Browse
Submit Data
Databases
API
Help

Dataset Information

10 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

The complete mitochondrial genome of the Thomas's horseshoe bat (Rhinolophus thomasi) using next-generation sequencing and Sanger sequencing.

ABSTRACT: The Thomas's horseshoe bat (Rhinolophus thomasi) is restricted to southeast Asia and few studies have been conducted on this species. Here we characterized the complete mitochondrial genome of R. thomasi using next-generation sequencing and Sanger sequencing. The whole mitogenome is 16,899 bp in length and contains 22 tRNA, 2 rRNA, 13 protein-coding genes and a non-coding control region. The tissue used in this study was taken from a sample collected 13 years ago and the genomic DNA was seriously degraded. Our study adds to a growing number of studies indicating that next-generation sequencing is powerful in generating genetic/genomic resources from museum samples.

SUBMITTER: Xing Y

PROVIDER: S-EPMC7800769 | biostudies-literature |

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Similar Datasets

The complete mitochondrial genome of the least horseshoe bat (Rhinolophus pusillus).

Project description:In this study, we generated the complete mitochondrial genome of Rhinolophus pusillus using next-generation sequencing. The mitochondrial genome was 16,833 bp in length and contained 13 protein-coding genes, 22 tRNA, 2 rRNA, and a non-coding control region. Phylogenetic analyses supported the taxonomic status of Rhinolophus pusillus among genus Rhinolophus, and the grouping with the sister taxon R. monoceros, which was highly restricted to Taiwan Island.

| S-EPMC7748457 | biostudies-literature

Heteroplasmy and ancient translocation of mitochondrial DNA to the nucleus in the Chinese Horseshoe Bat (Rhinolophus sinicus) complex.

Project description:The utility and reliability of mitochondrial DNA sequences in phylogenetic and phylogeographic studies may be compromised by widespread and undetected nuclear mitochondrial copies (numts) as well as heteroplasmy within individuals. Both numts and heteroplasmy are likely to be common across diverse taxa yet few studies have characterised their frequencies and variation at the intra-specific level. Here we report the presence of both numts and heteroplasmy in the mitochondrial control region of the Chinese horseshoe bat Rhinolophus sinicus. In total we generated 123 sequences from 18 bats, which contained two different numt clades (i.e. Numt-1 and Numt-2) and one mtDNA clade. The sequence divergence between Numt-1 and Numt-2 was 16.8% and each numt type was found in all four R. sinicus taxa, suggesting either two ancient translocations of mitochondrial DNA into the nucleus from the same source taxon, or a single translocation from different source taxa that occurred before the split of R. sinicus into different lineages. Within the mtDNA clade, phylogenetic relationships among the four taxa of R. sinicus were similar to those seen in previous results. Based on PCR comparisons, heteroplasmy was inferred between almost all individuals of R. sinicus with respect to sequence variation. Consistent with introgression of mtDNA between Central sinicus and septentrionalis, individuals from these two taxa exhibited similar signatures of repeated sequences in the control region. Our study highlights the importance of testing for the presence of numts and heteroplasmy when applying mtDNA markers to phylogenetic studies.

| S-EPMC4026475 | biostudies-literature

Complete mitochondrial genome sequence of E. suratensis revealed by next generation sequencing.

Project description:The complete mitochondrial genome of Etroplus suratensis, the Green chromide cichlid, was determined for the first time through NGS method. The genome is 16,467 bp (Accession no. KU301747) in length and consisted of 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes and one control region. Organization of genes and their order are in accordance with other vertebrates. The overall base composition on plus strand was A: 28.3%, G: 15.2%, C: 30.9%, T: 25.6%, and the A + T content 53.9%. The control region contains a putative termination-associated sequence and three conserved sequence blocks. This mitogenome sequence data would play an important role in population genetics and phylogenetics of cichlid fish of India.

| S-EPMC7800130 | biostudies-literature

Next-generation sequencing of the complete mitochondrial genome of the Nixi chicken (Gallus gallus).

