Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Sequencing and analysis of the complete mitochondrial genome of Hippopus porcellanus.

ABSTRACT: In this study, the complete mitochondrial genome of Hippopus porcellanus was reported. The whole mitochondrial genome was 21,565bp in length with a typical mitochondrial genomic structure including 13 protein-coding genes, 23 transfer RNA genes, 2 ribosomal RNA genes and 1 control region (D-loop). Mitogenome base composition was biased toward A + T content, at 60.3%. A phylogenetic tree based on complete mitogenome sequences revealed that, H. porcellanus is closely related to H. hippopus, both of which belong to the genus Hippopus.

SUBMITTER: Ma H

PROVIDER: S-EPMC8317960 | biostudies-literature | 2021

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

Sequencing and analysis of the complete mitochondrial genome of Hippopus porcellanus.

Ma Haitao H Zhang Baolu B Zhang Yuehuan Y Zhang Yang Y Qin Yanping Y Han Chenghui C Chen Shixi S Yu Ziniu Z

Mitochondrial DNA. Part B, Resources 20210726 9

In this study, the complete mitochondrial genome of Hippopus porcellanus was reported. The whole mitochondrial genome was 21,565bp in length with a typical mitochondrial genomic structure including 13 protein-coding genes, 23 transfer RNA genes, 2 ribosomal RNA genes and 1 control region (D-loop). Mitogenome base composition was biased toward A + T content, at 60.3%. A phylogenetic tree based on complete mitogenome sequences revealed that, H. porcellanus is closely related to H. ...[more]

PMID: 34368446

Similar Datasets

Complete mitochondrial genome of Andrias davidianus (Caudata: cryptobrachidae): sequencing and analysis.

Project description:In this study, the total mitochondrial genome sequence of Andrias davidianus (Caudata: Cryptobrachidae) was determined. The genome is 16,519 bases in length. It consists of 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes and 2 non-coding regions. These results will contribute to the natural resources conservation and species identification Of A. davidianus.

| S-EPMC7799949 | biostudies-literature

Sequencing and phylogenetic analysis of the Pyrgilauda ruficollis (Aves, Passeridae) complete mitochondrial genome.

Project description:In this study, both long PCR and conserved primers walking sequencing methods were used to determine the complete sequence of the of Pyrgilauda ruficollis mitochondrial genome (KC836121). The results showed that the complete mitochondrial genome of P. ruficollis is 1 6909 bp in length with 55.0% A+T content, harboring the typical 37 genes. The mitogenome had the same gene order with that of Podoces hendersoni. All protein coding genes started with ATG codon, except ND3 with GTG. For the stop codon usage, most genes terminate with codons TAA or TAG, but ND5 terminated with AGA, while ND1 and COI genes with AGG, and both the genes COⅢ and ND4 have an incomplete termination codon (T). The secondary structures of 22 tRNA genes were also predicted, showing that all tRNAs can form typical clover-leaf secondary structures, except for the tRNA(Ser) (AGN) which loses the DHU arm, while tRNA(Phe) harbor an extra nucleotide inserted in the TψC arm. The predicted secondary structures of 12S rRNA and 16S rRNA exhibit 47 helices in 4 domains and 60 helices in 6 domains respectively. The control region of P. ruficollis with the length of 1 305 bp was located between tRNA(Glu) and tRNA(Phe), and typical domains of which could be found as other bird groups. Using the data from 13 mitochondrial protein-coding genes, results of a final phylogenetic analysis strongly supports the traditional view that P. ruficollis is closely related with Passeridae and Fringillidae.

| S-EPMC5042932 | biostudies-literature

Sequencing and analysis of the complete mitochondrial genome in Anopheles sinensis (Diptera: Culicidae).

