Browse
Submit Data
Databases
API
Help

Dataset Information

27 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

The complete chloroplast genome of Acanthopanax brachypus (Araliaceae), a famous medicinal plant in China.

ABSTRACT: Acanthopanax brachypus (Araliaceae) is an important medicinal plant originated from China. Here, we reported the first chloroplast genome sequence of A. brachypus. The plastome of A. brachypu is 156,802 bp in length, including a large single-copy (LSC) of 86,742 bp, a small single-copy (SSC) of 18,184 bp, and a pair of inverted repeat regions (IRa and IRb) of 25,938 bp. It contains 113 unique genes consisting of 80 protein-coding genes, 29 tRNA genes, and 4 rRNA genes.

SUBMITTER: Ou XB

PROVIDER: S-EPMC7781937 | biostudies-literature |

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Similar Datasets

Complete chloroplast genome of Callicarpa formosana Rolfe, a famous ornamental plant and traditional medicinal herb.

Project description:Callicarpa formosana is a species of beauty-berry with large medicinal value belonging to the family Verbenaceae. In this study, the complete chloroplast genome of C. formosana was sequenced using Illumina Hiseq X Ten platform. The chloroplast genome was 1,54,210 bp in length, containing two short inverted repeat (IRa and IRb) regions of 25,701 bp, which was separated by a large single copy (LSC) region of 84,938 bp and a small single copy (SSC) region of 17,870 bp. The GC content of the whole chloroplast genome was 38.1%. The chloroplast DNA of C. formosana comprised 113 genes, including 79 protein-coding genes, 4 ribosomal RNA genes, and 30 transfer RNA genes. Phylogenetic analysis indicated that the genus Callicarpa L. was located in the basal position within the family Verbenaceae. The chloroplast genome (cpDNA) of C. formosana was closely related to Callicarpa nudiflora.

| S-EPMC7781935 | biostudies-literature

The complete mitochondrial genome of Panax ginseng (Apiales, Araliaceae): an important medicinal plant.

Project description:Ginseng (Panax ginseng C. A. Meyer) is a multifunctional medicinal herb used worldwide and is an economically important high-value crop in Korea. Here, we presented the mitochondrial genome of P. ginseng landrace 'Jakyung', which is one of the most common cultivars cultivated in Korean farms. The complete mitochondrial genome sequence was 464,661 bp in length and had a single circular form. The ginseng mitochondrial genome encoded 72 unique genes, including 45 protein-coding genes, 24 tRNA genes, and three rRNA genes. Nucleotide composition analysis revealed a GC content of 45.1%, with a slightly higher A + T bias (A, 27.1%; T, 27.8%; G, 22.5%; C, 22.6%). Phylogenetic analysis showed that P. ginseng was closely related to Daucus carota in the Apiales. This complete mitochondrial genome sequence of P. ginseng provides valuable genetic information for further studies of this important medicinal plant.

| S-EPMC8477949 | biostudies-literature

Complete chloroplast genome sequence of Mahonia duclouxiana (Berberidaceae), a medicinal plant in China.

Project description:Mahonia duclouxiana is a member of the genus Mahonia of Berberidaceae and is distributed in South Asia. Here, the complete chloroplast genome sequence of M. duclouxiana was reported. The complete chloroplast genome is 165,384 bp in length, which has a large single-copy (LSC) region of 73,477 bp, a small single-copy (SSC) region of 18,563 bp, and two inverted repeat (IR) regions of 36,672 bp. The G/C content in the chloroplast genome is 38.1%. The whole chloroplast genome contains 151 genes, including 38 unique tRNA genes, 105 unique protein-coding genes, and 8 unique rRNA genes. The phylogenetic analysis supported that this species should be included in Maddenia. The complete chloroplast genome sequence of M. duclouxiana will provide extremely important information in tracing the evolutionary history of the genus Mahonia and the development of the medicinal value.

| S-EPMC8475121 | biostudies-literature

The complete chloroplast genome of Berchemia lineata, an important medicinal plant from China.

Project description:Brechemia lineata is a well-known medicinal plant in the Rhamnaceae family and widely used in traditional Chinese medicine. Here, we sequenced the complete chloroplast genome using Illumina pair-end sequencing data. The chloroplast genome was 154,962 bp in length, consisting of a large single-copy (LSC) region of 82,928 bp, a small single-copy (SSC) region of 17,376 bp, and a pair of inverted repeat (IR) regions of 27,329 bp. The chloroplast genome consists of 112 unique genes, including 78 protein-coding genes, 30 transfer RNA, and 4 ribosomal RNA genes. The overall GC content of the chloroplast genome was 37.0%. The phylogenetic analysis suggests close relationship of B. lineata with other Berchemia species. These genomic resources will be valuable resource for systematic and phylogenetic studies of Berchemia genus.

| S-EPMC7782211 | biostudies-literature

Complete chloroplast genome sequences of Lagotis brevituba (Plantaginaceae): a famous Tibetan medicine plant.

Project description:Lagotis brevituba is a famous Tibetan medicine plant and its complete chloroplast genome is determined in this study. The complete chloroplast genome is 152,967 bp in length, with a large single-copy (LSC) region of 83,740 bp, a small single copy (SSC) region of 17,845 bp, and a pair of inverted repeats (IRs) of 25,691 bp. The whole genome contained 131 genes, including 86 protein-coding genes, 37 tRNA genes and 8 rRNA genes. The phylogenetic tree showed that L. brevituba clustered with L. yunnanensis in family Plantaginaceae.

| S-EPMC8143624 | biostudies-literature

The complete chloroplast genome of Eleutherococcus trifoliatus (Araliaceae): a wild edible plant in the coastal region of South China.