Project description:Nixi chicken is a type of Tibetan chickens who lives at high altitudes in China. In this study, we reported the first complete mitochondrial genome of Nixi chicken by using a next-generation sequencing method. The assembled complete mitogenome contains one control region, 2 ribosomal RNAs, 13 protein-coding genes and 22 transfer RNA genes. Our work provides a valuable source of data for the study of the evolution of the Gallus gallus mitochondrial genome and contributes to the Nixi chicken breeding improvement program.

| S-EPMC7781923 | biostudies-literature

Lineage divergence and historical gene flow in the Chinese horseshoe bat (Rhinolophus sinicus).

Project description:Closely related taxa living in sympatry provide good opportunities to investigate the origin of barriers to gene flow as well as the extent of reproductive isolation. The only two recognized subspecies of the Chinese rufous horseshoe bat Rhinolophus sinicus are characterized by unusual relative distributions in which R. s. septentrionalis is restricted to a small area within the much wider range of its sister taxon R. s. sinicus. To determine the history of lineage divergence and gene flow between these taxa, we applied phylogenetic, demographic and coalescent analyses to multi-locus datasets. MtDNA gene genealogies and microsatellite-based clustering together revealed three divergent lineages of sinicus, corresponding to Central China, East China and the offshore Hainan Island. However, the central lineage of sinicus showed a closer relationship with septentrionalis than with other lineages of R. s. sinicus, in contrary to morphological data. Paraphyly of sinicus could result from either past asymmetric mtDNA introgression between these two taxa, or could suggest septentrionalis evolved in situ from its more widespread sister subspecies. To test between these hypotheses, we applied coalescent-based phylogenetic reconstruction and Approximate Bayesian Computation (ABC). We found that septentrionalis is likely to be the ancestral taxon and therefore a recent origin of this subspecies can be ruled out. On the other hand, we found a clear signature of asymmetric mtDNA gene flow from septentrionalis into central populations of sinicus yet no nuclear gene flow, thus strongly pointing to historical mtDNA introgression. We suggest that the observed deeply divergent lineages within R. sinicus probably evolved in isolation in separate Pleistocene refugia, although their close phylogeographic correspondence with distinct eco-environmental zones suggests that divergent selection might also have promoted broad patterns of population genetic structure.

| S-EPMC3581519 | biostudies-literature

Pest consumption in a vineyard system by the lesser horseshoe bat (Rhinolophus hipposideros).

Project description:Herbivorous arthropods cause immense damage in crop production annually. Consumption of these pests by insectivorous animals is of significant importance to counteract their adverse effects. Insectivorous bats are considered amongst the most voracious predators of arthropods, some of which are known crop pests. In vineyard-dominated Mediterranean agroecosystems, several crops are damaged by the attack of insect pests. In this study we aimed 1) to explore the diet and pest consumption of the lesser horseshoe bat Rhinolophus hipposideros and 2) analyse whether the composition of pest species in its diet changes throughout the season. We employed a dual-primer DNA metabarcoding analysis of DNA extracted from faeces collected in three bat colonies of a wine region in Southwestern Europe during the whole active period of most pest species. Overall, 395 arthropod prey species belonging to 11 orders were detected; lepidopterans and dipterans were the most diverse orders in terms of species. Altogether, 55 pest species were identified, 25 of which are known to cause significant agricultural damage and 8 are regarded as pests affecting grapevines. The composition of pest species in faeces changed significantly with the season, thus suggesting several periods should be sampled to assess the pest consumption by bats. As a whole, the results imply that R. hipposideros acts as a suppressor of a wide array of agricultural pests in Mediterranean agroecosystems. Therefore, management measures favouring the growth of R. hipposideros populations should be considered.

| S-EPMC6638854 | biostudies-literature

Systematic Evaluation of Sanger Validation of Next-Generation Sequencing Variants.

