Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

The complete plastome sequence of Rumex japonicus Houtt.: a medicinal plant.

ABSTRACT: Rumex japonicus is a medicinal plant distributed in East Asia. Here, we report and characterize the complete plastid genome sequence of R. japonicus and size is 159,292 bp in length and contains the typical structure and gene content of other angiosperm plastomes, including two inverted repeat regions of 30,629 bp, a large single-copy region of 85,028 bp and a small single-copy region of 13,006 bp. There are 112 unique genes, including 78 protein-coding, 30 tRNAs and 4 rRNAs. We constructed a phylogenetic tree with 14 species and the phylogenetic topologies showed that R. japonicus was closely related to Rheum wittrockii.

SUBMITTER: Raman G

PROVIDER: S-EPMC7748881 | biostudies-literature | 2020 Jan

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

The complete plastome sequence of Rumex japonicus Houtt.: a medicinal plant.

Raman Gurusamy G Cho Soung Jae SJ Park SeonJoo S

Mitochondrial DNA. Part B, Resources 20200108 1

Rumex japonicus is a medicinal plant distributed in East Asia. Here, we report and characterize the complete plastid genome sequence of R. japonicus and size is 159,292 bp in length and contains the typical structure and gene content of other angiosperm plastomes, including two inverted repeat regions of 30,629 bp, a large single-copy region of 85,028 bp and a small single-copy region of 13,006 bp. There are 112 unique genes, including 78 protein-coding, 30 tRNAs and 4 rRNAs. We co ...[more]

PMID: 33366591

Similar Datasets

Complete plastome sequence of Mallotus japonicus (Linn. f.) Mull. Arg. (Euphorbiaceae): a medicinal plant species endemic in East Asia.

Project description:Mallotus japonicus is a shrub species in the family of Euphorbiaceae. The study of plastome would be helpful for its phylogenetic study and species identification. The total length of complete plastome for Mallotus japonicus is of 164,912 bp, with typical part-four structure and gene content of angiosperm plastome, including two inverted repeat (IR) regions of 27,829 bp, a large single-copy (LSC) region of 90,319 bp, and a small single-copy (SSC) region of 18,935 bp. The plastome contains 125 genes, consisting of 80 unique protein-coding genes, 31 unique tRNA gene, four unique rRNA genes (5S rRNA, 4.5S rRNA, 16S rRNA, and 23S rRNA), and five pseudogenes. The overall G/C content in the plastome of Mallotus japonicus is 40.2%. The phylogenetic analysis indicates that M. japonicus is closer to M. peltatus than other species in this study. The complete plastome sequence is conducive to the exploitation and utilization of Euphorbiaceae resources and the phylogenetic study in future.

| S-EPMC8079058 | biostudies-literature

The Hair Growth-Promoting Effect of Rumex japonicus Houtt. Extract.

Project description:Rumex japonicus Houtt. is traditionally used as a medicinal plant to treat patients suffering from skin disease in Korea. However, the beneficial effect of Rumex japonicus Houtt. on hair growth has not been thoroughly examined. Therefore, the present study aims to investigate the hair growth-promoting effect of Rumex japonicus (RJ) Houtt. root extract using human dermal papilla cells (DPCs), HaCaT cells, and C57BL/6 mice model. RJ induced antiapoptotic and proliferative effects on DPCs and HaCaT cells by increasing Bcl-2/Bax ratio and activating cellular proliferation-related proteins, ERK and Akt. RJ also increased β-catenin via the inhibition of GSK-3β. In C57BL/6 mice model, RJ promoted the anagen induction and maintained its period. Immunohistochemistry analysis demonstrated that RJ upregulated Ki-67 and β-catenin expressions, suggesting that the hair growth effect of RJ may be mediated through the reinforcement of hair cell proliferation. These results provided important insights for the possible mechanism of action of RJ and its potential as therapeutic agent to promote hair growth.

| S-EPMC5128716 | biostudies-literature

Complete plastome sequence of Callicarpa nudiflora Vahl (Verbenaceae): a medicinal plant.

