Browse
Submit Data
Databases
API
Help

Dataset Information

16 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

The complete chloroplast genome of a medical herb, Rheum lhasaense (Polygonaceae), from Qinghai-Tibet Plateau in China.

ABSTRACT: Rheum lhasaense (Polygonaceae) is one of the genuine medicinal herbs in Qinghai-Tibet Plateau, China. Here we report the first chloroplast (cp) genome of R. lhasaense using Illumina NovaSeq 6000 platform. The length of its complete cp genome is 161,820 bp, containing four sub-regions. A large single copy region (LSC) of 87,086 bp and a small single copy region (SSC) of 12,814 bp are separated by a pair of inverted repeat regions (IRs) of 30,960 bp. The complete cp genome of R. lhasaense contains 130 genes, including 85 protein-coding genes, 37 tRNA genes, and 8 rRNA genes. The overall GC content of the cp genome is 37.4%. The phylogenetic analysis, based on 28 cp genomes, suggested that R. lhasaense is closely related to R. acuminatum and R. pumilum.

SUBMITTER: Zhang R

PROVIDER: S-EPMC8774141 | biostudies-literature |

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Similar Datasets

The complete chloroplast genome of a medical herb, Halenia elliptica D.Don (Gentianaceae), from Qinghai-Tibet Plateau in China.

Project description:Halenia elliptica D.Don (Gentianaceae) is one of the genuine medicinal species in Qinghai-Tibet Plateau, China. Here we report the first chloroplast (cp) genome of H. elliptica using Illumina HiSeq X Ten platform. The length of its complete cp genome is 153,341 bp, containing four sub-regions; a large single-copy region (LSC) of 82,811 bp and a small single-copy region (SSC) of 18,278 bp, which are separated by a pair of inverted repeat regions (IRs) of 26,126bp each. The complete cp genome of H. elliptica contains 129 genes, including 84 protein-coding genes, 37 tRNA genes, and 8 rRNA genes. The overall GC content of the cp genome is 38.1%. The phylogenetic analysis, based on 15 cp genomes, suggested that H. elliptica is closely related to Halenia corniculata (L.) Cornaz and Swertia species.

| S-EPMC7707369 | biostudies-literature

The complete chloroplast genome of a medical herb, Potentilla parvifolia Fisch. (Rosaceae), from Qinghai-Tibet Plateau in China.

Project description:Potentilla parvifolia Fisch. (Rosaceae) is one of the genuine medicinal materials in Qinghai-Tibet Plateau, China. Here we report the first chloroplast (cp) genome of P. parvifolia using Illumina NovaSeq 6000 platform. The length of its complete cp genome is 152,898 bp, containing four sub-regions; a large single copy region (LSC) of 84,160 bp and a small single copy region (SSC) of 18,128 bp are separated by a pair of inverted repeat regions (IRs) of 25,305bp. The complete cp genome of P. parvifolia contains 130 genes, including 85 protein-coding genes, 37 tRNA genes, and 8 rRNA genes. The overall GC content of the cp genome is 37.2%. The phylogenetic analysis, based on 17 cp genomes, suggested that P. parvifolia is closely related to P. fruticosa L. and Fragaria species.

| S-EPMC7872539 | biostudies-literature

Characterization of the complete chloroplast genome of medicinal plant Rheum officinale (Polygonaceae).

Project description:The complete chloroplast (cp) genome of Rheum officinale Baill. was determined based on the Illumina Sequencing data. The cp genome is 161,563?bp in length. The overall G?+?C content of the cp genome was 37.31%. The R. officinale cp genome contains 129 genes, including 84 protein-coding genes, eight rRNA genes (four rRNA species), and 37 tRNA genes (20 tRNA species). A neighbour-joining phylogenetic tree clarified that the cp genome of R. officinale was closely related to that of R. palmatum in Polygonaceae.

| S-EPMC7687616 | biostudies-literature

The complete chloroplast genome of Abies georgei Orr var. smithii, a species endemic to the Qinghai-Tibet Plateau, China.

Project description:Abies georgei Orr var. smithii is an evergreen coniferous species of Pinaceae, and is endemic to the Qinghai-Tibet Plateau of China. Considering its vital ecological functions in this unique area, the complete chloroplast (cp) genome was constructed in this study to provide genetic information for its further study of conservation and evolution. The complete cp genome is 121,213 bp in length with GC content of 38.3%, and contains a tetrad structure, including a large single copy region of 76,278 bp, a small single copy of 42,575 bp, and two very short repeats of 1,180 bp for each. Besides, it contains 113 genes in total, including 74 CDSs, 35 tRNAs, and four rRNAs. This genome has been deposited in Genbank under accession number of MT527722.

| S-EPMC7783149 | biostudies-literature

Phylogenetic relationship and characterization of the complete chloroplast genome of the alpine leaf-warbler in Qinghai-Tibet Plateau.

