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 of Saussurea medusa maxim. (Asteraceae), an alpine Tibetan herb

ABSTRACT: Abstract Saussurea medusa is an important traditional Tibetan medicinal plant in China. In this study, we assembled the complete chloroplast (cp) genome of S. medusa. The complete S. medusa chloroplast genome is a circular molecular structure of 152,257 bp in length with coding GC 37.93%, consisting of two inverted repeats (25,204 bp) separated by a large single-copy region (83,334 bp) and a small single-copy region (18,515 bp). The complete chloroplast genome of S. medusa contained 130 genes, including 87 protein-coding genes, 35 tRNA genes, and eight rRNA genes. Phylogenetic analysis shows that S. medusa is most closely related to Saussurea inversa and Saussurea pseudoleucoma. The complete chloroplast genome sequence of S. medusa facilitates the phylogenetic studies of Asteraceae.

SUBMITTER: Wei Y

PROVIDER: S-EPMC8567947 | biostudies-literature |

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Similar Datasets

The complete chloroplast genome of Saussurea medusa (Asteraceae), a rare subnival plant in Qinghai-Tibetan Plateau.

Project description:Saussurea medusa Maxim. is a subnival plant of Asteraceae with abundant medicinal and ecological value. Until now, few studies have been conducted on S. medusa, especially in phylogenetic relationships and species identification. The S. medusa cp genome had a typical quadripartite structure with a conserved genome arrangement. It was 152,500 bp in size, consisting of a large single copy (LSC) region of 83,553 bp and a small single copy (SSC) region of 18,545 bp, separated by a pair of inverted repeats (IRs) of 25,201 bp. It contained 113 unique genes, including 80 protein-coding genes (PCGs), 29 tRNA and four rRNA genes. The overall GC content was 37.67%. Moreover, a phylogenetic analysis, based on 48 complete cp genomes using Maximum Likelihood (ML) method, indicated that S. medusa was relatively closed to S. pseudoleucoma and was well-clustered within genus Saussurea.

| S-EPMC7594724 | biostudies-literature

The Complete Chloroplast Genome of Ye-Xing-Ba (Scrophularia dentata; Scrophulariaceae), an Alpine Tibetan Herb.

Project description:Scrophularia dentata is an important Tibetan medicinal plant and traditionally used for the treatment of exanthema and fever in Traditional Tibetan Medicine (TTM). However, there is little sequence and genomic information available for S. dentata. In this paper, we report the complete chloroplast genome sequence of S. dentata and it is the first sequenced member of the Sect. Tomiophyllum within Scrophularia (Scrophulariaceae). The gene order and organization of the chloroplast genome of S. dentata are similar to other Lamiales chloroplast genomes. The plastome is 152,553 bp in length and includes a pair of inverted repeats (IRs) of 25,523 bp that separate a large single copy (LSC) region of 84,058 bp and a small single copy (SSC) region of 17,449 bp. It has 38.0% GC content and includes 114 unique genes, of which 80 are protein-coding, 30 are transfer RNA, and 4 are ribosomal RNA. Also, it contains 21 forward repeats, 19 palindrome repeats and 41 simple sequence repeats (SSRs). The repeats and SSRs within S. dentata were compared with those of S. takesimensis and present certain discrepancies. The chloroplast genome of S. dentata was compared with other five publicly available Lamiales genomes from different families. All the coding regions and non-coding regions (introns and intergenic spacers) within the six chloroplast genomes have been extracted and analysed. Furthermore, the genome divergent hotspot regions were identified. Our studies could provide basic data for the alpine medicinal species conservation and molecular phylogenetic researches of Scrophulariaceae and Lamiales.

| S-EPMC4938499 | biostudies-literature

Complete chloroplast genome of Saussurea inversa (Asteraceae) and phylogenetic analysis.