Project description:Callicarpa nudiflora Vahl is a medicinal plant occurring in Guangdong, Guangxi, Hainan provinces of China. Here, we report and characterize the complete plastid genome sequence of C. nudiflora in an effort to provide genomic resources useful for promoting its conservation. The complete plastome is 154,080 bp in length and contains the typical structure and gene content of angiosperm plastome, including two inverted repeat (IR) regions of 25,657 bp, a large single-copy (LSC) region of 84,949 bp, and a small single-copy (SSC) region of 17,817 bp. There are 113 genes annotated, including 79 unique protein-coding genes, 4 unique ribosomal RNA genes, and 30 transfer RNA genes. To investigate the evolution status of C. nudiflora, as well as Verbenaceae, we constructed a phylogenetic tree with C. nudiflora and other 11 species based on their complete chloroplast genomes. According to the phylogenetic topologies, C. nudiflora was closely related to Lancea hirstua.

| S-EPMC7687407 | biostudies-literature

Complete plastome sequence of Tetrataenium Candicans (tribe Tordylieae, Apiaceae): a medicinal plant.

Project description:Tetrataenium candicans is a Himalayan native medicinal plant species. In this study, we report and characterize the complete plastid genome sequence of T. candicans in order to provide genomic resources helpful for promoting its systematics research and conservation. The complete chloroplast (cp) genome is a circular structure and 147,335 bp in length, composing of one large single-copy (LSC) region of 92,996 bp, one small single-copy (SSC) region of 17,473 bp, and separated by a pair of inverted repeat (IR) regions of 18,433 bp each. It encodes 129 genes, including 85 protein-coding genes, 36 tRNA genes, and 8 rRNA genes. The GC content is 37.5%. Phylogenetic analysis of 31 representative plastomes indicated that the T. candicans was close to Semenovia gyirongensis.

| S-EPMC7707242 | biostudies-literature

Complete plastome sequence of Flueggea virosa (Roxburgh ex Willdenow) Voigt (Phyllanthaceae): a medicinal plant.

Project description:Flueggea virosa is a tropical plant of the Phyllanthaceae family, which has high medicinal value. Here, we report and characterize the complete plastome of F. virosa. The complete plastome is 154,961 bp in length and contains the typical structure and gene content of angiosperm plastome, including two inverted repeat (IR) regions of 27,575 bp, a large single-copy (LSC) region of 83,397 bp and a small single-copy (SSC) region of 16,414 bp. The plastome contains 130 genes, consisting of 80 unique protein-coding genes, 30 unique tRNA gene, 4 unique rRNA genes (5S rRNA, 4.5S rRNA, 23S rRNA and 16S rRNA). The overall A/T content in the plastome of F. virosa is 63.10%. The complete plastome sequence of F. virosa will provide a useful resource for the conservation genetics of this species as well as for phylogenetic studies in Phyllanthaceae.

| S-EPMC7782946 | biostudies-literature

The complete plastome sequence of Platanthera japonica (Orchidaceae): an endangered medicinal and ornamental plant.

Project description:Platanthera japonica (Thunb. ex A. Marray) Lindl belongs to the genus Platanthera within family Orchidaceae, is an endangered herbal species in the East Asia area. In this study, the complete plastome sequence (cpDNA) of P. japonica was determined by next-generation Illumina sequencing. The cpDNA of this herbal plant is 155,409 bp in size, with a pair of inverted repeat (IR) regions of 26,933 bp that separate a large single-copy (LSC) region of 84,049 bp and a small single-copy (SSC) region of 17,494 bp. The GC content in plastome is 36.9%, and the IR region (43.2%) is higher than that of the LSC and SSC region (34.4% and 29.7%, respectively), which is similar with other Orchidaceae plastomes. The assembled plastome encoded 133 genes, which included 38 tRNA genes, 8 rRNA genes, and 87 protein-coding genes. A total of 24 species were used to construct the phylogenetic relationships among P. japonica and other related species within Orchidaceae. The results showed that P. japonica is closely related to Platanthera chlorantha.

| S-EPMC7748498 | biostudies-literature

The complete chloroplast genome of a medicinal resource plant (Rumex crispus).

