Browse
Submit Data
Databases
API
Help

Dataset Information

15 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

The complete mitogenome of the Thai soldier crab Mictyris thailandensis Davie, Wisespongpand & Shih, 2013 (Crustacea: Decapoda: Mictyridae)

ABSTRACT: Abstract Mictyris thailandensis has been described recently in the family Mictyridae which is found only in the Andaman Sea, west coast of Thailand. In this study, we performed shotgun genome sequencing of a male M. thailandensis using a paired-end (150 bp) sequencing chemistry on MGISEQ-2000RS and report the complete mitochondrial genome of M. thailandensis (15,557 bp). A total of 37 genes have been annotated: 13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNAs), two ribosomal RNA genes (rRNAs), and a control region. Comparative phylogenetic analysis with 29 crustaceans based on 13 conserved genes demonstrated that M. thailandensis is closely related to other soldier crabs in the family Mictyridae. The mitogenome of M. thailandensis presented here provides useful genetic information to help understand the evolutionary relationships among the Mictyridae family members.

SUBMITTER: Sonthirod C

PROVIDER: S-EPMC8803110 | biostudies-literature |

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Similar Datasets

Crustacea (Decapoda)

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

| PRJNA596786 | ENA

The complete mitogenome of the Chionoecetes opilio (Crustacea: Decapoda: Oregoniidae) and its unique characteristics.

Project description:The complete mitochondrial genome of Chionoecetes opilio is a 16,067 bp long, circular molecule which contains 13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNAs), and 2 ribosomal RNA genes (rRNAs). Its gene contents and organization are generally similar to other majoid mitogenomes. However, the mitogenome shows unique characteristics; long terminal amino acids, loss or addition of 3 PCGs, a 1216 bp long putative D-loop region, and peculiar secondary structures of 5 tRNAs. The concatenated amino acid sequences of 13 PCGs were used to analyze the phylogenetic tree, which well supported the monophyly of brachyuran clades of Majoidea, Heterotremata, Thoracotremata, and Eubrachyura.

| S-EPMC7782958 | 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 mitogenome of Pentacheles validus (Decapoda: Polychelidae).

Project description:In this study, the complete mitogenome sequence of Pentacheles validus has been decoded for the first time. The overall base composition is 33.4% for A, 25.0% for C, 10.8% for G, and 30.9% for T and has low GC content of 35.8%. The assembled mitogenome, 16,079 bp in length, has unique 13 protein-coding genes (PCGs), 22 transfer RNAs and 2 ribosomal RNAs. The mitogenome shares 80% identity to Polycheles typhlops. The complete mitogenome of P. validus provides essential DNA molecular data for further phylogenetic and evolutionary analysis for Polychelidae and deep-sea faunas.

| S-EPMC7800303 | biostudies-literature

The complete mitochondrial genome sequence of the hydrothermal vent galatheid crab Shinkaia crosnieri (Crustacea: Decapoda: Anomura): a novel arrangement and incomplete tRNA suite.

Project description:BACKGROUND: Metazoan mitochondrial genomes usually consist of the same 37 genes. Such genes contain useful information for phylogenetic analyses and evolution modelling. Although complete mitochondrial genomes have been determined for over 1,000 animals to date, hydrothermal vent species have, thus far, remained excluded due to the scarcity of collected specimens. RESULTS: The mitochondrial genome of the hydrothermal vent galatheid crab Shinkaia crosnieri is 15,182 bp in length, and is composed of 13 protein-coding genes, two ribosomal RNA genes and only 18 transfer RNA genes. The total AT content of the genome, as is typical for decapods, is 72.9%. We identified a non-coding control region of 327 bp according to its location and AT-richness. This is the smallest control region discovered in crustaceans so far. A mechanism of cytoplasmic tRNA import was addressed to compensate for the four missing tRNAs. The S. crosnieri mitogenome exhibits a novel arrangement of mitochondrial genes. We investigated the mitochondrial gene orders and found that at least six rearrangements from the ancestral pancrustacean (crustacean + hexapod) pattern have happened successively. The codon usage, nucleotide composition and bias show no substantial difference with other decapods. Phylogenetic analyses using the concatenated nucleotide and amino acid sequences of the 13 protein-coding genes prove consistent with the previous classification based upon their morphology. CONCLUSION: The present study will supply considerable data of use for both genomic and evolutionary research on hydrothermal vent ecosystems. The mitochondrial genetic characteristics of decapods are sustained in this case of S. crosnieri despite the absence of several tRNAs and a number of dramatic rearrangements. Our results may provide evidence for the immigrating hypothesis about how vent species originate.

| S-EPMC2442616 | biostudies-literature

Complete mitochondrial genome of the spiny rock crab Thalamita crenata (ruppell, 1830) (Crustacea: Decapoda: Portunidae) from China coast and its phylogeny.

Project description:To understand the evolution of the swimming crab Thalamita crenata, the complete mitochondrial genome of T. crenata from China was sequenced and analyzed. The circular mitogenome sequence was 15,787?bp in length, made up of 13 protein-coding genes, 22 transfer RNA genes, two ribosomal RNA genes and a control region. The overall mitogenome composition was 34.40% for A, 11.55% for G, 35.31% for T, and 18.74% for C, respectively, with a high A?+?T content of 69.71%. Phylogenetic analysis showed that T. crenata was closest to the genus Charybdis.

| S-EPMC7800823 | 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

Geosesarmamirum, a new species of semi-terrestrial sesarmid crab (Crustacea, Decapoda, Brachyura) from central Taiwan.

Project description:A new species of semi-terrestrial sesarmid crab of the genus Geosesarma De Man, 1892, is described from central Taiwan. Geosesarmamirum sp. nov. is distinct in possessing a strong transverse crest on the inner surface of the male chela and a diagnostic male first gonopod which is relatively long and stout, with the distal chitinous part broad and spatuliform. Like most Geosesarma species, G.mirum sp. nov. has large eggs and direct development, contrasting with the only other species known from Taiwan, G.hednon Ng, Liu and Schubart, 2004, which has small eggs and planktotrophic larvae.

| S-EPMC6614171 | biostudies-literature

The complete mitogenome of freshwater gammarid Grandidierella taihuensis (Crustacea: Amphipoda).

Project description:The freshwater gammarid Grandidierella taihuensis is an important composition of benthic community. In this study, the complete mitogenome sequences of G. taihuensis are determined using next-generation and PacBio long-read sequencing. The mitogenome of G. taihuensis is 15,099 bp in size, and consisted of 13 protein-coding genes, two ribosomal RNA genes, 22 tRNA genes, and a putative control region. Gene arrangement is as same as that of G. rubroantennata. The base composition of the entire mitogenome showed a conspicuous A + T bias of 69.4%. The mitogenome data produced in this study provides a useful resource for future evolutionary and ecological studies.

| S-EPMC8043560 | biostudies-literature

Yuebeipotamon calciatile, a new genus and new species of freshwater crab from southern China (Crustacea, Decapoda, Brachyura, Potamidae).

Project description:A new genus and species of freshwater crab, Yuebeipotamon calciatile gen. n., sp. n., is described from southern China. While the carapace features are superficially similar to species of Sinopotamon Bott, 1967, Longpotamon Shih, Huang & Ng, 2016, and Tenuilapotamon Dai, Song, Li, Chen, Wang & Hu, 1984, the new genus possesses a distinctive combination of carapace, ambulatory leg, male thoracic sternal, male abdominal, and gonopodal characters that distinguish it from these and other genera. Molecular evidence derived from the mitochondrial 16S rDNA supports the establishment of a new genus.

| S-EPMC5027778 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

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