Browse
Submit Data
Databases
API
Help

Dataset Information

21 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

The complete mitochondrial genome of Psammomys obesus (Rodentia: Muridae).

ABSTRACT: The fat sand rats (Psammomys obesus) can easily induce obesity and acquire type 2 diabetes mellitus when they are fed with high-carbohydrate diets. P. obesus is often used as an animal model for studies on diabetes and obesity. We described 16,592 bp of P. obesus mtDNA that contains 13 protein-coding genes (PGCs), two rRNA genes (12S rRNA and 16S rRNA), 22 transfer RNA (tRNA) genes, and one control region (D-loop). The complete mitochondrial genome sequence provided here would be useful for further understanding the evolution of ratite and conservation genetics of P. obesus.

SUBMITTER: Lan Y

PROVIDER: S-EPMC7800552 | biostudies-literature |

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Similar Datasets

The complete mitochondrial genome of Niviventer sacer (Rodentia: Muridae).

Project description:Niviventer sacer (Rodentia: Muridae) had been regarded as a subspecies of N. confucianus, i.e. N. c. sacer, and was raised as a distinct species recently by our laboratory. We sequenced the complete mitochondrial genome of N. sacer first and annotated the genome structure. The total length of the genome was 16,308 base pairs (bp) containing 13 protein-coding genes (PCGs), two ribosomal RNA genes (rRNAs), 22 transfer RNA genes (tRNAs), and a control region. We also constructed the phylogenetic tree by maximum-likelihood method and it demonstrated that N. sacer was the sister clade of N. confucianus.

| S-EPMC9341373 | biostudies-literature

The complete mitochondrial genome of marmoset rats Hapalomys delacouri (Rodentia: Muridae).

Project description:The marmoset rats (Hapalomys delacouri) is a rarely investigated rodent. It occupies important ecological niche and phylogenetic position. The complete mitochondrial genome of H. delacouri was determined for the first time by long PCR and second-generation sequencing. The results showed that the entire mitogenome of H. delacouri was 16,316 bp long (deposited in GenBank with accession number MK850463). The gene order and orientation were the same as the most rodent. Only tRNALys (TTT) and tRNASer (AGN) of 22 transfer RNAs showed atypical cloverleaf structures, lacking a dihydrouridine (DHU) arm. The newly added H. delacouri mitogenome will benefit population genetic and phylogenetic studies in the rodent.

| S-EPMC7687551 | biostudies-literature

The complete mitochondrial genome of the Tamarisk gerbil, Meriones tamariscinus (Rodentia: Muridae).

Project description:The complete mitochondrial genome of the Tamarisk jird, Meriones tamariscinus, was sequenced. The 16,389bp genome contains 37 genes, typical for rodent mitogenomes, including 22 tRNA genes, 2 rRNA genes, and 13 protein-coding genes. The total GC content of the mitochondrial genome is 36.8%, with a base composition of 34.0% A, 24.5% C, 12.3% G, and 29.2% T. The phylogenetic analysis showed that M. tamariscinus was classified in the genus Meriones, Muridae.

| S-EPMC7800061 | biostudies-literature

Complete mitochondrial genome of the water vole, Microtus richardsoni (Cricetidae, Rodentia).

Project description:Water voles (Microtus richardsoni) are sensitive species distributed in the mountains of Canada (Alberta, British Columbia), and the United States of America (Idaho, Montana, Oregon, Utah, Washington, and Wyoming). We assembled the complete circular M. richardsoni mitogenome, which is 16,285 bp in length and encodes 13 protein-coding genes, 22 tRNA genes, and two rRNA genes. We estimated the phylogenetic tree of M. richardsoni and 24 related arvicoline species with two outgroup species: Phodopus roborovskii and Cricetus cricetus.

| S-EPMC7782294 | biostudies-literature

Assessment of three mitochondrial genes (16S, Cytb, CO1) for identifying species in the Praomyini tribe (Rodentia: Muridae).

Project description:The Praomyini tribe is one of the most diverse and abundant groups of Old World rodents. Several species are known to be involved in crop damage and in the epidemiology of several human and cattle diseases. Due to the existence of sibling species their identification is often problematic. Thus an easy, fast and accurate species identification tool is needed for non-systematicians to correctly identify Praomyini species. In this study we compare the usefulness of three genes (16S, Cytb, CO1) for identifying species of this tribe. A total of 426 specimens representing 40 species (sampled across their geographical range) were sequenced for the three genes. Nearly all of the species included in our study are monophyletic in the neighbour joining trees. The degree of intra-specific variability tends to be lower than the divergence between species, but no barcoding gap is detected. The success rate of the statistical methods of species identification is excellent (up to 99% or 100% for statistical supervised classification methods as the k-Nearest Neighbour or Random Forest). The 16S gene is 2.5 less variable than the Cytb and CO1 genes. As a result its discriminatory power is smaller. To sum up, our results suggest that using DNA markers for identifying species in the Praomyini tribe is a largely valid approach, and that the CO1 and Cytb genes are better DNA markers than the 16S gene. Our results confirm the usefulness of statistical methods such as the Random Forest and the 1-NN methods to assign a sequence to a species, even when the number of species is relatively large. Based on our NJ trees and the distribution of all intraspecific and interspecific pairwise nucleotide distances, we highlight the presence of several potentially new species within the Praomyini tribe that should be subject to corroboration assessments.

| S-EPMC3344912 | biostudies-literature

The complete mitochondrial genome of an Asian longicorn beetle, Neoplocaederus obesus (Gahan) (Coleoptera: Cerambycidae: Cerambycinae).

