Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Characterization of the complete mitochondrial genome of Laomedia astacina De Haan, 1841 (Decapoda: Laomediidae) and its phylogenetic implications.

ABSTRACT: In this study, we determined the complete mitochondrial genome (mitogenome) of Laomedia astacina De Haan, 1841 using next-generation sequencing technology. The total length of the mitogenome sequence of L. astacina is 14,795 base pairs, including 13 protein-coding genes (PCGs), 22 transfer RNA genes, and two ribosomal RNA genes. The overall composition of the mitogenome is estimated to be 35.3% A, 38.0% T, 13.8% C, and 12.9% G, indicating that the L. astacina mitogenome is rich in A + T (73.3%). The phylogenetic relationships of 13 decapod species were constructed based on the 13 PCGs by the maximum-likelihood approach using IQtree software.

SUBMITTER: Guo D

PROVIDER: S-EPMC8956301 | biostudies-literature | 2022

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

Characterization of the complete mitochondrial genome of Laomedia astacina De Haan, 1841 (Decapoda: Laomediidae) and its phylogenetic implications.

Guo Dong D Zhang Dandan D Tu Zhong Z Song Lun L Dong Jing J Wang Weikuang W

Mitochondrial DNA. Part B, Resources 20220322 3

In this study, we determined the complete mitochondrial genome (mitogenome) of Laomedia astacina De Haan, 1841 using next-generation sequencing technology. The total length of the mitogenome sequence of L. astacina is 14,795 base pairs, including 13 protein-coding genes (PCGs), 22 transfer RNA genes, and two ribosomal RNA genes. The overall composition of the mitogenome is estimated to be 35.3% A, 38.0% T, 13.8% C, and 12.9% G, indicating that the L. astacina mitogenome is r ...[more]

PMID: 35342794

Similar Datasets

The complete mitochondrial genome and phylogenetic analysis of Upogebia major (De Haan, 1841).

Project description:The complete mitochondrial (mt) genome of Upogebia major (De Haan, 1841) is 16,131 bp in length, comprising 13 protein-coding genes (PCGs), 22 transfer RNA genes, and two ribosomal RNA genes. The nucleotide composition for U. major is 34.3% of A, 36.6% of T, 10.9% of C, and 18.3% of G. All PCGs are initiated by ATN codons, except for the cox1 gene, which was not determined. Nine PCGs use a common stop codon of TAA or TAG, the other four end with an incomplete stop codon (a single stop nucleotide T). Phylogenetic tree analysis showed that U. major had a close relationship with the species from the family Thalassinidae. The study will provide an important theoretical basis for further analysis of mt genome evolution and the phylogenetic relationships of the order Decapoda.

| S-EPMC7995815 | biostudies-literature

The complete mitochondrial genome of Aesop slipper lobster Scyllarides haanii (De Haan, 1841).

Project description:The complete mitochondrial genome of Scyllarides haanii from South China Sea was first determined and characterized. With a length of 15,666 bp, the circular mitogenome of S. haanii consists of 22 tRNA genes, two rRNA genes, 13 protein-coding genes (PCGs), and one control region. The nucleotide composition is significantly biased (A, G, T, and C was 32.05%, 12.45%, 33.97%, and 21.53%, respectively) with A + T contents of 66.02%. Two PCGs used an unusual initiation codon, and five PCGs were ended with an uncomplete or abnormal stop codon. One microsatellite was identified in the mitogenome located in ND4 gene. Phylogenetic analysis demonstrated that S. haanii was first clustered with Scyllarides squammosus, then together with Scyllarides latus.

| S-EPMC7782161 | biostudies-literature

The complete mitochondrial genome of Hemigrapsus penicillatus (De Haan, 1835) (Decapoda, Varunidae).

