

ABSTRACT: Here, we present the complete mitochondrial genome of the sakura shrimp, Sergia lucens (Crustacea, Decapoda, Sergestidae). The circular genome is 16,087 base pairs in length and contains 13 protein-coding genes, 22 tRNA genes, and two rRNA genes. The nucleotide composition of the S. lucens mitogenome is biased towards A?+?T (69.9%). The gene arrangement was identical to penaeid shrimps. Maximum likelihood phylogenetic analysis using the nucleotide sequences of 13 protein-coding genes placed S. lucens next to Acetes chinensis, supporting the conventional taxonomic relationship of Sergia and Acetes.

SUBMITTER: Kawato S

PROVIDER: S-EPMC7800779 | biostudies-literature | 2018 Apr

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

The complete mitochondrial genome sequence of the sakura shrimp, Sergia lucens (Crustacea, Decapoda, Sergestidae).

Kawato Satoshi S Nozaki Reiko R Kondo Hidehiro H Hirono Ikuo I

Mitochondrial DNA. Part B, Resources 20180402 1

Here, we present the complete mitochondrial genome of the sakura shrimp, Sergia lucens (Crustacea, Decapoda, Sergestidae). The circular genome is 16,087 base pairs in length and contains 13 protein-coding genes, 22 tRNA genes, and two rRNA genes. The nucleotide composition of the S. lucens mitogenome is biased towards A + T (69.9%). The gene arrangement was identical to penaeid shrimps. Maximum likelihood phylogenetic analysis using the nucleotide sequences of 13 protein-cod ...[more]

PMID: 33474198

Similar Datasets

The complete mitochondrial genome of the Argentine red shrimp Pleoticus muelleri (Bate, 1888) (Crustacea, Decapoda, Solenoceridae).

Project description:The complete mitochondrial genome of Argentine red shrimp, Pleoticus muelleri (Bate, 1888) was determined using the MiSeq platform. Its mitogenome (16,189 bp) encoded the canonical 13 protein-coding genes, 22 tRNA genes, two rRNA genes. Start codons of all protein-coding genes were ATN except for ATP8, while incomplete stop codons (T-) were identified in six genes including COXI, COXII, COXIII, NAD3, NAD5, and NAD6. The mitogenome of P. muelleri showed highest sequence identity with Parapenaeopsis hardwickii (82%) and Solenocera crassicornis (81%). Phylogenetic analysis showed three shrimps in Solenoceridae including P. muelleri were grouped together from those in Penaeidae, which suggests taxonomic reexamination for those in those family.

| S-EPMC7800069 | biostudies-literature

The complete mitochondrial genome of Chionoecetes japonicus (Crustacea: Decapoda: Majoidea).

Project description:The complete mitochondrial genome of Chionoecetes japonicus was sequenced using a specimen collected offshore in the East Sea. The genome includes 13 protein-coding genes (PCGs), 22 transfer RNA (tRNA) genes, two ribosomal RNA (rRNA) genes, and a control region (D-loop), with a total length of 16,060 bp. The overall nucleotide composition was 34.91% A, 17.29% C, 10.93% G, and 36.87% T, with 71.78% A + T. In the phylogenetic tree was constructed using maximum-likelihood and Bayesian inference analyses, C. japonicus and C. japonicus pacificus formed a genetic clade that was sister to C. opilio.

| S-EPMC7782079 | biostudies-literature

Complete mitochondrial genome of Kishi velvet shrimp, Metapenaeopsis dalei (Rathbun, 1902) (Crustacea: Decapoda: Penaeidae) in the East China Sea.

Project description:We determined the complete mitochondrial genome of Metapenaeopsis dalei (Rathbun, 1902), which is collected from East China Sea (124°E and 33.5°N). Total mitochondrial genome length of M. dalei was 15 939 bp, in which 13 proteins, two ribosomal RNAs, 22 transfer RNAs and a putative control region were encoded. The gene arrangement of M. dalei was well conserved with nine known Penaeidae mitochondrial genomes from COX1 to tRNATyr . The protein-coding genes started with ATN except for COX1 in which ACG is used. Four genes (COX2, COX3, ND3 and ND5) exhibited an incomplete stop codon. Nucleotide sequence identity of M. dalei mitochondrial genome to those of nine Penaeidae species ranged from 78% to 80%. Based on the COI region, M. dalei is most closely related to Penaeus notialis.

| S-EPMC7871848 | biostudies-literature

Complete mitochondrial genome of Oregonia gracilis Dana, 1851 (Crustacea: Decapoda: Majoidea).

Project description:The complete mitochondrial genome of the majoid crab, Oregonia gracilis, was determined from a specimen collected in Korea. The mitochondrial genome is 15,737 bp long and contains 13 protein-coding genes (PCGs), 22 transfer RNA (tRNA) genes, and two ribosomal RNA (rRNA) genes. A maximum-likelihood phylogenetic tree based on the 13 PCGs of the mitochondria showed that O. gracilis is closely related to the genus Chinoecetes. The complete mitochondrial genome of O. gracilis provides valuable information on the mitochondrial evolution of majoid crabs.

| S-EPMC8008944 | biostudies-literature

The complete mitochondrial genome of the peppermint shrimp Lysmata wurdemanni (Decapoda: Lysmatidae).

