Browse
Submit Data
Databases
API
Help

Dataset Information

36 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

The complete chloroplast genome of Epimedium pubescens Maxim. (Berberidaceae), a traditional Chinese medicine herb.

ABSTRACT: Epimedium pubescens Maxim. is a well-known traditional Chinese medicine herb. In this study, the complete chloroplast genome of E. pubescens was sequenced. The genome was 158 956 bp in length, with a large single-copy region of 86,345 bp, a small single-copy region of 17,075 bp, and 2 inverted repeat regions of 27,768 bp. The genome consisted of 113 genes, including 79 protein-coding genes, 30 tRNA genes, and 4 rRNA genes. The GC contents were 38.82%. Phylogenetic analysis showed that E. pubescens of series Brachyrcerae was firstly clustered with E. acumiantum Franch. of ser. Dolichocerae, but not with E. brevicornu Maxim. from the same series.

SUBMITTER: Huang R

PROVIDER: S-EPMC7781925 | biostudies-literature |

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Similar Datasets

The complete chloroplast genome of Epimedium brevicornu Maxim (Berberidaceae), a traditional Chinese medicine herb.

Project description:Epimedium brevicornu Maxim. is a traditional Chinese medicine herb with good effects on many diseases. In the present paper, the complete chloroplast genome of E. brevicornu was sequenced. The complete chloroplast genome of E. brevicornu was 159572 bp in length with 38.83% GC content, including four distinct regions: large single-copy region (86535 bp), small single-copy region (17641 bp), and a pair of inverted repeat regions (27698 bp). The chloroplast genome encoded 112 unique genes, which included 78 protein-coding genes, 30 tRNA genes, and 4 rRNA genes. Phylogenetic analysis with the previously reported chloroplast genomes of Epimedium showed that E. brevicornu with small flowers at first clustered with large-flowered E. acuminatum into a strongly supported branch, but not with Epimedium species having similar floral characters.

| S-EPMC7748679 | biostudies-literature

The complete chloroplast genome of Epimedium sagittatum (Sieb. Et Zucc.) Maxim. (Berberidaceae), a traditional Chinese herb.

Project description:Epimedium sagittatum is an important traditional medicinal plant in China. In this study, we assembled the complete chloroplast (cp) genome of E. sagittatum. The whole cp genome of E. sagittatum is 157,114?bp in length, comprising a pair of inverted repeat (IR) regions (25,775?bp) separated by a large single copy (LSC) region (88,507?bp) and a small single copy (SSC) region (17,057?bp). The E. sagittatum cp genome contains 133 genes, of which 82 protein-coding genes, 38 tRNA genes, 8 rRNA genes and 5 pseudogenes. Phylogenetic analysis shows that E. sagittatumis closely clustered with E. lishihchenii. This genome provides a wealth of information for distinguishing of Epimedium species.

| S-EPMC7706818 | biostudies-literature

The complete chloroplast genome of Epimedium brevicornu (Berberidaceae), a traditional Chinese medicinal herb.

Project description:Epimedii Folium has been used as a common traditional Chinese medicine for more than 2000 years in China. In this study, we assembled the complete chloroplast (cp) genome of Epimedium brevicornu. The whole cp genome of E. brevicornu is 158,658 bp in length, comprising a pair of inverted repeat (IR) regions (27,699 bp) separated by a large single copy (LSC) region (86,558 bp) and a small single copy (SSC) region (16,702bp). The E. brevicornu cp genome contains 129 genes, of which 84 protein-coding genes, 37 tRNA genes, and eight rRNA genes. Phylogenetic analysis shows that E. brevicornu is closely clustered with E. wushanense, E. lishihchenii, and E. sagittatum. The published E. brevicornu chloroplast genome will provide useful information for the phylogenetic and evolutionary study on Epimedium family of Berberidaceae.

| S-EPMC7748714 | biostudies-literature

The complete chloroplast genome of Epimedium wushanense T. S. Ying. (Berberidaceae), a traditional Chinese medicinal herb.

Project description:Epimedium wushanense is a well-known medicinal plant in Berberidaceae in China. In this study, we sequenced the complete chloroplast (cp) genome of E. wushanense. The results showed that the cp genome of E. wushanense was 157,283 bp in length, which is composed of a large single-copy region (LSC, 88,579 bp) and a small single-copy region (SSC, 17,082 bp) that were separated by a pair of inverted repeat regions (IRa and IRb, 25,811 bp). The chloroplast genome of E. wushanense contains 112 unique genes, of which are 78 protein-coding genes, 30 tRNA genes, and 4 rRNA genes. The overall GC content was 38.78%. The phylogenetic tree analysis showed that E. wushanense was closely related to E. pseudowushanense, E. lishihchenii, and E. sagittatum.

| S-EPMC7748643 | biostudies-literature

The complete chloroplast genome of Plagiorhegma dubia Maxim., a traditional Chinese medicinal herb.