Project description:BackgroundNext-generation sequencing (NGS) data are used for both clinical care and clinical research. DNA sequence variants identified using NGS are often returned to patients/participants as part of clinical or research protocols. The current standard of care is to validate NGS variants using Sanger sequencing, which is costly and time-consuming.MethodsWe performed a large-scale, systematic evaluation of Sanger-based validation of NGS variants using data from the ClinSeq® project. We first used NGS data from 19 genes in 5 participants, comparing them to high-throughput Sanger sequencing results on the same samples, and found no discrepancies among 234 NGS variants. We then compared NGS variants in 5 genes from 684 participants against data from Sanger sequencing.ResultsOf over 5800 NGS-derived variants, 19 were not validated by Sanger data. Using newly designed sequencing primers, Sanger sequencing confirmed 17 of the NGS variants, and the remaining 2 variants had low quality scores from exome sequencing. Overall, we measured a validation rate of 99.965% for NGS variants using Sanger sequencing, which was higher than many existing medical tests that do not necessitate orthogonal validation.ConclusionsA single round of Sanger sequencing is more likely to incorrectly refute a true-positive variant from NGS than to correctly identify a false-positive variant from NGS. Validation of NGS-derived variants using Sanger sequencing has limited utility, and best practice standards should not include routine orthogonal Sanger validation of NGS variants.

| S-EPMC4878677 | biostudies-literature

Next-generation sequencing yields the complete mitochondrial genome of Microhyla beilunensis (Anura: Microhylidae).

Project description:The complete mitochondrial genome (mtDNA) of Microhyla beilunensis (Anura: Microhylidae) was sequenced and annotated. The length of mtDNA sequences of M. beilunensis was 16,721 bp, and encoded 13 protein-coding genes (PCGs), 22 transfer RNA (tRNA) genes, 2 ribosomal RNA (rRNA) genes, and a control region. The overall nucleotide composition of this genome was 29.1% A, 24.5% C, 14.5% G, 31.9% T, with a total A + T content of 61%. Phylogenetic analysis using Bayesian Inference (BI) method revealed that M. beilunensis was closely related with other 8 species from the genus Microhyla. The mtDNA dataset could be utilized for studying the molecular ecology and population genetics of Microhylid frogs.

| S-EPMC7782835 | biostudies-literature

Complete mitochondrial genome of the three Colombian Caribbean loggerhead sea turtles, using next-generation sequencing.

Project description:The loggerhead turtle, Caretta caretta (Linnaeus, 1758), is an endangered sea turtle in Colombian Caribbean beach. In the present study was sequenced the complete mitochondrial DNA of three loggerhead turtles using Illumina next-generation sequencing (NGS). The average nucleotide frequency was A: 35% T: 26%, C: 27% and G: 12%. This genome provides knowledge to the study of genetic variations and evolution of mitochondrial genomes of C. caretta. The sequences were deposited at the GenBank database under the accession number MF554690.1, MF579504.1 and MF579505.1.

| S-EPMC7800953 | biostudies-literature

Next-generation sequencing yields the complete mitochondrial genome of Pterygoplichthys pardalis (Loricariidae; Siluriformes).

Project description:In this study, we report the complete mitochondrial genome of Pterygoplichthys pardalis has derived by next-generation sequencing. The complete mitochondrial genome of P. pardalis contains 16,425 bp encompassing 13 protein-coding genes, 22 transfer RNA genes, two ribosomal RNA genes, and one control region (D-loop). The base composition is A 31.79%, C 26.89%, G 14.63%, and T 26.69%, and its gene arrangement is consistent with mitochondrial genomes derived from other representatives of Loricariidae. A phylogenetic tree of 24 Loricariidae species constructed based on the 13 coding genes shows that P. pardalis is clustered with other Pterygoplichthys genus. It suggests that the molecular classification results confirm its external morphological characteristics. These results have reference value for the further study of phylogenetic relationship, taxonomic classification, and phylogeography of Loricariidae.

| S-EPMC8530479 | 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