Project description:BackgroundAnopheles sinensis (Diptera: Culicidae) is a primary vector of Plasmodium vivax and Brugia malayi in most regions of China. In addition, its phylogenetic relationship with the cryptic species of the Hyrcanus Group is complex and remains unresolved. Mitochondrial genome sequences are widely used as molecular markers for phylogenetic studies of mosquito species complexes, of which mitochondrial genome data of An. sinensis is not available.MethodsAn. sinensis samples was collected from Shandong, China, and identified by molecular marker. Genomic DNA was extracted, followed by the Illumina sequencing. Two complete mitochondrial genomes were assembled and annotated using the mitochondrial genome of An. gambiae as reference. The mitochondrial genomes sequences of the 28 known Anopheles species were aligned and reconstructed phylogenetic tree by Maximum Likelihood (ML) method.FindingsThe length of complete mitochondrial genomes of An. sinensis was 15,076 bp and 15,138 bp, consisting of 13 protein-coding genes, 22 transfer RNA (tRNA) genes, 2 ribosomal RNA (rRNA) genes, and an AT-rich control region. As in other insects, most mitochondrial genes are encoded on the J strand, except for ND5, ND4, ND4L, ND1, two rRNA and eight tRNA genes, which are encoded on the N strand. The bootstrap value was set as 1000 in ML analyses. The topologies restored phylogenetic affinity within subfamily Anophelinae. The ML tree showed four major clades, corresponding to the subgenera Cellia, Anopheles, Nyssorhynchus and Kerteszia of the genus Anopheles.ConclusionsThe complete mitochondrial genomes of An. sinensis were obtained. The number, order and transcription direction of An. sinensis mitochondrial genes were the same as in other species of family Culicidae.

| S-EPMC5625653 | biostudies-literature

Sequencing and Analysis of the Complete Mitochondrial Genome of Lentipes ikeae.

Project description:We sequenced and analyzed the complete mitochondrial genome of Lentipes ikeae and explored the phylogenetic relationships among Sicydiinae based on mitochondrial genome sequences. The complete mitochondrial genome sequence of L. ikeae was determined using the Illumina HiSeq X Ten sequencing platform, and the gene structural characteristics and base composition were analyzed. Based on the mitochondrial genome sequences of 28 Sicydiinae species published in GenBank and mitochondrial protein-coding genes (PCGs), Acanthogobius flavimanus (Gobionellinae) was selected as an outgroup to construct phylogenetic trees of Sicydiinae using the maximum likelihood and Bayesian inference methods. The mitochondrial genome of L. ikeae (GenBank number: OP764680) has a total length of 16,498 bp and encodes 13 PCGs, 22 transfer RNA genes, two ribosomal RNA genes, and a D-loop (control) region. Gene rearrangement is not observed. The mitochondrial genome of L. ikeae exhibits an AT preference, with AT skew > 0 and GC skew < 0 across the entire genome. The phylogenetic relationships of Sicydiinae based on 13 mitochondrial PCG sequences are Sicydium + (Stiphodon + (Sicyopus + Lentipes)) + Sicyopterus, indicating that Sicydium, Sicyopterus, Lentipes, and Stiphodon are all monophyletic groups.

| S-EPMC10967545 | biostudies-literature

Sequencing and analysis of the complete mitochondrial genome of Coenobita brevimanus.

Project description:Coenobitidae is one of the most important families in Anomura. However, systematic classification and taxonomic studies are still limited. In this study, we determined the complete mitochondrial genome (mitogenome) of Coenobita brevimanus and further explored the phylogenetic relationships of Anomura. In the whole mitogenome of C. brevimanus (16388 bp), the AT-skew is negative and the GC-skew is positive.The phylogenetic tree was constructed using MrBayes method based on the 13 PCGs, which showed that Coenobitidae is monophyletic with maximal support value. Our phylogenetic analysis can be used to provide a basis for studies of the mitochondrial evolution of Anomura.

| S-EPMC7706557 | biostudies-literature

Complete mitochondrial genome sequencing and preliminary phylogenetic analysis of Chromis notata.