Project description:Eleutherococcus trifoliatus (L.) S. Y. Hu is a wild edible plant and widely used in the coastal region of South China. Here, we report the complete chloroplast genome of E. trifoliatus. The length of the cp genome was determined to be 156751 bp with a small single copy (SSC) region of 18316 bp, a large single copy (LSC) region of 86747 bp and two separated inverted region of 25844 bp, respectively. Totally, 132 unique genes were identified of this genome, including 87 protein-coding genes, 37 tRNA genes and eight rRNA genes. The GC contents of this genome is 38%. Chloroplast phylogenomics analysis indicates that E. trifoliatus is closely related to E. gracilistylus (W.W. Sm.) S.Y. Hu.

| S-EPMC7748804 | biostudies-literature

The complete chloroplast genome of Polygala japonica Houtt. (Polygalaceae), a medicinal plant in China.

Project description:Polygala japonica Houtt. (Polygalaceae) is a perennial herbaceous plant widely distributed in south China. Here, we assembled and characterized the complete chloroplast (cp) genome of P. japonica using sequencing data. The complete cp genome of P. japonica was 165,439 bp in length, with a GC content of 36.7%. The complete cp genome shows a typical quadripartite structure with a pair of inverted repeats (IRs) of 36,786 bp, separated by a large single copy region (LSC) of 83,722 bp, and a small single copy region (SSC) of 8,145 bp. A total of 135 genes were annotated in the cp genome of P. japonica, consisting of 89 protein-coding genes, 8 rRNA genes, and 38 tRNA genes. The phylogenetic analysis showed P. japonica had a closer relationship with P. tenuifolia.

| S-EPMC7832591 | biostudies-literature

The complete chloroplast genome of Tetrastigma planicaule, one important folk medicinal plant in China.

Project description:We announce here the first complete chloroplast genome sequence of Tetrastigma planicaule, one important Chinese folk medicinal plant. This complete chloroplast genome is 160,323 bp in length. In total, 131 genes were identified, including 86 protein-coding genes, 37 tRNA genes, and 8 rRNA genes. The results of phylogenetic analysis indicated that Tetrastigma is a separate genus and is closely related to Vitis.

| S-EPMC8158278 | biostudies-literature

The complete chloroplast genome sequence of the medicinal plant Salvia miltiorrhiza.

Project description:Salvia miltiorrhiza is an important medicinal plant with great economic and medicinal value. The complete chloroplast (cp) genome sequence of Salvia miltiorrhiza, the first sequenced member of the Lamiaceae family, is reported here. The genome is 151,328 bp in length and exhibits a typical quadripartite structure of the large (LSC, 82,695 bp) and small (SSC, 17,555 bp) single-copy regions, separated by a pair of inverted repeats (IRs, 25,539 bp). It contains 114 unique genes, including 80 protein-coding genes, 30 tRNAs and four rRNAs. The genome structure, gene order, GC content and codon usage are similar to the typical angiosperm cp genomes. Four forward, three inverted and seven tandem repeats were detected in the Salvia miltiorrhiza cp genome. Simple sequence repeat (SSR) analysis among the 30 asterid cp genomes revealed that most SSRs are AT-rich, which contribute to the overall AT richness of these cp genomes. Additionally, fewer SSRs are distributed in the protein-coding sequences compared to the non-coding regions, indicating an uneven distribution of SSRs within the cp genomes. Entire cp genome comparison of Salvia miltiorrhiza and three other Lamiales cp genomes showed a high degree of sequence similarity and a relatively high divergence of intergenic spacers. Sequence divergence analysis discovered the ten most divergent and ten most conserved genes as well as their length variation, which will be helpful for phylogenetic studies in asterids. Our analysis also supports that both regional and functional constraints affect gene sequence evolution. Further, phylogenetic analysis demonstrated a sister relationship between Salvia miltiorrhiza and Sesamum indicum. The complete cp genome sequence of Salvia miltiorrhiza reported in this paper will facilitate population, phylogenetic and cp genetic engineering studies of this medicinal plant.

| S-EPMC3584094 | biostudies-literature

The Complete Chloroplast Genome Sequences of the Medicinal Plant Pogostemon cablin.

Project description:Pogostemon cablin, the natural source of patchouli alcohol, is an important herb in the Lamiaceae family. Here, we present the entire chloroplast genome of P. cablin. This genome, with 38.24% GC content, is 152,460 bp in length. The genome presents a typical quadripartite structure with two inverted repeats (each 25,417 bp in length), separated by one small and one large single-copy region (17,652 and 83,974 bp in length, respectively). The chloroplast genome encodes 127 genes, of which 107 genes are single-copy, including 79 protein-coding genes, four rRNA genes, and 24 tRNA genes. The genome structure, GC content, and codon usage of this chloroplast genome are similar to those of other species in the family, except that it encodes less protein-coding genes and tRNA genes. Phylogenetic analysis reveals that P. cablin diverged from the Scutellarioideae clade about 29.45 million years ago (Mya). Furthermore, most of the simple sequence repeats (SSRs) are short polyadenine or polythymine repeats that contribute to high AT content in the chloroplast genome. Complete sequences and annotation of P. cablin chloroplast genome will facilitate phylogenic, population and genetic engineering research investigations involving this particular species.

| S-EPMC4926354 | 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