Browse
Submit Data
Databases
API
Help

Dataset Information

30 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

The complete mitochondrial genome of Thor amboinensis (Hippolytidae, Decapoda).

ABSTRACT: The complete mitochondrial genome of Thor amboinensis was obtained and described in this study. This complete mitochondrial genome is 15,553 bp in length and consists of 13 protein-coding genes, 2 ribosomal RNA genes, and 22 transfer RNA genes. Twenty-two genes were encoded by the heavy strand. The overall base composition of the heavy-strand was 36.09% A, 12.36% G, 14.54% C, and 37.01% T, with a high G + C content of 26.90%. The phylogenetic analysis suggested that T. amboinensis was closest to Lebbeus groenlandicus. The newly described mitochondrial genome may provide valuable data for phylogenetic analysis for Hippolytidae.

SUBMITTER: Wang Y

PROVIDER: S-EPMC7782259 | biostudies-literature |

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Similar Datasets

Characterization of the complete mitochondrial genome of Lysmata amboinensis (Hippolytidae, Decapoda) and its phylogenetic analysis.

Project description:The complete mitochondrial genome of Lysmata amboinensis was obtained and described in this study. This complete mitochondrial genome is 16,735 bp in length and consists of 13 protein-coding genes (PCGs), 2 ribosomal RNA genes (rRNA), and 22 transfer RNA genes (tRNA). A total of 23 genes were encoded by the heavy strand. The overall base composition of the heavy-strand was 31.68% A, 14.31% G, 21.65% C, and 32.36% T, with a high A + T content of 64.05%. The phylogenetic analysis suggested that hippolytidae shrimp may be considered as the polyphyletic taxon. These results are useful for understanding the phylogenetic relationships and evolution of Hippolytidae shrimp.

| S-EPMC7759256 | biostudies-literature

Characterization of the complete mitochondrial genome of Lysmata vittata (Decapoda: Hippolytidae).

Project description:Lysmata vittata is widely distributed in the Indian and Pacific oceans. In this study, we sequenced the mitochondrial genome of L. vittata using Illumina HiSeq. The complete mitochondrial genome of L. vittata was 20,837 bp in length, including 13 protein-coding genes, 22 transfer RNA genes, and two ribosomal RNA genes. The contents of the four bases in the mitochondrial DNA were A (31.68%), T (32.36%), C (21.65%), and G (14.31%). Phylogenetic analysis of 41 shrimp showed that L. vittata was clustered with other Hippolytidae shrimp.

| S-EPMC8174479 | biostudies-literature

Characterization of the complete mitochondrial genome of Lysmata debelius (Decapoda: Hippolytidae).

Project description:Despite its wide distribution in the Indo-Pacific region and its popularity as an aquarium species, genetic studies on Lysmata debelius remain very limited. In this study, we obtained and characterized the complete mitochondrial genome (mitogenome) of L. debelius. Results showed that the mitogenome was 16,757 bp in length and consisted of 37 genes, including 13 protein-coding genes (PCGs), 22 transfer RNA genes, and two ribosomal RNA genes. Fourteen genes were light-strand encoded and 23 genes were heavy-strand encoded. The A + T content of the heavy strand was 67.16%. All PCGs had ATN as the start codon. Eight PCGs terminated with a complete stop codon of TAN, and five PCGs (ND3, ND5, ND4, Cox2, and Cytb) had an incomplete stop codon. The phylogeny of 42 shrimp species showed that all three Lysmata species were clustered together. The newly described mitogenome should provide valuable data for phylogenetic analysis of Hippolytidae.

| S-EPMC8231415 | biostudies-literature

Characterization of the complete mitochondrial genome of Saron marmoratus (Hippolytidae, Decapoda) and its phylogenetic analysis.

Project description:The complete mitochondrial genome of shrimp Saron marmoratus was obtained and characterized in this study. This complete mitochondrial genome is 16,330 bp in size and comprises 13 protein-coding genes (PCGs), two ribosomal RNA genes, and 22 transfer RNA genes. Fourteen genes were encoded by light strand and another 23 genes were encoded by heavy strand. The A + T content of the heavy-strand was 67.89%. Most PCGs had ATN as the start codon except ND4 initiated with GAT. Eleven PCGs terminated with a complete stop codon TAN, but two PCGs (ND5 and Cytb) had an incomplete stop codon. The phylogenetic analysis suggested that Hippolytidae shrimp may be considered as the polyphyletic taxon. These results are useful for understanding the phylogenetic relationships and evolution of Hippolytidae shrimp.

| S-EPMC7808751 | biostudies-literature

Complete mitochondrial genome of Leptodius sanguineus (Decapoda, Xanthidae).

