Browse
Submit Data
Databases
API
Help

Dataset Information

33 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

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

ABSTRACT: 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.

SUBMITTER: Liu X

PROVIDER: S-EPMC8547808 | biostudies-literature |

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Similar Datasets

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

Project description:Epimedium davidii, which belongs to Berberidaceae, is mainly distributed in the southwest of China. In this study, the complete chloroplast genome of E. davidii was sequenced and assembled. The circular genome is 159,715 bp in length, which comprises a large single-copy region (LSC, 85,862 bp), a small single-copy region (SSC, 17,081 bp), and a pair of inverted repeat regions (IRa and IRb, 28,386 bp). The chloroplast genome of E. davidii contains 112 unique genes, of which 78 protein-coding genes, 30 tRNA genes, and 4 rRNA genes. Phylogenetic analysis indicated that E. davidii was closely related to Epimedium acuminatum.

| S-EPMC7748688 | biostudies-literature

The complete chloroplast genome of Epimedium fargesii Franch. (Berberidaceae), a rare plant species endemic to China.

Project description:Epimedium L. is a medicinally important herbaceous genus in the family Berberidaceae. Epimedium fargesii Franch. is only narrowly inhabited in the Daba Mountains in China. Here, we sequenced and assembled the first complete chloroplast genome of Epimedium fargesii Franch. The chloroplast genome of E. fargesii was 157,208 bp in length, with a total GC content of 38.77%. A total of 112 unique genes were identified, including 78 protein-coding genes, 30 tRNA genes, and four rRNA genes. Phylogenetic analysis indicated that E. fargesii formed a sister relationship with E. wushanense T. S. Ying. Our results provided fundamental data for further taxonomic and phylogenetic research of the genus Epimedium.

| S-EPMC8555541 | 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

The complete chloroplast genome of Epimedium flavum Stearn (Berberidaceae).

Project description:Epimedium flavum Stearn, which belongs to Berberidaceae, is mainly distributed in the Sichuan province of China. In this study, the complete chloroplast genome of E. flavum was reported for the first time. The whole genome of E. flavum was 159,134 bp in length, and revealed a typical quadripartite structure, including two copies of an inverted repeat (IR) region of 27,735 bp separating a large single-copy region (LSC, 86,576 bp) and a small single-copy region (SSC, 17, 088 bp). The chloroplast genome contained 112 unique genes, including 78 protein-coding genes, 30 tRNA genes, and 4 rRNA genes. Phylogenetic analysis showed that E. flavum of series Davidianae was firstly clustered with E. brevicornu of ser. Brachyerae.

| S-EPMC8330771 | biostudies-literature

The complete chloroplast genome of Epimedium mikinorii Stearn. (Berberidaceae).

Project description:Epimedium mikinorii is a vulnerable species in the Epimedium genus of Berberaceae. Here, we sequenced the complete chloroplast genome of E. mikinorii, which is 157,136 bp in length, and is a typical quadripartite circular molecule composed of two inverted repeats (IRs) of 25,896 bp for each, a large single-copy region (LSC) of 88,395 bp, and a small single-copy region (SSC) of 16,949 bp. The complete chloroplast genome of E. mikinorii contains 134 genes, including 83 protein-coding genes, 38 tRNA genes, 8 rRNA genes, and 5 pseudogenes. Phylogenetic analysis showed that E. mikinorii was closely related to E. dolichostemon.

| S-EPMC7748847 | biostudies-literature

Characterization of the complete chloroplast genome of Epimedium brevicornu (Berberidaceae).

Project description:The complete chloroplast genome sequence of Epimedium brevicornu, a common medicinal plant is widely distributed in South China. The plastome is 156,947?bp in length, with one large single-copy region of 88,535?bp, one small single-copy region of 17,012?bp, and two inverted repeat (IR) regions of 27,700?bp. It contains 132 genes, including 83 protein-coding genes, 8 ribosomal RNA, and 38 transfer RNA. Phylogenetic tree shows that this species is a sister to Epimedium acuminatum. The published plastome of E. brevicornu provides important insight into conservation and restoration efforts for E. brevicornu.

| S-EPMC7707583 | biostudies-literature

The complete chloroplast genome of Epimedium xichangense Y. J. Zhang (Berberidaceae).

Project description:Epimedium xichangense, a critically endangered herb with limited population, mainly distributes in Sichuan province, China. In our study, we obtained the complete chloroplast genome of E. xichangense with a length of 158,955 bp, including a large single copy region of 86,478 bp, small single copy region of 17,027 bp, and a pair of inverted repeat regions of 27,725 bp. The GC content in the whole chloroplast genome of E. xichangense is 38.81%. Among the 112 unique genes in the circular genome, 30 tRNA, four rRNA and 78 protein-coding genes were successfully annotated. We constructed the Maximum likelihood (ML) tree with 26 species, and came to the conclusion that E. xichangense was phylogenetically closely related to E. acuminatum and E. chlorandrum.

| S-EPMC7748833 | biostudies-literature

The complete chloroplast genome sequences of two ornamental Epimedium species (Berberidaceae).

Project description:Both Epimedium sutchuenense Franch. 1894 and E. fargesii Franch. 1894 are perennial herbs with excellent ornamental values due to their showy flowers. However, little molecular research has been done on these species. Here, the complete chloroplast (cp) genome of E. sutchuenense and E. fargesii was analyzed and reported. The cp genome sizes of E. sutchuenense and E. fargesii were 157, 263 and 157, 133 bp, respectively. Both the two cp genomes contained a pair of inverted repeat regions (IRs) (25,782 and 25,796 bp), separated by the small single-copy (SSC) region (17,106 and 17,071 bp) and a large single-copy (LSC) region (88,593 and 88,470 bp). A total of 113 unique genes were annotated in each of the two cp genomes, including 79 protein-coding genes, 30 tRNA genes, and four rRNA genes. Phylogenetic analysis supported a close relationship between E. sutchuenense and E. wushanense, while E. fargesii had no clear clustering branch.

| S-EPMC9176344 | 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

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