Project description:Rumex crispus has high medicinal value which belongs to the family Polygonaceae. We sequenced the complete chloroplast genome of R. crispus, which is 158,851 bp in length. A total of 111 unique genes have been predicted in the chloroplast genome of this species, consisting of 77 protein-coding sequences, 30 tRNA and 4 rRNA genes. A maximum likelihood (ML) phylogenetic tree based on 80 protein-coding genes of 18 Polygonaceae species showed the phylogenetic position of R. crispus within the family Polygonaceae. These results facilitate population and biological studies of R. crispus and benefit further investigations of this important species.

| S-EPMC7706888 | biostudies-literature

Rumex japonicus Houtt. alleviates dextran sulfate sodium-induced colitis by protecting tight junctions in mice.

Project description:BackgroundRumex japonicus Houtt. (RJ) is widely distributed in Korea, Japan, and China. The root of RJ has traditionally been used to treat constipation, jaundice, hematemesis, dysfunctional uterine bleeding, and gastrointestinal diseases. According to recent studies, plants of the genus Rumex have beneficial functionalities such as anti-microbial, antioxidative, and anti-inflammatory effects. Inflammatory bowel disease, including Crohn's disease and ulcerative colitis, is a chronic inflammatory disease characterized by an abnormal immune response and epithelial barrier dysfunction. This study evaluates the protective effect of RJ against dextran sulfate sodium (DSS)-induced colitis.MethodsMale 8-week-old C57BL/6 N mice were treated with methanolic extract of RJ for 14 days, and DSS-induced groups were administered 2.5% DSS for last 7 days. After sacrifice, the length and weight of the colon were measured, and colon sections were subjected to H&E staining, immunohistochemistry and Western blotting to investigate the changes of inflammatory cytokines, tight junction and apoptosis-related factors.ResultsThe colon of DSS-treated mouse was significantly shorter and heavier than the normal mouse. Moreover, DSS exposure induced an increase of tumor necrosis factor-α, interleukin (IL)-1β, IL-6, occludin, zonula occludens-1, p21, p53 and Bcl-2, and decreased the expressions of IL-10, claudin-2 and cleaved caspase-3 in the colon tissue. These DSS-induced changes were inhibited by RJ treatment.ConclusionOur results indicate that RJ effectively suppresses DSS-induced colitis by protecting tight junction connections in the colonic tissue. We therefore infer that RJ has the potential as a medicine or ingredient for treating colitis.

| S-EPMC7168767 | biostudies-literature

The complete plastome sequence of Atractylodes macrocephala (Asteraceae: Cardueae), an important medicinal plant in East Asia.

Project description:Atractylodes macrocephala is one of the most commonly used herbs in China, which is famous for its high medicinal value. In this study, we analyzed and characterized the complete plastome sequence of A. macrocephala. Sequence analysis indicated that the entire genome is 153,265 bp in length, consisting of a large single-copy (LSC, 84,311 bp) and a small single-copy (SSC, 18,674 bp) region separated by a pair of inverted repeat (IR) regions of 25,140 bp for each. The genome contains 107 unique genes, including 80 different protein-coding genes, 23 tRNA genes, and 4 rRNA genes. The overall GC content of the genome is 37.7%. The phylogenetic analysis revealed a monophyletic Atractylodes and Cardueae. This research reports the complete plastome genome of Atractylodes macrocephala, which provides a better understanding of this important herb.

| S-EPMC7748879 | biostudies-literature

Complete plastome sequence of Pseuderanthemum haikangense C.Y. Wu & H.S. Lo (Acanthaceae): a medicinal plant in South China.

Project description:Pseuderanthemum haikangense (Acanthaceae) is a shrubs native to Guangdong, Hainan, Yunnan province of China. In this study, we report and characterize the complete plastome sequence of P. haikangense in order to provide genomic resources helpful for promoting its conservation and medicinal utilization. The complete plastome is 152,849 bp in length and contains the typical quadripartite structure of angiosperm, including two Inverted Repeat (IRs) regions of 25,849 bp, a Large Single-Copy (LSC) region of 83,878 bp and a Small Single-Copy (SSC) region of 17,273 bp. The plastome contains 113 genes, consisting of 79 unique protein-coding genes, 30 unique tRNA gene and 4 unique rRNA genes. The overall A/T content in the plastome of P. haikangense is 61.60%. The complete plastome sequence of P. haikangense will provide a useful resource for the conservation and garden utilization of this species as well as for the phylogenetic studies of Acanthaceae.

| S-EPMC7782011 | biostudies-literature