Project description:Hemigrapsus penicillatus is a small grapsoid crab which is found in Japan, Taiwan, Korea, and China coasts. In this study a complete mitogenome of Korean H. penicillatus was analyzed and phylogenetic relationships in the family Varunidae were investigated. The mitogenome size is 16,486 bp with 34.1% A, 18.1% C, 11.4% G, and 36.4% T nucleotide distributions. Genome structure and gene orientations are identical with previous records from the family and mitochondrial protein-coding gene based phylogenetic tree suggested that the closest species to H. penicillatus is H. sanguineus. This is the second complete mitogenome record from the genus Hemigrapsus and the first record for the species.

| S-EPMC7800518 | biostudies-literature

Analysis of complete mitochondrial genome of fiddler crab Uca (Tubuca) arcuata (De Haan, 1835) (Arthropoda, Malacostraca, Decapoda).

Project description:In this study complete nucleotide sequences of the mitochondrial genome of fiddler crab Uca arcuata (De Haan, 1835) were determined and characterized. The length of mitochondrial genome for U. arcuata is 15,955 bp. This is the third and the longest record of complete mitochondrial genome from the family Ocypodidae. Furthermore, phylogenetic relationships were evaluated due to mitochondrial protein-coding genes. Phylogenetic tree suggests that U. arcuata belongs to the monophyletic family Ocypodidae and has sister group relationship with the genus Ocypode.

| S-EPMC7800788 | biostudies-literature

Characterization and Phylogenetic Implications of the Complete Mitochondrial Genome of Syrphidae.

Project description:In this study, the complete mitochondrial genomes (mitogenomes) of two hoverfly species of Korinchia angustiabdomena (Huo, Ren, and Zheng) and Volucella nigricans Coquillett (Diptera: Syrphidae) were determined and analyzed. The circular mitogenomes were 16,473 bp in K. angustiabdomena (GenBank No. MK870078) and 15,724 bp in V. nigricans (GenBank No. MK870079). Two newly sequenced mitogenomes both contained 37 genes, and the gene order was similar with other syrphine species. All the protein-coding genes (PCGs) were started with the standard ATN codons; and most of PCGs were terminated with a TAA stop codon, while ND1 in K. angustiabdomena ended with a TAG codon, and ND5 terminated with truncated T stop codons in both species. The phylogenetic relationship between K. angustiabdomena and V. nigricans with related lineages was reconstructed using Bayesian inference and Maximum-likelihood analyses. The monophyly of each family considered within Muscomorpha was confirmed by the clades in the phylogenetic tree, and superfamily of the Oestroidea (Calliphoridae, Sarcophagidae, and Oestridae) was unexpectedly found to be a paraphyletic group based on our selected data. This mitogenome information for K. angustiabdomena and V. nigricans could facilitate future studies of evolutionarily related insects.

| S-EPMC6723807 | biostudies-literature

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 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 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

Characterization of the complete mitochondrial genome of Cryptotermes domesticus (Blattodea: Kalotermitidae): Genome description and phylogenetic implications.

Project description:The complete mitochondrial genome of Cryptotermes domesticus (Haviland) was sequenced and annotated to study its characteristics and the phylogenetic relationship of C. domesticus to other termite species. The mitogenome of C. domesticus is a circular, close, and double-stranded molecule with a length of 15,655 bp. The sequenced mitogenome contains 37 typical genes, which are highly conserved in gene size, organization, and codon usage. Transfer RNA genes (tRNAs) also have typical secondary structures. All of the 13 protein-coding genes (PCGs) start with an ATN codon, except for nad4, which starts with GTG and terminates with the terminal codon TAA and TAG or the incomplete form T-- (cox2 and nad5). Most tRNAs have a typical cloverleaf structure, except for trnS1, in which this form is replaced by a simple loop and lacks the dihydrouridine (DHU) arm. The nucleotide diversity (Pi) and nonsynonymous (Ka)/synonymous (Ks) mutation rate ratios indicate that nad1, cox1, and cox3 are the most conserved genes, and that cox1 has the lowest rate of evolution. In addition, an 89 bp repeated sequence was found in the A + T-rich region. Phylogenetic analysis was performed using Bayesian inference (BI) and maximum likelihood (ML) methods based on 13 PCGs, and the monophyly of Kalotermitidae was supported.

| S-EPMC10078508 | biostudies-literature