Project description:Plagiorhegma dubia Maxim. is a traditional Chinese medicinal herb from Plagiorhegma, Berberidaceae, which is distributed in the northeast of China, Korea, Russia. The complete chloroplast genome is 152,468 bp in length, with large single copy (LSC 82,257 bp) and small single copy (SSC 16,599 bp) regions separated by a pair of inverted repeats (IR 26 805 bp). The genome has a total of 113 genes including 79 protein-coding genes, 30 tRNA genes, and 4 rRNA genes. Phylogenetic analysis shows that P. dubia is closely related with Sinopodophyllum hexandrum and Epimedium species. The results are of great implication for the development and utilization of P. dubia and the phylogenetic researches on Berberidaceae.

| S-EPMC7800371 | biostudies-literature

The complete chloroplast genome of Berberis weiningensis (Berberidaceae), an endemic and traditional Chinese medicinal herb.

Project description:Berberis weiningensis is a frequently-used traditional Chinese medicinal herb that included various active alkaloids. In this study, we assembled the complete chloroplast (cp) genome of B. weiningensis. The complete cp genome of B. weiningensis is 166,275 bp in length, and has a typical structure with large single-copy (LSC 73,624 bp) and small single-copy (SSC 18,608 bp) regions separated by a pair of inverted repeats (IRs 37,019 bp) of large size. The B. weiningensis cp genome contains 147 genes, of which 101 protein-coding genes, 8 rRNA genes, and 38 tRNA genes. The phylogenetic analysis revealed that Berberis species closely clustered with Mahonia species, which obviously support that Mahonia and Berberis are not monophyletic.

| S-EPMC7995825 | biostudies-literature

The complete chloroplast genome of Asarum heterotropoides Fr. Schmidt var. mandshuricum (Maxim.) Kitag. (Aristolochiaceae), a traditional Chinese medicine herb.

Project description:The complete chloroplast genome of A. heterotropoides var. mandshuricum reported herein was a circular DNA molecule of 160,262 bp in length. The typical quadripartite structure of the genome consisted of a pair of inverted repeats (IRs) of 27,262 bp separated by a large single-copy (LSC) region of 88,927 bp and a small single-copy region (SSC) of 16,811 bp. The overall GC content of the genome is 38.45%, with 36.7%, 33.1%, and 43.0% in LSC, SSC, IR regions, respectively. The cp genome encoded 125 genes, including 83 protein-coding genes, 34 tRNA genes, and 8 rRNA genes. 138 SSRs were identified in the genome. Phylogenetic anlysis showed the position of A. heterotropoides var. mandshuricum is closely related to A. heterotropoides.

| S-EPMC8344226 | biostudies-literature

The complete chloroplast genome of Epimedium sutchuenense Franch. (Berberidaceae)

Project description:Abstract Epimedium L. is the largest herbaceous genus in the family Berberidaceae which comprises more than 60 species. Epimedium sutchuenense Franch. is narrowly inhabited in the Daba Mountains of China. In the current study, we assembled the first complete chloroplast genome of E. sutchuenense through Illumina paired-end sequencing. The complete chloroplast genome of E. sutchuenense was 157,218 bp in length and the total GC content was 38.78%. A total of 112 unique genes were identified, including 78 protein-coding genes, 30 tRNA genes and 4 rRNA genes. The phylogenetic analysis demonstrated that E. sutchuenense was sister to Epimedium wushanense T. S. Ying. Our results provided valuable information for further phylogenetic research and germplasm exploration of Epimedium genus.

| S-EPMC8547808 | biostudies-literature

The complete chloroplast genome of Epimedium muhuangense (Berberidaceae).

Project description:Epimedium muhuangense S. Z. He & Y. Y. Wang 2017, one of the rare unifoliolate species in the Epimedium genus of Berberidaceae, is distributed in the Guizhou province of China. In present research, we sequenced the complete chloroplast genome of E. muhuangense with Illumina sequencing technology. The whole genome was 157,264 bp in length, which consisted of a large single-copy region (LSC, 88,588 bp), a small single-copy region (SSC, 17,036 bp), and a pair of inverted repeat regions (IRa and IRb, 25,820 bp). A total of 112 unique genes were successfully annotated, consisting of 78 protein-encoding genes, 30 rRNA, and four tRNA. Phylogenetic analysis demonstrated that E. muhuangense is closely related to E. elachyphyllum.

| S-EPMC9116252 | biostudies-literature

The complete chloroplast genome of Epimedium tianmenshanense (Berberidaceae).

Project description:In this study, the complete chloroplast (cp) genome of Epimedium tianmenshanense was sequenced and assembled. The circular genome is 157,066 bp in size. The whole chloroplast genome of E. tianmenshanense contains 112 unique genes, of which 78 protein-coding genes, 30 tRNA genes, and four rRNA genes. The phylogenetic analysis based on 17 complete chloroplast genomes demonstrated a closer relationship between E. tianmenshanense and E. lishihchenii.

| S-EPMC7748789 | 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