Project description:Saussurea inversa Raab-Straube is a small perennial and polycarpic herb that is distributed on the rocky slopes of the Qinghai-Tibetan plateau (QTP) at an altitude of 3700-5400 meters. It has a chloroplast genome structure similar to that of other species of Saussurea. It is 152,102 bp in size, including a large single-copy (LSC) region of 83,450 bp, a small single-copy (SSC) region of 18,286 bp and a pair of inverted repeats (IRs) of 25,183 bp. The chloroplast genome of S. inversa encodes 113 genes, containing 80 protein-coding genes (PCGs), 29 tRNA and four rRNA genes. Phylogenetic analysis shows that S. inversa is clustered with S. pseudosimpsoniana and S. laniceps.

| S-EPMC7801092 | biostudies-literature

The complete chloroplast genome of Petasites japonicus (Siebold & Zucc.) Maxim. (Asteraceae).

Project description:The complete chloroplast (cp) genome sequence of Petasites japonicus (Asteraceae) was determined. The cp genome is 150,445 bp and consists of a large single-copy region (82,910 bp), a small single-copy region (17,907 bp), and a pair of inverted repeats (24,814 bp). It encodes a set of 114 genes, consisting of 80 protein-coding genes, 30 tRNA genes, and four rRNA genes. Phylogenetic inference confirmed that P. japonicus is sister to the genus Ligularia in the tribe Senecioneae of Asteraceae.

| S-EPMC8635567 | 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 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 pubescens Maxim. (Berberidaceae), a traditional Chinese medicine herb.

Project description: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.

| S-EPMC7781925 | biostudies-literature

The complete chloroplast genome of Triosteum himalayanum (Caprifoliaceae), a perennial alpine herb.

Project description:Triosteum himalayanum is a perennial herb which is distributed in the eastern Himalayas, Hengduan Mountains, and central China. The complete chloroplast genome of T. himalayanum is studied for the first time, which is 154,579?bp in length and is divided into four regions: two inverted repeat (IRA and IRB) regions of 23,370?bp, a small single copy (SSC) region of 18,682?bp and a large single copy (LSC) region of 89,157?bp. The plastid genome contains 133 genes, including 86 protein-coding genes, 39 tRNA genes, and 8 rRNA genes. The overall CG content in the chloroplast genome of T. himalayanum is 38.38%. The phylogenetic analysis on the complete plastome sequence of T. himalayanum will help to show the intergeneric diversity of Caprifoliaceae.

| S-EPMC7707766 | biostudies-literature

The complete chloroplast genome of Phlomoides younghushandii (Lamiaceae), a traditional Tibetan medicinal herb.

Project description:The species Phlomoides younghushandii is a medicinal herb mainly distributed in southwest China. The first complete plastid genome sequence of P. younghushandii reported here was 151,747 bp long, with the large single copy (LSC) region of 83,181 bp, the small single copy (SSC) region of 17,372 bp and two inverted repeats (IRa and IRb) of 25,597 bp. The plastome contained 114 genes, including 80 protein-coding genes, four encoding rRNAs, and 30 encoding tRNAs. The overall GC content was 38.5%. Phylogenetic analysis of Lamiaceae based on a whole plastome matrix suggested that Phlomoides is closely related to the genus Phlomis as members of subfamily Lamioideae.

| S-EPMC7995819 | biostudies-literature

The complete chloroplast genome of Phlomoides betonicoides (Lamiaceae), a traditional Tibetan medicinal herb.

Project description:The species Phlomoides betonicoides is used medicinally and mainly distributed in southwest China. The first complete plastid genome sequence of P. betonicoides reported here was 151,777 bp long, with the large single copy (LSC) region of 83,205 bp, the small single copy (SSC) region of 17,370 bp and two inverted repeats (IRa and IRb) of 25,601 bp. The plastome contained 114 genes, including 80 protein-coding genes, four ribosomal RNA genes, and 30 transfer RNA genes. The overall GC content was 38.5%. Result from phylogenetic analysis suggests that tribe Phlomideae (Phlomoides) is closely related to tribe Lamieae and tribe Leonureae in present study.

| S-EPMC7721044 | 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