Browse
Submit Data
Databases
API
Help

Dataset Information

25 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 sequence of a vulnerable legume species Dalbergia tonkinensis prain in Vietnam.

Project description:Dalbergia tonkinensis is a critically vulnerable tree species that is distributed in Vietnam and Hainan Island of China. The complete chloroplast genome sequence of D. tonkinensis was characterized using Illumina pair-end sequencing. The cpDNA is 156,086 bp in length and contains a pair of 25,720 bp inverted repeats, one large single copy region of 85,761 bp, and one small single copy region of 18,885 bp. It contains 131 genes including 86 protein-coding genes, 36 tRNAs, eight rRNAs, and one pseudogene. The overall G + C content of the whole genome is 36.1%. Phylogenetic analysis based on 35 chloroplast genomes of Papilionoideae including Cercis glabra (as an outgroup) indicates that all the species of the Dalbergioids sensu lato formed a monophyletic clade and D. tonkinensis formed a sister relationship with the D. hainanensis and D. odorifera group.

| S-EPMC7706621 | biostudies-literature

Deciphering the complete chloroplast genome sequence of Meconopsis torquata Prain: Insights into genome structure, comparative analysis and phylogenetic relationship.

Project description:In the present study, we have characterized the complete chloroplast (Cp) genome of Meconopsis torquata Prain (family Papaveraceae), revealing the plastome size of 153,290 bp, and a GC content of 38.72 %. The cp genome features the typical circular quadripartite structure found in flowering plants, including a pair of inverted repeat regions (25,816 bp), isolated by a small single-copy region (17,740 bp) and a large single-copy (83,918 bp). Genome annotation revealed 132 genes: 87 protein-coding genes, 37 tRNAs and eight rRNAs. This comparative study demonstrated that the genome structure, gene number and GC ratio are consistent with several other cp genomes of Meconopsis and Papaver genera. A total of 120 SSRs were detected in the plastome, the majority (111) of which were mononucleotide repeats. Among the longer repeats, palindromic sequences were most common, followed by forward, reverse, and complement repeats. The whole genome alignment revealed the conserved nature of the inverted repeat region over single-copy zones. Nucleotide diversity unveiled hypervariable sites (ycf1, rps16, accD, atpB and psbD) in both the small and large single-copy regions, which could be useful for designing molecular markers for taxonomic identification. Phylogenetic analysis revealed a close alliance of M. torquata with other Meconopsis species, such as M. pinnatifolia and M. paniculata, with strong bootstrap support. Molecular dating suggests that M. torquata originated during the Tortonian age of the Miocene epoch of the Cenozoic era. These findings provide valuable insights for biological research, especially in understanding the genetic and evolutionary divergence within the Papaveraceae family.

| S-EPMC11367419 | 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 complete chloroplast genome of Aucuba obcordata (Rehder) Fu ex W. K. Hu et Soong (Garryaceae) from China.

Project description:Aucuba obcordata is an endemic species and traditional Chinese medicine in China. The complete chloroplast genome sequence of A. obcordata was generated by de novo assembly using whole genome next generation sequencing. The complete chloroplast genome was 157,993 bp in length, contained four parts: a large single copy (LSC) region of 87317 bp, a small single copy (SSC) region of 18483 bp, and two inverted repeat (IRs) regions of 26,094 bp each. The genome annotation contained a total of 113 genes, including 79 protein-coding genes, 30 tRNA genes, and four rRNA genes. The overall GC content was 37.8%. Phylogenetic analysis of chloroplast genomes clustered A. obcordata with Eucommia ulmoides Oliver.

| S-EPMC7687530 | 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 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 of Flemingia macrophylla (Willd.) Prain (Fabaceae) from Guangxi, China.

Project description: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 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

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