Project description:Chromis notata (Temminck and Schlegel, 1843), commonly known as the pearl-spot chromis, is a damselfish that inhabits the northwestern region of the Pacific Ocean and the East China Sea. Interestingly, C. notata has been found to have morphological variations depending on the geographical area of collection. However, because there are insufficient molecular studies on C. notata, in this study, we determined its complete mitochondrial genome using PCR and phylogenetic analyses. The mitochondrial genome of C. notata was found to be 16,600 bp long, which consisted of 22 tRNA genes, 2 rRNA genes, 13 protein-coding genes, and 1 control region (D-loop). The base composition was 27.6% A, 24.8% T, 31.0% C, and 16.6% G. A phylogenetic tree reconstructed with the neighbor-joining method depicted a clone relationship with seven species of family Pomacentridae and our previous study based on CO1 gene sequences. The complete mitochondrial genome is a valuable resource in classifying and conserving C. notata.

| S-EPMC9037164 | biostudies-literature

Sequencing and analysis of the complete mitochondrial genome of Gymnogobius laevis.

Project description:Gymnogobius laevis (Steindachner, 1879) is a small, benthic freshwater fish. In a previous study, it was reported as a rare resident in Heilongjiang Province. In this study, the mitochondrial genome of G. laevis was sequenced. It is 16,519 base pairs (bp) in length and contains 13 protein-coding genes, two ribosomal RNA genes (12S rRNA and 16S rRNA), 22 transfer RNA genes (tRNA), and two non-coding control regions. The A + T content is 55.71% in the G. laevis mitochondrial genome. A phylogenetic tree shows that G. laevis is closely related to the family Gobiinae based on complete mitogenome sequences.

| S-EPMC9176352 | biostudies-literature

Complete mitochondrial genome sequencing of central Indian domestic pig.

Project description:Domestic pig (Sus scrofa domesticus) is one of the important farm animal contributing 7% of the country's total animal protein sources in India. In the present study, random hexamer primer was used to amplify the complete mitochondrial genome of Central Indian domestic pig and resolved the complete mitochondrial sequence by shotgun sequencing followed by de novo assembly in MIRA version 4.0.5. The sequence assembly revealed to be 15,827 bp mitogenome of pig (accession no. KT965278). The mitogenome in the present study has 99% homology with previously reported mitogenome of pigs from different parts of the world. The present study is the first report of complete sequence of mitogenome of pig from Indian subcontinent. Mitogenome analysis by MITOS web server revealed similarity of gene order, organization with the other pig breeds and vertebrates, comprising of 13 protein-coding genes, 22 tRNAs, 2 rRNAs and a control region. It was concluded that modified random hexamer can be successfully used for whole mitogenome sequencing using NGS without designing mitogenome-specific primer, thereby reducing cost and labor.

| S-EPMC7801016 | biostudies-literature

Sequencing and analysis of the complete mitochondrial genome of Datnioides campbelli (Datnioididae).

Project description:In this study, the complete mitochondrial genome sequence of the New Guinea tiger fish Datnioides campbelli (Whitley 1938) (Lobotiformes: Datnioididae) was sequenced by next-generation sequencing method. The assembled mitochondrial genome consists of 13 protein-coding genes, 22 transfer RNA genes, and two ribosomal RNA genes, with a length of 16,416 bp. The total base composition of the mitogenome of D. campbelli was 29.31% for A, 29.02% for C, 15.14% for G and 26.54% for T. A phylogenetic tree based on 13 protein-coding genes (PCGs) provides important molecular data for further phylogeographic and evolutionary analysis of Lobotiformes.

| S-EPMC9661975 | biostudies-literature

Sequencing and analysis of the complete mitochondrial genome of Metrioptera bonneti (Orthoptera: Tettigoniidae).

Project description:Here, we report the complete mitochondrial genome sequence of Metrioptera bonneti and its phylogenetic status. The complete mitogenome of M. bonneti is 16,273 bp in size and consisted of 13 protein-coding genes, 22 tRNA genes, two rRNA genes, and one D-loop. The overall nucleotide composition of the mitogenome was 35% A, 20.4% C, 11.7% G, and 32.9% T, with an A + T bias of 67.9%. Using the 13 PCGs and two rRNA of M. bonneti, together with 39 Tettigoniidae and two outgroup species, we constructed a phylogenetic tree based on the Bayesian inference method. The tree showed that M. bonneti forms a sister clade with Metrioptera ussuriana and supported the monophyly of Tettigoniinae.

| S-EPMC7799858 | biostudies-literature