Project description:In this study, the complete 16,979 bp mitochondrial genome of Lysmata wurdemanni (Gibbes, 1850) was determined from a specimen collected from Apalachee Bay, U.S. The mitogenome contains 37 genes, and consists of 32.33% A, 35.01% T, 19.55% C, and 13.10% G, with a total G + C content of 32.65%. A maximum likelihood phylogenetic tree based on mitochondrial protein-coding genes suggested L. wurdemanni is clustered with Lysmata vittata and Lysmata amboinensis, based on available mitochondrial sequences of relatives. These data are useful in determining phylogenetic relationships between Lysmatidae and Thoridae. The sequenced mitochondrial genome may also assist in understanding evolutionary distinctions and breeding strategies in hermaphroditic species.

| S-EPMC8211131 | biostudies-literature

The complete mitochondrial genome of Helicana japonica (Crustacea, Decapoda, Varunidae) from South Korea.

Project description:Helicana japonica mainly inhabits burrowed holes in the mudflats and intertidal zones. Specimens from the Republic of Korea were collected and whole genomic DNA from the cheliped muscle tissue was extracted. We determined the complete mitochondrial genome using Illumina HiSeq X Ten. The mitogenome is 16,535 bp in length and consists of 13 protein-coding genes, 2 rRNA genes, and 22 tRNA genes. A phylogenetic tree was reconstructed using the maximum-likelihood of phylogeny methods. H. japonica formed a sister clade with Helicana wuana, which is another Helicana species.

| S-EPMC10434999 | biostudies-literature

Complete mitochondrial genome of Penaeus acehensis (Crustacea, Decapoda, Penaeidae) from Aceh province, Indonesia.

Project description:Penaeid shrimps are widely distributed from Indian to western Pacific Oceans and some which are economically important. In this study, we reported full mitochondrial genome of an endemic shrimp species, Penaeus acehensis, which inhabits exclusively in the coastal water of Aceh, Indonesia. Full length of circular mitogenome of P. acehensis was 15,991 bp in length, which contained 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes, and a control region. Start codons of all protein-coding genes were ATN except for COX1 in which ACG was used. Incomplete stop codon (T- -) was found in five genes including COX2, COX3, NAD5, NAD4, and NAD4L. Among its relatives, P. acehensis was most closely related to Penaeus monodon showing 89% sequence identity in its mitogenome, which was corresponding to morphological analysis. Phylogenetic tree result showed that P. acehensis was clustered together with those were distributed in Indo-West Pacific region (clade II), which is distinct from Eastern Pacific region (clade I).

| S-EPMC7800247 | biostudies-literature

The complete mitochondrial genome of Somanniathelphusa boyangensis and phylogenetic analysis of Genus Somanniathelphusa (Crustacea: Decapoda: Parathelphusidae).

Project description:In this study, the authors first obtained the mitochondrial genome of Somanniathelphusa boyangensis. The results showed that the mitochondrial genome is 17,032bp in length, included 13 protein-coding genes, 2 rRNAs genes, 22 tRNAs genes and 1 putative control region, and it has the characteristics of the metazoan mitochondrial genome A+T bias. All tRNA genes display the typical clover-leaf secondary structure except tRNASer(AGN), which has lost the dihydroxyuridine arm. The GenBank database contains the mitochondrial genomes of representatives of approximately 22 families of Brachyura, comprising 56 species, including 4 species of freshwater crab. The authors established the phylogenetic relationships using the maximum likelihood and Bayesian inference methods. The phylogenetic relationship indicated that the molecular taxonomy of S. boyangensis is consistent with current morphological classification, and Parathelphusidae and Potamidae are derived within the freshwater clade or as part of it. In addition, the authors used the COX1 sequence of Somanniathelphusa in GenBank and the COX1 sequence of S. boyangensis to estimated the divergence time of this genus. The result displayed that the divergence time of Somanniathelphusa qiongshanensis is consistent with the separation of Hainan Island from mainland China in the Beibu Gulf, and the divergence time for Somanniathelphusa taiwanensis and Somanniathelphusa amoyensis is consistent with the separation of Taiwan Province from Mainland China at Fujian Province. These data indicate that geologic events influenced speciation of the genus Somanniathelphusa.

| S-EPMC5810993 | biostudies-literature

Sequencing of complete mitochondrial genome of sword prawn Parapenaeopsis hardwickii (Miers) (Crustacea, Decapoda, Penaeidae).

Project description:The sword prawn Parapenaeopsis hardwickii (Miers) (Crustacea, Decapoda, Penaeidae) is an important commercial fishery species, distributed in the East China Sea. In this study, we described the complete mitochondrial genome of P. hardwickii. The genome is 15,922 bp in length, encoding the standard set of 13 protein-coding genes, 22 tRNA genes and two rRNA genes, with circular organization. The overall A + T content is 67.20%; nucleotide frequency of the gene is as follows: A, 35.01%; C, 20.83%; G, 11.98%; T, 32.19%. The gene order of P. hardwickii is the same as Penaeus monodon and Fenneropenaeus chinensis, and it mainly retains as the Penaeidae ground pattern. The complete mitogenome sequence information of P. hardwickii would play an important part for further studies on molecular systematics and population genetics.

| S-EPMC7871835 | biostudies-literature

Crustacea (Decapoda)

Project description:Transcriptomes from four species of decapod crustaceans: Panulirus argus, Homarus americanus, Procambarus clarkii, and Callinectes sapidus

| PRJNA596786 | ENA