Browse
Submit Data
Databases
API
Help

Dataset Information

21 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

The complete chloroplast genome sequence of Rhodiola sacra (Prain ex Hamet) S. H. Fu.

ABSTRACT: Rhodiola sacra (Prain ex Hamet) S. H. Fu is a traditional natural plant pharmaceutical with anti-hypoxia effect and mainly distributed in Yunnan and Tibet (China). The complete chloroplast sequence of R. sacra was determined in our study. The cpDNA was 150,941 bp in length, containing a pair of inverted repeats (IRs) of 25,873 bp each separated by a large and small single copy (LSC and SSC) regions of 82,161 bp and 17,034 bp, respectively. The genome contained 84 protein coding genes, eight rRNA genes and 36 tRNA genes. Phylogenetic tree revealed that R. sacra closely related to Rhodiola kirilowii and Rhodiola crenulata.

SUBMITTER: Zhao K

PROVIDER: S-EPMC7706779 | biostudies-literature |

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Similar Datasets

Characterization of the complete chloroplast genome of Corydalis inopinata Prain ex Fedde (Papaveraceae).

Project description:The complete chloroplast genome of Corydalis inopinata Prain ex Fedde was assembled and characterized in this study. The chloroplast genome was 181,335 bp in length, consisting of a large single-copy (LSC) region of 91,727 bp, a small single-copy (SSC) region of 1502 bp, and a pair of inverted repeat (IR) regions of 44,053 bp. It encoded 110 unique genes, including 68 protein-coding genes, 29 tRNA genes, 4 rRNA genes, and 9 pseudogenes. Phylogenetic analyses by maximum likelihood (ML) and Bayesian inference (BI) revealed that C. inopinata was closely related to C. conspersa Maxim. with full support in the present sampling. The complete plastid genome provided in this work would be useful for elucidating the taxonomy, phylogeny, and evolution of C. inopinata and other related species.

| S-EPMC7782898 | biostudies-literature

The complete chloroplast genome sequence of the Dioscorea persimilis Prain et Burkill (Dioscoreaceae).

Project description:Dioscorea persimilis belongs to Dioscorea genus, which is considered as one of the most popular food and traditional folk medicine in China. The complete chloroplast genome of D. persimilis was determined in this study. The total genome size was 153,219 bp in length, containing a pair of inverted repeats (IRs) of 25,477 bp, which were separated by large single copy (LSC) and small single copy (SSC) of 83,448 bp and 18,817 bp, respectively. The GC content is 37.01%. A total of 129 genes were predicted including 84 protein-coding genes, eight rRNA genes and 37 tRNA genes. Phylogenetic tree analysis of 24 species in the genus Dioscorea indicated that D. persimilis was closer to Chinese yam, but has remote phylogenetic relationship with Guinea yam.

| S-EPMC7748837 | biostudies-literature

The complete chloroplast genome of Flemingia macrophylla (Willd.) Prain (Fabaceae) from Guangxi, China

Project description:Abstract Flemingia macrophylla (Willd.) Prain is an ethnomedicinal plant with high nutritional and medicinal values. In this study, we report the complete chloroplast genome of F. macrophylla. The chloroplast genome has a typical quadripartite structure with a genome size of 152,988 bp, including a large single-copy (LSC) of 83,634 bp, a small single-copy (SSC) of 17,774 bp and two inverted repeats (IRs) of 25,790 bp. The genome contains 129 genes, including 84 protein-coding, 37 tRNA and 8 rRNA genes. The overall GC content is 35.1%. Phylogenetic analysis showed that F. macrophylla grouped with a clade containing the genera of Fagelia, Dolichos, Eriosema, Dunbaria and Cajanus in Fabaceae. This study provides essential data and insight for understanding the phylogenetic placement of Flemingia.

| S-EPMC8583843 | biostudies-literature

The complete chloroplast genome sequence of Potentilla tanacetifolia Willd. ex Schltdl.

Project description:Potentilla tanacetifolia Willd. ex Schltdl. is a perennial herb in China, which has high ecological and economic values. Its complete chloroplast genome was reported in this study for the first time. The whole chloroplast genome was 157, 051 base pairs in length with 129 genes, including 84 protein-coding genes, 37 tRNAs, and 8 rRNAs. In addition, phylogenetic analysis showed a sister relationship between P. tanacetifolia and P. chinensis.

| S-EPMC7889225 | biostudies-literature

The First Chloroplast Genome Sequence of Boswellia sacra, a Resin-Producing Plant in Oman.

