Browse
Submit Data
Databases
API
Help

Dataset Information

49 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Characterization and phylogenetic analysis of the complete chloroplast genome of Ilex rotunda, traditional Chinese medicine plant.

ABSTRACT: Ilex rotunda is a traditional Chinese medicine plant. In this study, we characterized the complete chloroplast (cp) genome sequence of I. rotunda to investigate its phylogenetic relationship. The cp genome of I. rotunda was 157,743 bp in length with 37.62% overall GC content, including a large single-copy (LSC) region of 87,060bp, a small single-copy (SSC) region of 18,432 bp, which were separated by a pair of inverted repeats (IRS) of 26,121 bp. The cp genome contained 133 genes, including 88 protein-coding genes, 37 tRNA genes, and 8 rRNA genes. Phylogenetic analysis based on whole cp genome sequences showed that I. rotunda is closely related to I. pubescens and I. polyneura.

SUBMITTER: Chen H

PROVIDER: S-EPMC8425722 | biostudies-literature | 2021

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

Characterization and phylogenetic analysis of the complete chloroplast genome of Ilex rotunda, traditional Chinese medicine plant.

Chen Hong H Chong Xinran X Zhou Yanwei Y Sun Linhe L Zhang Fan F Lu Xiaoqing X Li Naiwei N Zhou Ting T Li Yunlong Y

Mitochondrial DNA. Part B, Resources 20210831 10

Ilex rotunda is a traditional Chinese medicine plant. In this study, we characterized the complete chloroplast (cp) genome sequence of I. rotunda to investigate its phylogenetic relationship. The cp genome of I. rotunda was 157,743 bp in length with 37.62% overall GC content, including a large single-copy (LSC) region of 87,060bp, a small single-copy (SSC) region of 18,432 bp, which were separated by a pair of inverted repeats (IRS) of 26,121 bp. The cp genome contained 133 ...[more]

PMID: 34514128

Similar Datasets

Complete chloroplast genome sequence of Ilex latifolia (Aquifoliaceae), a traditional Chinese tea.

Project description:Ilex latifolia (Aquifoliaceae), commonly known as 'kudingcha', is an evergreen tree widely distributed in southwest China. It is well known for its health function due to possess antioxidant, antidiabetic, antihypertensive, anti-inflammatory, and anti-ischemic activities. Here, we first report and characterize its complete chloroplast genome based on Illumina paired-end sequencing data. The complete plastid genome was 157,601 bp, which contained inverted repeats (IR) of 26,077 bp separated by a large single-copy (LSC) and a small single copy (SSC) of 87,020 bp and 18,427 bp, respectively. The cpDNA contains 143 genes, comprising 95 protein-coding genes, 40 tRNA genes, and eight rRNA genes. The overall GC content of the plastome is 37.6%. The phylogenetic analysis of 18 selected chloroplast genomes demonstrated that I. latifolia is closely related to the congeneric I. integra.

| S-EPMC7748568 | biostudies-literature

Complete chloroplast genome sequence of Pueraria thomsonii, an important traditional Chinese medicine plant.

Project description:Pueraria thomsonii is a leguminous plant with high root yield and starch content. It is also a medicinal material in the Chinese pharmacopeia. However, the raw materials of P. thomsonii are often confused with some non-medicinal Pueraria plants. To enrich the genetic resources of P. thomsonii and guide its molecular identification, the complete chloroplast genome was sequenced and reported. The total genome of P. thomsonii is 153,434 bp in length. consisting of two inverted repeat regions (IRS, 25,640 bp each) separated by a large single-copy (LSC, 84,155 bp) and a small single-copy region (SSC, 17,999 bp). The overall GC content is 35.41%. It contains 130 genes, including 85 protein coding genes, 8 rRNA genes and 37 tRNA genes. Phylogenetic analysis showed that P. thomsonii could be distinguished from other plants and closely related to the legume Pachyrhizus erosus. This study enriches the genetic information of P. thomsonii and contributes to the screening of excellent germplasm.

| S-EPMC7707730 | biostudies-literature

The complete chloroplast genome sequence of a traditional Chinese medicine plant Bulbophyllum disciflorum Rolfe (Orchidaceae).

Project description:Bulbophyllum disciflorum is one of Orchidaceae species, which has important ornamental and economic value. Here, we reported the first chloroplast genome sequence of Bulbophyllum. The genome of B. disciflorum is 148,554 bp in length, including a large single-copy (LSC) of 79,001 bp, a small single-copy (SSC) of 16,797 bp, and a pair of inverted repeat regions (IRa and IRb) of 26,378bp. It contains 108 unique genes consisting of 74 protein-coding genes, 30 tRNA genes, and 4 rRNA genes. The phylogenetic analysis revealed that Bulbophyllum is sister to the genus of Dendrobium.

| S-EPMC7720722 | biostudies-literature

Characterization of the complete chloroplast genome of Glycyrrhiza uralensis (Leguminosae), a traditional Chinese medicine.

Project description:Glycyrrhiza uralensis is a tradational Chinese medicine of Leguminosae, which contains many chemicals, such as glycyrrhizin, liquiritin glycyrol, melatonin (N-acetyl-5-methoxy tryptamine), glycyrrhizol A, glycyrrhizol B and four known isoflavonoids (5-O-methylglycryol, isoglycyrol, 6,8-diisoprenyl-5,7,4'-trihydroxy isoflavone, gancaonin). Illumina paired-end reads data was used to assemble the complete chloroplast (cp) genome. About 15,445,866 raw Paired-End Reads and the length distribution in 127,702 bp (GC content accounts for 34.3%). Eight PCG genes and six tRNA genes possess a single intron, while ycf3 has a couple of introns. Based on the concatenated coding sequences of cp PCGs, the phylogenetic analysis showed that Glycyrrhiza uralensis and Glycyrrhiza inflata (MH321931) are closely related to each other within the family Leguminosae.

| S-EPMC7706715 | biostudies-literature

Characterization of the complete chloroplast genome of Euphorbia lathyris (Euphorbiaceae), a traditional Chinese medicine.