Project description:In this study, the complete mitochondrial genome of the Neoplocaederus obesus (GenBank accession number: MT525962) was sequenced. The 15,683 bp long genome has the standard metazoan complement of 38 genes. These genes contain 13 protein-coding genes, 22 transfer RNA genes, 2 ribosomal RNA genes, and 1 control region. The nucleotide composition of the N. obesus mitogenome was A: 37.20%, T: 32.19%, G: 12.10%, C: 18.52%. The A＋T content was 69.39%, showing strong AT skew.

| S-EPMC7782181 | biostudies-literature

Phylogeographic study of Apodemus ilex (Rodentia: Muridae) in Southwest China.

Project description:BACKGROUND:The Mountains of southwest China have complex river systems and a profoundly complex topography and are among the most important biodiversity hotspots in the world. However, only a few studies have shed light on how the mountains and river valleys promote genetic diversity. Apodemus ilex is a fine model for investigating this subject. METHODOLOGY/PRINCIPAL FINDINGS:To assess the genetic diversity and biogeographic patterns of Apodemus ilex, the complete cytochrome b gene sequences (1,140 bp) were determined from 203 samples of A. draco/ilex that were collected from southwest China. The results obtained suggested that A. ilex and A. draco are sistergroups and diverged from each other approximately 2.25 million years ago. A. ilex could be divided into Eastern and Western phylogroups, each containing two sub-groups and being widespread in different geographical regions of the southern Hengduan Mountains and the western Yunnan - Guizhou Plateau. The population expansions of A. ilex were roughly from 0.089 Mya to 0.023 Mya. CONCLUSIONS:Our result suggested that A. ilex is a valid species rather than synonym of A. draco. As a middle-high elevation inhabitant, the phylogenetic pattern of A. ilex was strongly related to the complex geographical structures in southwest China, particularly the existence of deep river valley systems, such as the Mekong and Salween rivers. Also, it appears that the evolutionary history of A. ilex, such as lineage divergences and population expansions were strongly affected by climate fluctuation in the Late Pleistocene.

| S-EPMC3274519 | biostudies-literature

Dietary ecology of Murinae (Muridae, Rodentia): a geometric morphometric approach.

Project description:Murine rodents represent a highly diverse group, which displays great ecological versatility. In the present paper we analyse the relationship between dental morphology, on one hand, using geometric morphometrics based upon the outline of first upper molar and the dietary preference of extant murine genera, on the other. This ecomorphological study of extant murine rodents demonstrates that dietary groups can be distinguished with the use of a quantitative geometric morphometric approach based on first upper molar outline. A discriminant analysis of the geometric morphometric variables of the first upper molars enables us to infer the dietary preferences of extinct murine genera from the Iberian Peninsula. Most of the extinct genera were omnivore; only Stephanomys showed a pattern of dental morphology alike that of the herbivore genera.

| S-EPMC3827291 | biostudies-literature

Complete Mitochondrial Genome of Three Species of the Genus Microtus (Arvicolinae, Rodentia).

Project description:The 65 species of the genus Microtus have unusual sex-related genetic features and a high rate of karyotype variation. However, only nine complete mitogenomes for these species are currently available. We describe the complete mitogenome sequences of three Microtus, which vary in length from 16,295 bp to 16,331 bp, contain 13 protein-coding genes (PCGs), two ribosomal RNA genes, 22 transfer RNA genes and a control region. The length of the 13 PCGs and the coded proteins is the same in all three species, and the start and stop codons are conserved. The non-coding regions include the L-strand origin of replication, with the same sequence of 35 bp, and the control region, which varies between 896 bp and 930 bp in length. The control region includes three domains (Domains I, II and III) with extended termination-associated sequences (ETAS-1 and ETAS-2) in Domain I. Domain II and Domain III include five (CSB-B, C, D, E and F) and three (CSB-1, CSB-2, and CSB-3) conserved sequence blocks, respectively. Phylogenetic reconstructions using the mitochondrial genomes of all the available Microtus species and one representative species from another genus of the Arvicolinae subfamily reproduced the established phylogenetic relationships for all the Arvicolinae genera that were analyzed.

| S-EPMC7696944 | biostudies-literature

Complete mitochondrial genome of Perny's long-nosed squirrel Dremomys pernyi (Rodentia: Sciuridae).

Project description:The complete mitochondrial genome of Perny's long-nosed squirrel (Dremomys pernyi) was firstly sequenced and characterized. The genome was 16,573 bp in length, and its composition and arrangement of genes were analogous to other rodents. The sequences of 13 protein-coding genes were used to construct phylogenetic tree for D. pernyi and other 13 sciurid species available on GenBank. To date, this is the first species whose complete mitochondrial genome sequence was sequenced in genus Dremomys. Our results will provide information for further molecular studies.

| S-EPMC7800828 | 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