Browse
Submit Data
Databases
API
Help

Dataset Information

22 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

The complete chloroplast genome of Saposhnikovia divaricata.

ABSTRACT: Saposhnikovia divaricata (Trucz.) Schischk. is a traditional Chinese herbal medicine widely distributed in Eastern Siberia and Northern Asia. In this research, we assembled and characterized the complete chloroplast genome sequence of S. divaricata from high-throughput sequencing data. The chloroplast genome was 147,834 bp in length, consisting of large single-copy (LSC) and small single-copy (SSC) regions of 93,202 bp and 17,324 bp, respectively, which were separated by a pair of 18,654 bp inverted repeat (IR) regions. The genome is expected to contain 129 genes, including 85 protein-coding genes, 36 tRNA genes, and 8 rRNA genes. The total GC content of the genome is 37.5%. A phylogenetic tree reconstructed by 40 chloroplast genomes reveals that S. divaricata is mostly related to Ledebouriella seseloides.

SUBMITTER: Bao Z

PROVIDER: S-EPMC7748531 | biostudies-literature |

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Similar Datasets

The Chloroplast Genome of Wild <i>Saposhnikovia divaricata</i>: Genomic Features, Comparative Analysis, and Phylogenetic Relationships.

Project description:Saposhnikovia divaricata, a well-known Chinese medicinal herb, is the sole species under the genus Saposhnikovia of the Apiaceae subfamily Apioideae Drude. However, information regarding its genetic diversity and evolution is still limited. In this study, the first complete chloroplast genome (cpDNA) of wild S. divaricata was generated using de novo sequencing technology. Similar to the characteristics of Ledebouriella seseloides, the 147,834 bp-long S. divaricata cpDNA contained a large single copy, a small single copy, and two inverted repeat regions. A total of 85 protein-coding, 8 ribosomal RNA, and 36 transfer RNA genes were identified. Compared with five other species, the non-coding regions in the S. divaricata cpDNA exhibited greater variation than the coding regions. Several repeat sequences were also discovered, namely, 33 forward, 14 reverse, 3 complement, and 49 microsatellite repeats. Furthermore, phylogenetic analysis using 47 cpDNA sequences of Apioideae members revealed that L. seseloides and S. divaricata clustered together with a 100% bootstrap value, thereby supporting the validity of renaming L. seseloides to S. divaricata at the genomic level. Notably, S. divaricata was most closely related to Libanotis buchtormensis, which contradicts previous reports. Therefore, these findings provide a valuable foundation for future studies on the genetic diversity and evolution of S. divaricata.

| S-EPMC9141249 | biostudies-literature

Characterization of the complete plastome of <i>Saposhnikovia divaricata</i> (Turcz.) Schischk.

Project description:Saposhnikovia divaricata is traditional herbal medicine with a long history in China. We reported the complete chloroplast genome of S. divaricate using the next generation sequencing. A total of 115 unique genes were annotated, consisting of 81 protein coding genes, 30 tRNA and 4 rRNA. The overall AT content was 69.2%. The molecular phylogenetic tree reveals that S. divaricate is closely related to Peucedanum in tribe Selineae.

| S-EPMC7748655 | biostudies-literature

Saposhnikovia divaricata

Project description:Saposhnikovia divaricata (Turcz.) Schischk. transcriptome

| PRJNA1060493 | ENA

Saposhnikovia divaricata

Project description:Saposhnikovia divaricata Raw sequence reads

| PRJNA756825 | ENA

Saposhnikovia divaricata

Project description:Saposhnikovia divaricata overview

| PRJNA757171 | ENA

Saposhnikovia divaricata

Project description:Saposhnikovia divaricata Raw sequence reads

| PRJNA1108193 | ENA

Saposhnikovia divaricata

Project description:Saposhnikovia divaricata Raw sequence reads

| PRJNA876052 | ENA

Saposhnikovia divaricata

Project description:Saposhnikovia divaricata Raw sequence reads

| PRJNA906183 | ENA

Saposhnikovia divaricata-An Ethnopharmacological, Phytochemical and Pharmacological Review.

Project description:Saposhnikovia divaricata (Turcz.) Schischk., a perennial herb belonging to the family Umbelliferae, is widely distributed in Northeast Asia. Its dried root (Radix Saposhnikoviae) is used as a Chinese herbal medicine for the treatment of immune system, nervous system, and respiratory diseases. Phytochemical and pharmacological studies have shown that the main constituents of S. divaricata are chromones, coumarins, acid esters, and polyacetylenes, and these compounds exhibited significant anti-inflammatory, analgesic, antioxidant, antiproliferative, antitumor, and immunoregulatory activities. The purpose of this review is to provide comprehensive information on the botanical characterization and distribution, traditional use and ethnopharmacology, phytochemistry, and pharmacology of S. divaricata for further study concerning its mechanism of action and development of better therapeutic agents and health products from S. divaricata.

| S-EPMC7176574 | biostudies-literature

Comparative analysis of the chloroplast and mitochondrial genomes of Saposhnikovia divaricata revealed the possible transfer of plastome repeat regions into the mitogenome.

Project description:BackgroundSaposhnikovia divaricata (Turcz.) Schischk. is a perennial herb whose dried roots are commonly used as a source of traditional medicines. To elucidate the organelle-genome-based phylogeny of Saposhnikovia species and the transfer of DNA between organelle genomes, we sequenced and characterised the mitochondrial genome (mitogenome) of S. divaricata.ResultsThe mitogenome of S. divaricata is a circular molecule of 293,897 bp. The nucleotide composition of the mitogenome is as follows: A, 27.73%; T, 27.03%; C, 22.39%; and G, 22.85. The entire gene content is 45.24%. A total of 31 protein-coding genes, 20 tRNAs and 4 rRNAs, including one pseudogene (rpl16), were annotated in the mitogenome. Phylogenetic analysis of the organelle genomes from S. divaricata and 10 related species produced congruent phylogenetic trees. Selection pressure analysis revealed that most of the mitochondrial genes of related species are highly conserved. Moreover, 2 and 46 RNA-editing sites were found in the chloroplast genome (cpgenome) and mitogenome protein-coding regions, respectively. Finally, a comparison of the cpgenome and the mitogenome assembled from the same dataset revealed 10 mitochondrial DNA fragments with sequences similar to those in the repeat regions of the cpgenome, suggesting that the repeat regions might be transferred into the mitogenome.ConclusionsIn this study, we assembled and annotated the mitogenome of S. divaricata. This study provides valuable information on the taxonomic classification and molecular evolution of members of the family Apiaceae.

| S-EPMC9364500 | 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