Project description:Euphorbia lathyris is a biennial herb plant in China. The seed is commonly used in well-known traditional Chinese medicine, and it has anti-tumor, p-glycoprotein and tyrosinase inhibitory activities. The length of circular chloroplast genome was 162,571 bp, containing a large single-copy region of 91,946 bp, a small single-copy region of 17,301 bp and two inverted repeat regions of 26,662 bp. The chloroplast genome contained 128 genes, including 85 protein-coding, 8 rRNA, and 35 tRNA genes. Phylogenetic tree analysis showed that E. lathyris, E. kansui and E. esulaare are closely related to each other.

| S-EPMC7510639 | biostudies-literature

Characterization of the complete chloroplast genome of Ephedra sinica Stapf (Ephedraceae), a traditional Chinese medicine.

Project description:Ephedra sinica Stapf is a traditional Chinese medicine of Ephedraceae in China, which contains many chemicals, such as ephedrine and pseudoephedrine, flavonoids, polysaccharides, phenolic compounds, and proanthocyanidins. It shows significant activity in asthma, fever, rheumatoid arthritis, and also promotes diuresis and sweat.

| S-EPMC7707388 | biostudies-literature

Characterization of the complete chloroplast genome of Euphorbia helioscopia Linn. (Euphorbiaceae), a traditional Chinese medicine.

Project description:Euphorbia helioscopia Linn. known as a traditional Chinese medicine of Euphorbiaceae, which contains terpenes, steroids, flavonoids, acetophenones, tannins, phenylpropanoids, cerebrosides and so on. Euphorbia helioscopia L. was used to treat malignant tumors and chronic obstructive pulmonary diseases such as cough, phlegm-turbidity, asthma, and chronic bronchitis. The complete chloroplast genome was assembled by Illumina paired-end reads data. The length of circular cp genome distribution in 160,041 bp, containing a large single-copy region (LSC) of 88,832 bp, a small single-copy region (SSC) of 17,145 bp and a pair of inverted repeat (IR) regions of 27,032 bp. In addition, 11 genes possess a single intron, while the other two genes (ycf3, clpP) have a couple of introns. The GC content of entire Euphorbia helioscopia L. cp genome, LSC, SSC and IR regions are 35.9, 33.1, 30.3, and 42.3%, respectively. From the NJ phylogenetic tree analysis showed that Euphorbia helioscopia L. and Euphorbia esula are closely related to each other within the family Euphorbiaceae.

| S-EPMC7707446 | biostudies-literature

Complete chloroplast genome of Ilex dabieshanensis: Genome structure, comparative analyses with three traditional Ilex tea species, and its phylogenetic relationships within the family Aquifoliaceae.

Project description:Ilex dabieshanensis K. Yao & M. B. Deng is not only a highly valued tree species for landscaping, it is also a good material for making kuding tea due to its anti-inflammatory and lipid-lowering medicinal properties. Utilizing next-generation and long-read sequencing technologies, we assembled the whole chloroplast genome of I. dabieshanensis. The genome was 157,218 bp in length, exhibiting a typical quadripartite structure with a large single copy (LSC: 86,607 bp), a small single copy (SSC: 18,427 bp) and a pair of inverted repeat regions (IRA and IRB: each of 26,092 bp). A total of 121 predicted genes were encoded, including 113 distinctive (79 protein-coding genes, 30 tRNAs, and 4 rRNAs) and 8 duplicated (8 protein-coding genes) located in the IR regions. Overall, 132 SSRs and 43 long repeats were detected and could be used as potential molecular markers. Comparative analyses of four traditional Ilex tea species (I. dabieshanensis, I. paraguariensis, I. latifolia and I. cornuta) revealed seven divergent regions: matK-rps16, trnS-psbZ, trnT-trnL, atpB-rbcL, petB-petD, rpl14-rpl16, and rpl32-trnL. These variations might be applicable for distinguishing different species within the genus Ilex. Phylogenetic reconstruction strongly suggested that I. dabieshanensis formed a sister clade to I. cornuta and also showed a close relationship to I. latifolia. The generated chloroplast genome information in our study is significant for Ilex tea germplasm identification, phylogeny and genetic improvement.

| S-EPMC9119449 | biostudies-literature

traditional chinese medicine

Project description:traditional chinese medicine Targeted loci

| PRJNA796441 | ENA

The complete chloroplast genome sequence of traditional Chinese medicine Uncaria macrophylla (Rubiaceae).

Project description:Uncaria macrophylla (Rubiaceae) is a medicinal vine plant of the Rubiaceae family that was distributed in East Asia and Southeast Asia. The first complete chloroplast genome of Uncaria macrophylla was sequenced and assembled in this study. The genome is 155,138 bp in length and contained 129 encoded genes in total, including 79 protein-coding genes, eight ribosomal RNA genes, and 37 transfer RNA genes. The phylogenomic analysis showed that U. macrophylla was closely related to Uncaria rhynchophylla according to the current sampling extent.

| S-EPMC9045754 | biostudies-literature