Project description:The complete mitochondrial genome sequenced from a xanthid crab, Leptodius sanguineus which was collected from a rocky intertidal area in Chuuk lagoon. The mitochondrial genome size of L. sanguineus evaluated as 15,480 bp with 33.6% A, 24% C, 11.2% G and 31.2% T and mitochondrial gene order of L. sanguineus is typical to brachyuran species. Phylogenetic analysis shows that the family Xanthidae has sister group relationship with a lineage including the families Portunidae and Menippidae in the subsection Heterotremata. This is the first report for the complete mitochondrial genome from the xanthid crabs.

| S-EPMC7799469 | biostudies-literature

The complete mitogenome of Lysmata vittata (Crustacea: Decapoda: Hippolytidae) with implication of phylogenomics and population genetics

Project description:In this study, the complete mitogenome of Lysmata vittata (Crustacea: Decapoda: Hippolytidae) has been determined. The genome sequence was 22003 base pairs (bp) and it included thirteen protein-coding genes (PCGs), twenty-two transfer RNA genes (tRNAs), two ribosomal RNA genes (rRNAs) and three putative control regions (CRs). The nucleotide composition of AT was 71.50%, with a slightly negative AT skewness (-0.04). Usually the standard start codon of the PCGs was ATN, while cox1, nad4L and cox3 began with TTG, TTG and GTG. The canonical termination codon was TAA, while nad5 and nad4 ended with incomplete stop codon T, and cox1 ended with TAG. The mitochondrial gene arrangement of eight species of the Hippolytidae were compared with the order of genes of Decapoda ancestors, finding that the gene arrangement order of the Lebbeus groenlandicus had not changed, but the gene arrangement order of other species changed to varying degrees. The positions of the two tRNAs genes (trnA and trnR) of the L. vittata had translocations, which also showed that the Hippolytidae species were relatively unconserved in evolution. Phylogenetic analysis of 50 shrimp showed that L. vittata formed a monophyletic clade with Lysmata/Exhippolysmata species. This study should be helpful to better understand the evolutionary status, and population genetic diversity of L. vittata and related species.

| S-EPMC8568142 | biostudies-literature

The complete mitochondrial genome of Penaeus semisulcatus (Decapoda: Penaeidae).

Project description:The green tiger prawn, Penaeus semisulcatus, is one of the economically important penaeid shrimp due to its larger body size compared with other shrimps in Penaeidae family. However, the taxonomic revision studies of Penaeidae have been one of the most controversial issues in recent years. Moreover, there are at least two morphotypes of the green tiger prawn, one with banded antenna, another with non-banded antenna. In this study, we report the complete mitochondrial genome of P. semisulcatus. The mitogenome has 16,002 base pairs (68.6% A?+?T content) and made up of total of 37 genes (13 protein-coding, 22 transfer RNAs and 2 ribosomal RNAs), and a control region. This study adds one more available complete mitogenomes of Penaeus and will provide useful genetic information for future evolutionary and taxonomic classification of Penaeidae.

| S-EPMC7706530 | biostudies-literature

The complete mitochondrial genome of Metapenaeopsis mogiensis (Decapoda: Penaeidae).

Project description:Metapenaeopsis is one of most important genera of Penaeidae. However, the systemically classification and taxonomic studies have so far been limited. In this study, we report the complete mitochondrial genome sequence of M. mogiensis. The mitogenome has 15,973 base pairs (66.7% A?+?T content) and made up of total of 37 genes (13 protein-coding, 22 transfer RNAs and two ribosomal RNAs), and a putative control region. This study was the second available complete mitogenomes of Metapenaeopsis and will provide useful genetic information for future phylogenetic and taxonomic classification of Metapenaeopsis.

| S-EPMC7510666 | biostudies-literature

The complete mitochondrial genome of Scylla paramamosain (Decapoda: Portunidae).

Project description:The mud crab Scylla paramamosain (Decapoda:Portunidae) is a commercially important crustacean species in China, which is broadly distributed along the southeastern coastal regions of China. In previous studies, the population from Beibu Bay showed distinct genetic lineage. Here, we report the complete mitochondrial genome sequence of S. paramamosain from Beibu Bay. The mitogenome has 15,816 base pairs 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 mitogenome in the Beibu Bay population was shorter than that in the Shenzhen population, because the non-coding region between tRNA-Glu and tRNA-His was shorter in the former, and there were 59 mutations sites between these two populations. This study adds a distinct mitogenomes of S. paramamosain and will provide useful genetic information for future genetic variation identification and genetic diversity evaluation of this economic valuable crab.

| S-EPMC7799674 | biostudies-literature

The complete mitochondrial genome of Thalamita sima (Decapoda: Portunidae).

Project description:Thalamita is one of most important genera of Portunidae. However, the systemically classification and taxonomic studies have so far been limited. In this study, we report the complete mitochondrial genome sequence of T. sima. The mitogenome has 15,831 base pairs (71.7% 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. This study was the second available complete mitogenomes of Thalamita and will provide useful genetic information for future phylogenetic and taxonomic classification of Thalamita.

| S-EPMC7799605 | 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