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 and phylogenetic analysis of Upogebia major (De Haan, 1841).

ABSTRACT: 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.

SUBMITTER: Sun X

PROVIDER: S-EPMC7995815 | biostudies-literature | 2021 Mar

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

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

Sun Xiaoyue X He Jun J

Mitochondrial DNA. Part B, Resources 20210318 3

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 s ...[more]

PMID: 33796702

Similar Datasets

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

Project description: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.

| S-EPMC8956301 | 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

Complete mitochondrial genome and phylogenetic analysis of Ixodes persulcatus (taiga tick).

Project description:Ixodes persulcatus is a species of hard tick which is a predominant tick species that spreads a wide array of serious human and animal pathogens. Here, we first assemble the complete mitogenome of I. persulcatus of China. The total length of the mitogenome was 14,539 bp included 36 genes and with a mitogenome structure similar to other ticks. Phylogenetic tree was constructed based on the complete mitogenome of I. persulcatus and closely related 19 species ticks to assess their phylogenic relationship and evolution. We also analyze the differences between the mitogenomes of I. persulcatus of Japan and China. The complete mitogenome data would be useful for further study of I. persulcatus.

| S-EPMC7800817 | biostudies-literature

Complete mitochondrial genome and phylogenetic analysis of Dollfustrema vaneyi (Trematoda: Bucephalidae).

Project description:BackgroundThe Bucephalidae is a large family of digenean trematodes but most previous analyses of its phylogenetic position have relied on a single mitochondrial gene or morphological features. Mitochondrial genomes (mitogenomes) remain unavailable for the entire family. To address this, we sequenced the complete mitogenome of Dollfustrema vaneyi and analyzed the phylogenetic relationships with other trematodes.ResultsThe circular genome of Dollfustrema vaneyi spanned 14,959 bp and contained 12 protein-coding genes, 22 transfer RNA genes, 2 ribosomal RNA genes, and a major non-coding region. We used concatenated amino acid and nucleotide sequences of all 36 genes for phylogenetic analyses, conducted using MrBayes, IQ-TREE and PhyloBayes. We identified pronounced topological instability across different analyses. The addition of recently sequenced two mitogenomes for the Aspidogastrea subclass along with the use of a site-heterogeneous model stabilized the topology, particularly the positions of Azygiidae and Bucephalidae. The stabilized results indicated that Azygiidae was the closest lineage to Bucephalidae in the available dataset, and together, they clustered at the base of the Plagiorchiida.ConclusionsOur study provides the first comprehensive description and annotation of the mitochondrial genome for the Bucephalidae family. The results indicate a close phylogenetic relationship between Azygiidae and Bucephalidae, and reveal their basal placement within the order Plagiorchiida. Furthermore, the inclusion of Aspidogastrea mitogenomes and the site-heterogeneous model significantly improved the topological stability. These data will provide key molecular resources for future taxonomic and phylogenetic studies of the family Bucephalidae.

| S-EPMC11403940 | biostudies-literature

The complete mitochondrial genome of Aspiorhynchus laticeps and its phylogenetic analysis.

Project description:The complete nucleotide sequence of the mitochondrial genome (mitogenome) of Aspiorhynchus laticeps was determined. The length of the complete mitochondrial DNA sequence of A. laticeps is 16,591 bp, which consists of 13 protein-coding genes, 22 transfer RNA (tRNA) genes, two ribosomal RNA (rRNA) genes, and a non-coding region 'D-loop'. Except for the D-loop, another non-coding region named replication origin of L-strand (OL) region was also found. According to the phylogenetic analysis, A. laticeps has a closer relationship with Schizothorax.

| S-EPMC4287850 | biostudies-literature

Complete mitochondrial genome and phylogenetic analysis of Triplophysa jianchuanensis (Cypriniformes: Cobitidae).

Project description:We used the Illumina MiSeq platform to sequence the complete mitochondrial genome of Triplophysa jianchuanensis (Cypriniformes: Cobitidae). The mitochondrial genome of T. jianchuanensis is 16,569 bp in length, and its genetic constitution and arrangement are consistent with those of the teleost taxon, containing 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes, an origin of light-strand replication, and a control region. The overall nucleotide base composition was 28.33% A, 27.25% T, 17.77% G, and 26.65% C. Phylogenetic analysis showed that T. jianchuanensis was grouped with T. venusta. These findings are valuable for further studies on the evolution, genetic diversity, and taxonomy of Triplophysa.

| S-EPMC10776075 | biostudies-literature

Complete mitochondrial genome of Hemiptelea davidii (Ulmaceae) and phylogenetic analysis.

Project description:Hemiptelea davidii (Hance) Planch is a potential valuable forest tree in arid sandy environments. Here, the complete mitochondrial genome of H. davidii was assembled using a combination of the PacBio Sequel data and the Illumina Hiseq data. The mitochondrial genome is 460,941 bp in length, including 37 protein-coding genes, 19 tRNA genes, and three rRNA genes. The GC content of the whole mitochondrial genome is 44.84%. Phylogenetic analyses indicated that H. davidii is close with Cannabis and Morus species.

| S-EPMC7706575 | biostudies-literature

The complete mitochondrial genome and phylogenetic analysis of Pealius mori (Hemiptera: Aleyrodidae)

Project description: Not available

| S-EPMC11229734 | biostudies-literature