Project description:Boswellia sacra (Burseraceae), a keystone endemic species, is famous for the production of fragrant oleo-gum resin. However, the genetic make-up especially the genomic information about chloroplast is still unknown. Here, we described for the first time the chloroplast (cp) genome of B. sacra. The complete cp sequence revealed a circular genome of 160,543 bp size with 37.61% GC content. The cp genome is a typical quadripartite chloroplast structure with inverted repeats (IRs 26,763 bp) separated by small single copy (SSC; 18,962 bp) and large single copy (LSC; 88,055 bp) regions. De novo assembly and annotation showed the presence of 114 unique genes with 83 protein-coding regions. The phylogenetic analysis revealed that the B. sacra cp genome is closely related to the cp genome of Azadirachta indica and Citrus sinensis, while most of the syntenic differences were found in the non-coding regions. The pairwise distance among 76 shared genes of B. sacra and A. indica was highest for atpA, rpl2, rps12 and ycf1. The cp genome of B. sacra reveals a novel genome, which could be used for further studied to understand its diversity, taxonomy and phylogeny.

| S-EPMC5235384 | biostudies-literature

The complete chloroplast genome sequence of Cypripedium tibeticum King Ex Rolfe (Orchidaceae).

Project description:In this study, we determined the complete chloroplast genome of Cypripedium tibeticum, an endangered species in China. The plastome is 159,223 bp in length, with a large single-copy region (LSC) of 86,537 bp, a small single-copy region (SSC) of 17,552 bp, and a pair of inverted repeat regions (IRs) of 27,567 bp each. It contains 133 genes, including 87 protein-coding genes, 38 tRNA genes, and 8 rRNA genes. The overall GC content was 36.9%, while the corresponding values in the LSC, SSC, and IR regions are 34.6, 30.4, and 42.6%, respectively. The phylogenetic analysis showed that C. tibeticum was closely related to its congeners and the classification of five subfamilies of Orchidaceae was also highly supported.

| S-EPMC7720939 | biostudies-literature

The complete chloroplast genome sequence of spleen amaranth (Amaranthus dubius Mart. ex Thell., Amaranthaceae).

Project description:Amaranthus dubius is a leafy vegetable widely cultivated in Asia and Africa. The complete chloroplast genome of Amaranthus dubius was sequenced and assembled in this study. The complete chloroplast genome is 150,520 bp. A total of 130 genes were identified, including 85 protein-coding genes, eight rRNA genes, and 37 tRNA genes. The overall GC content of this genome was 36.6%. The phylogenetic tree based on 10 chloroplast genomes in Amaranthaceae supports that A. dubius is sister to A. hypochondriacus and A. caudatus.

| S-EPMC8547846 | biostudies-literature

Complete chloroplast genome sequence of Schima superba (Teaceae)

Project description:Abstract Schima superba is the dominant species of subtropical evergreen broad-leaved forest which has the characteristics of ecological fire prevention function. In this study, we report the complete chloroplast genome sequence of S. superba. The cp genome was 157,205 bp in length with a GC content of 37.40%, including a large single-copy (LSC 87,161 bp), a small single-copy (SSC 18,092 bp), and a pair of inverted repeats (IR 25,976 bp). The genome encoded 133 functional genes, including 88 protein-coding genes, 37 tRNA genes, and 8 rRNA genes. The phylogenetic analysis showed that S. superba was closely related to Schima sinensis, Schima multibracteata, Schima crenata, and Schima remotisertata.

| S-EPMC8725924 | biostudies-literature

Complete mitochondrial genome of Laudakia sacra (Reptilia: Agamidae).

Project description:The complete mitochondrial genome (mitogenome) sequence of Laudakia sacra was determined by using a PCR-based method. The total length of mitogenome is 16,555?bp, and contains 13 typical vertebrate protein-coding genes, 22 transfer RNA genes, 2 ribosomal RNA genes and 2 control regions. Only ND6 gene and 8 tRNA genes on the L-strand other than are encoded on the H-strand. The phylogenetic tree of L. sacra and 13 other species were built. The DNA data present here will facilitate future taxonomic work of the genus Laudakia.

| S-EPMC7687532 | biostudies-literature

Complete chloroplast genome sequence of Prunus mahaleb.

Project description:Prunus mahaleb (L.) Mill. is a kind of ornamental species which originated from Europe and Western Asia. Here, we use Illumina paired-end sequencing to obtain the complete chloroplast genome of P. mahaleb. The complete cp genome of P. mahaleb with a size of 157,824?bp in length is a circular molecular genome, including a pair of inverted repeat (IR) region of 26,410?bp each, separated by a large single copy (LSC) region of 85,926?bp and a small single-copy (SSC) region of 19,078?bp. The genome consisted of 129 genes, including 84 protein-codon genes (PCGs), 37 tRNA genes, and eight rRNA genes. The GC content of the whole chloroplast genome is 36.7%. Phylogenetic analysis revealed that P. mahaleb was the closest related to P. cerasoides and P. maximowiczii.

| S-EPMC7687457 | 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