Browse
Submit Data
Databases
API
Help

Dataset Information

11 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

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

ABSTRACT: 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.

SUBMITTER: Wang Y

PROVIDER: S-EPMC7759256 | biostudies-literature |

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Similar Datasets

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 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

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

Project description: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.

| S-EPMC7782259 | 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

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 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 and phylogenetic analysis of Cancer pagurus (Decapoda, Cancridae).

Project description:The complete mitochondrial genome of Cancer pagurus was obtained using next-generation sequencing. The circular genome was 42,736?bp in length, consisting of 13 protein-coding genes, 26 transfer RNA genes, and 2 ribosomal RNA genes. The control region was not found in mitochondrial genome. Of the 41 genes, 21 were encoded by the heavy strand, while the others were encoded by the light strand. The genome composition with A?+?T bias (74.10%). The phylogenetic analysis suggested that C. pagurus was closest to Austinograea alayseae. The newly described mitochondrial genome may provide valuable data for phylogenetic analysis for Cancridae.

| S-EPMC7707713 | biostudies-literature

The complete mitochondrial genome and phylogenetic analysis of Cancer magister (Decapoda, Cancridae).

Project description:The complete mitochondrial (mt) genome of Cancer magister was obtained using next-generation sequencing. The circular genome was 39,658 bp in length, consisting of 13 protein-coding genes, 26 transfer RNA genes, and 2 ribosomal RNA genes. Unfortunately, the control region was not found in mitochondrial genome. Of the 41 genes, 24 were encoded by the heavy strand, while the others were encoded by the light strand. The genome composition with A + T bias (69.90%). The phylogenetic analysis showed that C. magister and Cancer pagurus was clustered together, then grouped with A. alayseae and Gandalfus puia, which may suggest Cancroidea was close with Bythograeidae. The newly described mitochondrial genome may provide valuable data for phylogenetic analysis for Cancridae.

| S-EPMC7707678 | biostudies-literature

The complete mitochondrial genome and phylogenetic analysis of Matuta planipes (Decapoda: Brachyura: Matutidae).

Project description:The complete mitochondrial genome of Matuta planipes was obtained using long and conventional PCR method. The circular genome was 15,760?bp in length, consisting of 13 protein-coding genes, 22 transfer RNA genes, 2 ribosomal RNA genes and a control region. Of the 37 genes, 23 were encoded by the heavy strand, while the others were encoded by the light strand. The genome composition with A?+?T bias (70.82%) and gene arrangement were largely identical to those observed in most arthropods, such as the mud crab (Scylla paramamosain). The phylogenetic analysis suggested that M. planipes was closest to Ashtoret lunaris. The newly described mitochondrial genome may provide valuable data for phylogenetic analysis for Matutidae.

| S-EPMC7800499 | biostudies-literature

Analysis of complete mitochondrial genome of Etisus anaglyptus (Arthropoda, Decapoda, Xanthidae) with phylogenetic consideration.

Project description:The complete mitochondrial genome is sequenced and analyzed from a xanthid crab Etisus anaglyptus, which is the first complete mitochondrial genome for the genus. The mitochondrial genome length of E. anaglyptus is 16,435 bp and it is composed of 13 protein coding genes, two ribosomal RNA genes, and 22 tRNA genes. The structure and gene orientation of the mitochondrial genome is identical with the other brachyuran records. Furthermore, phylogenetic relationships of the infraorder Brachyura evaluated by mitochondrial protein coding genes. The phylogenetic study showed that E. anaglyptus is positioned in the superfamily Xanthoidea and the closest species to E. anaglyptus is Leptodius sanguineus.

| S-EPMC7800804 | 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