Browse
Submit Data
Databases
API
Help

Dataset Information

16 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

The complete mitochondrial genome of Pedetontus zhejiangensis (Microcoryphia: Machilidae) and its phylogeny.

ABSTRACT: The complete mitochondrial genome of Pedetontus zhejiangensis (Microcoryphia: Machilidae) was successfully sequenced. The mitochondrial genome of P. zhejiangensis was a circular molecule of 15,602 bp in length, containing 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes, and the control region, which showed the typical insect mitochondrial genome arrangement. The AT content of the whole genome was 73.8% and the length of the control region was 671 bp with 82.5% AT content. In BI and ML phylogenetic trees, P. zhejiangensis was a sister group to Pedetontus silvestrii, and the monophyly of Pedetontus was strongly supported. The genus Pedetontinus was a sister group to Pedetontus.

SUBMITTER: Shen SQ

PROVIDER: S-EPMC7782177 | biostudies-literature |

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Similar Datasets

The complete mitochondrial genome of Neurigona zhejiangensis (Diptera: Dolichopodidae).

Project description:The long-legged fly Neurigona zhejiangensis belongs to the subfamily Neurigoninae of Dolichopodidae. The mitogenome (GenBank accession number: MT921956) of N. zhejiangensis was sequenced, the first representative complete mitogenome from this subfamily. The complete mitogenome is 17,141 bp, includes 13 protein-coding genes, 2 rRNAs, and 22 transfer RNAs. All genes have the same location and coding strand as in other published species of Dolichopodidae. Nucleotide composition is biased toward A and T, which together made up 77.3% of the entire genome. Bayesian inference strongly supported the monophyly of Empidoidea, Empididae and Dolichopodidae, with the phylogenetic relationships within Empidoidea: (Dolichopodinae + Neurigoninae) + ((Empidinae + (Trichopezinae + Oreogetoninae)) + Ocydromiinae).

| S-EPMC7819116 | biostudies-literature

Complete mitochondrial genome and phylogeny of Pleistocene mammoth Mammuthus primigenius.

Project description:Phylogenetic relationships between the extinct woolly mammoth (Mammuthus primigenius), and the Asian (Elephas maximus) and African savanna (Loxodonta africana) elephants remain unresolved. Here, we report the sequence of the complete mitochondrial genome (16,842 base pairs) of a woolly mammoth extracted from permafrost-preserved remains from the Pleistocene epoch--the oldest mitochondrial genome sequence determined to date. We demonstrate that well-preserved mitochondrial genome fragments, as long as approximately 1,600-1700 base pairs, can be retrieved from pre-Holocene remains of an extinct species. Phylogenetic reconstruction of the Elephantinae clade suggests that M. primigenius and E. maximus are sister species that diverged soon after their common ancestor split from the L. africana lineage. Low nucleotide diversity found between independently determined mitochondrial genomic sequences of woolly mammoths separated geographically and in time suggests that north-eastern Siberia was occupied by a relatively homogeneous population of M. primigenius throughout the late Pleistocene.

| S-EPMC1360101 | biostudies-literature

Complete mitochondrial genome of Pelecanus crispus and its phylogeny.

Project description:The Dalmatian Pelican (Pelecanus crispus), in the order Pelecaniformes, its habitat is distributed in Europe, Asia, and Africa. It is a large waterfowl that is of international concern. In this study, we first sequenced and described the complete mitochondrial genome and phylogeny of P. crispus. The results showed that the whole genome of P. crispus was 16,131 bp in length, and contained 13 protein-coding genes, 22 transfer RNA genes, two ribosome RNA genes, and one non-coding control region. The overall base composition of the mitochondrial DNA was 30.48% for A, 23.15% for T, 31.68% for C, and 14.69% for G, with a GC content of 46.37%. A phylogenetic tree of P. crispus in Pelecaniformes confirmed that P. crispus was sister to C. occidentalis. This information will be useful in the current understanding of the phylogeny and evolution of Pelecaniformes.

| S-EPMC7706529 | biostudies-literature

Molecular phylogeny of selected dorid nudibranchs based on complete mitochondrial genome.

Project description:Dorid nudibranchs are a large group of mollusks with approximately 2,000 recorded species. Although agreement exists on the monophyletic nature of the dorid nudibranch group, the interfamily relationships of the suborder are subject to debate. Despite efforts to elucidate this issue using short molecular markers, the conclusiveness of the findings has been hindered by branching polytomy. Mitogenomes are known to be effective markers for use in phylogenetic investigations. In this study, eight mitogenomes of dorid nudibranchs were decoded and analyzed. Gene content and structure showed little change among species, reflecting the conserved mitogenomes of dorid nudibranchs. For most genes, the direction was typical for nudibranchs; nevertheless, tRNACys had an inverse direction in Cadlinidae species. Phylogenetic trees based on nucleotide and amino acid datasets revealed a relatively consistent pattern of interfamily relationships with little difference for positions of Phyllidiidae and Cadlinidae. Species of Cadlinidae were clustered together and did not form a clade with Chromododidae. Additionally, Goniodorididae was sister to Aegiridae, whereas Discodoridae was sister to Dorididae. This finding was supported by tree topology test based on mitogenome data. The results of the present study indicate that complete mitogenomes are promising markers for investigating interfamily relationships among dorid nudibranchs.

| S-EPMC9637207 | biostudies-literature

The complete mitochondrial genome of Sarcocheilichthys davidi and its phylogeny.