Project description:The Alpine Leaf-warbler (Phylloscopus occisinensis) is a small-sized and poorly-known songbird endemic to China. In this study, we sequenced and described the whole mitochondrial genome of the Alpine leaf-warbler. The entire mitochondrial sequence was determined by long-range PCR and conserved primer walking approaches. The results demonstrated that the whole mitochondrial genome of P. occisinensis was 16,879 bp in length with 53.1% A + T content; the genome harboured the same gene order as that of other passerine birds, including 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes and non-coding control region. The control region (D-loop) of P. rubicilloides include two portions that one was located between tRNA-Gln and tRNA-Phe (219 bp in length) and the other is between tRNA-Thr and tRNA- Pro (1087 bp in length), which is similar to other Leaf-warblers. Phylogenetic analysis indicated that the genome of Phylloscopus species clustered within a clade and is closer related to Aegithalidae species than Paridae species. These mitochondrial data are potentially important for the further studies on molecular evolution and conservation genetics on leaf warbler species.

| S-EPMC7707335 | biostudies-literature

Qinghai-Tibet Plateau soil

Project description:Qinghai-Tibet Plateau soil

| PRJNA658924 | ENA

Mosquitoes and mosquito-borne arboviruses in the Qinghai-Tibet Plateau--focused on the Qinghai area, China.

Project description:An investigation was conducted to identify the distribution of mosquitoes and mosquito-borne arboviruses in the Qinghai-Tibet Plateau, China from July to August in 2007. A total of 8,147 mosquitoes representing six species from three genera (Aedes, Culex, and Anopheles) were collected in three locations (Geermu city, altitude of 2,780 m; Xining city, 2,200 m; Minhe county, 1,700 m). Six virus isolates were obtained including Tahyna virus (TAHV), Liaoning virus, and Culex pipiens pallens Densovirus. A serosurvey showed immunoglobulin G antibodies by immunofluorescence assay (IFA) against TAHV in residents of all three locations. The IFA-positive human samples were confirmed by 90% plaque-reduction neutralization tests (PRNT(90)) against TAHV with titers ranging from 1:20 to 1:10,240. In addition, TAHV seropositive cows, sheep, and swine were found in these locations. This investigation represents the first isolation of TAHV from Ae. (Och.) detritus and the first evidence of TAHV infection in residents and livestock in the Qinghai-Tibet Plateau.

| S-EPMC2844569 | biostudies-literature

Characteristics of complete chloroplast genome of a high-quality forage on Qinghai-Tibet Plateau, Medicago archiducis-nicolai Sirj. (Fabaceae：Trifolieae).

Project description:Medicago archiducis-nicolai Sirj. is a well-known high-quality forage as its good palatability and strong tolerance to drought, cold and saline-alkali stress. Here, the complete chloroplast genome sequence of M. archiducis-nicolai was reported. The size of the complete chloroplast genome is 127,072 bp in length. The chloroplast genome has no inverted repeat (IR) regions, which is very common in the family Fabaceae. The M. archiducis-nicolai chloroplast genome encodes 106 genes: 72 protein-coding genes, 30 tRNAs, and 4 rRNAs. The phylogenetic analysis result strongly suggested that M. archiducis-nicolai is a distinct lineage in Medicago, being sister to highly supported clade composed of three species (M. hybrida, M. papillosa and M. sativa).

| S-EPMC7836982 | biostudies-literature

The complete chloroplast genome sequence of Rheum tanguticum, an endangered Chinese medicinal plant (Polygonaceae).

Project description:Rheum tanguticum is a valuable medicinal plant endemic to the Qinghai-Tibetan Plateau. It has been listed classified under the IUCN Red List categories of Vulnerable due to the low reproductive rate and heavy exploitation. In this study, the complete chloroplast (cp) genome of R. tanguticum has been assembled using data from the whole-genome Illumina sequencing. The cp genome is 161,515?bp in size and contains two inverted repeat regions of 30,823?bp each, which is separated by a large single-copy region of 86,675?bp and a small single-copy region of 13,194?bp. The cp genome contains 87 protein-coding genes, 37 tRNA genes, and 8 rRNA genes. Phylogenetic analysis revealed that the cp genome of R. tanguticum was closely related to that of the R. palmatum.

| S-EPMC7707752 | biostudies-literature

Tahyna virus infection, a neglected arboviral disease in the Qinghai-Tibet Plateau of China.

Project description:Tahyna virus (TAHV) was first isolated from mosquitoes collected in the suburbs of Geermu city in the Qinghai-Tibet Plateau of China in 2007. Since then, TAHV antibodies have been detected in local livestock in Geermu, Qinghai. To determine whether the disease caused by TAHV was present in local residents, an investigation was conducted in the summer of 2009. During this investigation, ward inspections were conducted in rural clinics, and clinical information and specimens were collected from patients who complained mainly of acute fever. The collected samples were tested by serological and molecular methods. The results showed that four samples were positive for TAHV immunoglobulin M and had four-fold or higher levels of TAHV-neutralizing antibody titers between convalescent-phase and acute-phase, and that TAHV nucleotide sequences were detected in two acute sera. Clinical features of TAHV infection commonly included fever, accounting for 100%. Among all other symptoms, the one with the highest frequency was pharyngitis (80%), followed by malaise, inappetence, arthralgia, headache, and drowsiness. Follow-up surveys revealed that all cases recovered in 2-5 days after onset, and no serious or deadly cases were observed. This is the first time that the disease caused by TAHV infection has been reported in China. TAHV infection is another known mosquito-borne arboviral disease in China.

| S-EPMC4024839 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

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