Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

The first complete chloroplast genome of a traditional Chinese medicinal herb Odontosoria chinensis (Lindsaeaceae).

ABSTRACT: It is the first report on complete chloroplast genome of Odontosoria chinensis, a traditional Chinese medicinal herb. The genome size is 156,293?bp, containing a pair of inverted repeats (IRs) (25,198?bp) separated by a small single-copy (SSC) region (20,649?bp) and a large single-copy (LSC) region (85,248?bp), respectively. The plastome has 128 genes, including 87 protein-coding genes, 32 tRNA genes, eight rRNA genes, and one pseudogene. The overall GC content is 40.43%. Maximum likelihood tree reveals that O. chinensis is basal lineages of polypods. The study will provide powerful molecular information for further phylogenetic analysis.

SUBMITTER: Xu R

PROVIDER: S-EPMC7799563 | biostudies-literature | 2018 Feb

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

The first complete chloroplast genome of a traditional Chinese medicinal herb Odontosoria chinensis (Lindsaeaceae).

Xu Ruixiang R Liu Shanshan S Wang Zhen Z Wang Ting T Su Yingjuan Y

Mitochondrial DNA. Part B, Resources 20180226 1

It is the first report on complete chloroplast genome of Odontosoria chinensis, a traditional Chinese medicinal herb. The genome size is 156,293 bp, containing a pair of inverted repeats (IRs) (25,198 bp) separated by a small single-copy (SSC) region (20,649 bp) and a large single-copy (LSC) region (85,248 bp), respectively. The plastome has 128 genes, including 87 protein-coding genes, 32 tRNA genes, eight rRNA genes, and one pseudogene. The overall GC content is 40.43%. Maximum likeliho ...[more]

PMID: 33474148

Similar Datasets

The complete chloroplast genome of Chinese medicinal herb Belamcanda chinensis (L.) Redoute (Iridaceae).

Project description:The species of Belamcanda chinensis (L.) Redouté. is one of the Chinese traditional medicinal herb. In this study, we first report the complete chloroplast (cp) genome of B. chinensis. The chloroplast (cp) genome was determined to be 153,735 bp and the GC contents was 37.9%. The sequence includes a large single-copy (LSC) region of 83, 199 bp, a small single-copy (SSC) region of 18,168 bp, and two separated inverted regions of 26,184 bp each. It contains 132 genes, including 86 protein-coding genes, 38 tRNA genes, and 8 rRNA genes. Based on 10 chloroplast genomes data, the maximum likelihood phylogenetic analysis revealed that B. chinensis was sister to Iris (Bootstrap = 100%) within Iridaceae. This result will be helpful for the conservation and breeding programs of the B. chinensis.

| S-EPMC7889214 | 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

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 Berberis weiningensis (Berberidaceae), an endemic and traditional Chinese medicinal herb.

Project description:Berberis weiningensis is a frequently-used traditional Chinese medicinal herb that included various active alkaloids. In this study, we assembled the complete chloroplast (cp) genome of B. weiningensis. The complete cp genome of B. weiningensis is 166,275 bp in length, and has a typical structure with large single-copy (LSC 73,624 bp) and small single-copy (SSC 18,608 bp) regions separated by a pair of inverted repeats (IRs 37,019 bp) of large size. The B. weiningensis cp genome contains 147 genes, of which 101 protein-coding genes, 8 rRNA genes, and 38 tRNA genes. The phylogenetic analysis revealed that Berberis species closely clustered with Mahonia species, which obviously support that Mahonia and Berberis are not monophyletic.

| S-EPMC7995825 | biostudies-literature

Complete chloroplast genome sequence of Pueraria lobata (Willd.) Ohwi (Fabaceae): a traditional Chinese medicinal herb.

Project description:Pueraria lobata is a traditional Chinese herb which has been used medically since ancient times. In this study, we sequenced the complete chloroplast genome of P. lobata based on next-generation sequencing and used the data to assess genomic resources. The chloroplast genome of P. lobata is 153,411 bp in length consisting of large and small single-copy regions of length 84,142 and 17,989 bp, separated by two IR regions of 25,640 bp. The overall GC content was 35.4%. De novo assembly and annotation showed the presence of 112 unique genes with 78 protein-coding genes, 30 tRNA genes, and four rRNA genes. A maximum-likelihood phylogenomic analysis showed that Pueraria was sister to Pediomelum + Glycine.

| S-EPMC7720969 | biostudies-literature

Characterization of the complete chloroplast genome of Arisaema erubescens (Wall.) Schott, a traditional Chinese medicinal herb.

Project description:Arisaema erubescens is a well-known medicinal plant in China. In this study, we sequenced the complete chloroplast (cp) genome sequence of A. erubescens to investigate its phylogenetic relationship in the family Araceae. The cp genome was 167,607 bp in length, consisting of a pair of inverted repeats (IRa and IRb: 26,193 bp) separated by a large single-copy region (LSC: 93,660 bp) and a small single-copy region (SSC: 21,561 bp). The GC content of whole cp genome is 35.3%. De novo assembly and annotation showed the presence of 114 unique genes with 80 protein-coding genes, 30 tRNA genes, and four rRNA genes. Phylogenetic analysis indicated that A. erubescens was closely related to A. franchetianum, and the genus Arisaema was sister to the genus Pinellia.

| S-EPMC7782955 | biostudies-literature

The complete chloroplast genome of Epimedium wushanense T. S. Ying. (Berberidaceae), a traditional Chinese medicinal herb.

Project description:Epimedium wushanense is a well-known medicinal plant in Berberidaceae in China. In this study, we sequenced the complete chloroplast (cp) genome of E. wushanense. The results showed that the cp genome of E. wushanense was 157,283 bp in length, which is composed of a large single-copy region (LSC, 88,579 bp) and a small single-copy region (SSC, 17,082 bp) that were separated by a pair of inverted repeat regions (IRa and IRb, 25,811 bp). The chloroplast genome of E. wushanense contains 112 unique genes, of which are 78 protein-coding genes, 30 tRNA genes, and 4 rRNA genes. The overall GC content was 38.78%. The phylogenetic tree analysis showed that E. wushanense was closely related to E. pseudowushanense, E. lishihchenii, and E. sagittatum.

| S-EPMC7748643 | 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

The complete chloroplast genome of Isodon rubescens, a traditional Chinese herb.

Project description:Isodon rubescens (Hemsley) H. Hara is a kind of traditional medical herb which can be used for cancer treatment. In this study, the complete chloroplast genome sequence of I. rubescens was assembled. Its complete circular chloroplast DNA length was 152,761 bp. The genome was made up of a large single-copy region of 83,655 bp, a small single-copy region of 17,660 bp, and a pair of inverted repeat regions of 25,723 bp. The genome totally encoded 129 genes, containing 85 protein-coding genes, 36 tRNA genes, and eight rRNA genes. Phylogenetic analysis indicated that I. rubescens had a close relationship with basil (Ocimum basilicum).

| S-EPMC7872541 | biostudies-literature