Project description:Sarcocheilichthys davidi is a small-size ornamental freshwater species. In the present study, the complete mitochondrial genome of S. davidi was first determined using the next-generation sequencing technology. The result showed that the circular mitogenome was 16,675 bp in length, contained 13 protein-coding genes (PCGs), two ribosomal RNA (rRNA) genes, 22 transfer RNA (tRNA) genes, and two non-coding regions: origin of light-strand replication (OL) and displacement loop locus (D-loop). In addition to ND6 and eight tRNA genes, most mitochondrial genes were encoded on the heavy strand. Furthermore, the overall base composition was 29.97% A, 26.12% T, 26.86% C, 17.04% G, respectively, and showed AT-rich feature (56.09%). Moreover, phylogenetic analysis based on the tandem 13 PCGs nucleotide sequences indicated that S. davidi had a close relationship with S. snigripinnis and S. variegatus wakiyae. The complete mitogenome sequence of S. davidi would contribute to the better understanding of molecular systematics, selection, conservation, species identification and evolution of this species.

| S-EPMC7799733 | biostudies-literature

Complete mitochondrial genome of the snakehead (Channa gachua) and its phylogeny.

Project description:In present study, the mitochondrial genome (mitogenome) of Channa gachua was determined and the phylogenetic relationship of Channidae fish was reconsidered. The mitogenome of the C. gachua is 16547?bp in length, containing 13 protein coding genes (PCGs), 22 transfer RNA genes (tRNAs), two ribosome RNA genes (rRNAs), a control region (D-loop) and an origin region of replication on the light-strand (OL). The overall nucleotide composition is 28.32% A, 26.58% T, 29.41% C, 15.69% G, with 54.90% AT, respectively. Phylogenetic analyses revealed that C. gachua belongs to the genus Channa and shares a close relationship with C. marulius and C. striata.

| S-EPMC7707787 | biostudies-literature

The complete mitochondrial genome and phylogeny of Diacronema viridis (Pavlovales, Pavlovophyceae).

Project description:The complete mitochondrial genome of the pavlovophycean microalga Diacronema viridis CCMP 620 was sequenced and characterized. The circular mitogenome is a total 29,282 bp in length with 39.2% GC content and contains 47 genes, including 20 protein-coding, three rRNA, and 24 tRNA genes. The gene synteny of D. viridis and D. lutheri has been highly conserved; however, the gene content (absence of introns and ORFs) and repeat regions (3.7 kbp) of D. viridis contributed to significant difference of mitogenomes within the Diacronema.

| S-EPMC8158218 | biostudies-literature

The complete mitochondrial genome of Epeorus herklotsi (Ephemeroptera: Heptageniidae) and its phylogeny.

Project description:The mitochondrial genome of Epeorus herklotsi (Ephemeroptera: Heptageniidae) is a circular molecule of 15,801?bp in length with a base composition of 32.7% A, 32.9% T, 21.5% C, 13.0% G, including extra tRNAMet gene. The IMQM tRNA cluster is found in E. herklotsi as well as Parafornuru youi and two species of Epeorus (KM244708, KJ493406), while the typical IQM tRNA cluster is found in Paegniodes cupulatus. In BI and ML phylogenetic trees, the monophyly of the families Heptageniidae, Baetidae, and Ephemerellidae are highly supported. E. herklotsi is a sister clade to Epeorus sp2. (KJ493406).

| S-EPMC7800082 | biostudies-literature

The complete mitochondrial genome of Menticirrhus littoralis (Sciaenidae, Perciformes) and its phylogeny.

Project description:We describe the mitochondrial genome of the Menticirrhus littoralis and infer the phylogenetic position of Menticirrhus in the family Sciaenidae. The genome contains 16,499 base pairs distributed in gene regions (13 protein-coding regions, 2 rRNAs and 22 tRNAs) and a control region (CR). Our phylogenetic analysis suggests, with strong statistical support, that Menticirrhus is a sister group of the other sciaenids.

| S-EPMC7510665 | biostudies-literature

Complete mitochondrial genome of Chroicocephalus brunnicephalus from India: phylogeny with other Larids.

Project description:The complete mitogenome sequence of the brown-headed gull, Chroicocephalus brunnicephalus was determined in this study. The 16,771 bp genome consists of 13 protein-coding genes (PCGs), two ribosomal RNA (rRNA) genes, and 22 transfer RNA (tRNA) genes, and a control region (CR). The decoded mitogenome was AT-rich (54.77%) with nine overlapping and 17 intergenic spacer regions. Most of the PCGs were started by a typical ATG initiation codon except for cox1 and nad3. Further, the usual termination codons (AGG, TAG, TAA, and AGA) were used by 11 PCGs except for cox3 and nad4. The concatenated PCGs based Bayesian phylogeny clearly discriminates all the Laridae species and reflects the sister relationship of C. brunnicephalus with C. ridibundus. The present mitogenome-based phylogeny was congruent with the earlier hypothesis and confirmed the evolutionary position of the brown-headed gull as masked species. The generated mitogenome of C. brunnicephalus is almost identical to the previously generated mitogenome from China except for two base pairs in CR. To visualize the population structure of this migratory species, we propose more sampling from different geographical locations and the generation of additional molecular data to clarify the reality.

| S-EPMC7872550 | 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