Browse
Submit Data
Databases
API
Help

Dataset Information

19 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

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

ABSTRACT: 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.

SUBMITTER: Zuo Y

PROVIDER: S-EPMC7832591 | biostudies-literature |

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Similar Datasets

The complete chloroplast genome characteristics of Polygala crotalarioides Buch.-Ham. ex DC. (Polygalaceae) from Yunnan, China.

Project description:Polygala crotalarioides Buch.-Ham. ex DC. (Polygalaceae) is a perennial herbaceous plant widely distributed in southwest China. Its chloroplast genome sequence was obtained using Illumina NovaSeq sequencing technology, and then was assembled, annotated, and characterized. The total length of chloroplast genome is 164,269 bp and it contained a large (LCS, 82,697 bp) and a small (SSC, 8083 bp) single copy region, separated by a pair of inverted repeats (IRA/IRB, 36,744 bp). The overall GC content of genome was 36.8% and corresponding values of the LSC, SSC, and IR regions are 34.9%, 29.5%, and 39.7%, respectively. There are 135 genes that were predicted including 89 protein-coding, 38 tRNA, and 8 rRNA genes. The maximum-likelihood (ML) phylogenetic tree reconstructed by IQ-TREE indicated that P. crotalarioides had a strong genetic relationship with P. tenuifolia, P. sibirica, and P. japonica. In summary, the complete chloroplast genome of P. crotalarioides is reported for the first time, which is of great significance for future research on the evolutionary phylogeny and protection of Polygala.

| S-EPMC8425772 | biostudies-literature

The complete chloroplast genome of a Chinese medicinal plant, Peristrophe japonica (Thunb.) Bremek. (Lamiales: Acanthaceae) from Nanjing, China.

Project description:Peristrophe japonica (Thunb.) Bremek. is a widely distributed medicinal plant species in China and Japan. In this study, the complete chloroplast genome sequence of P. japonica was assembled and characterized from high-throughput sequencing data. The chloroplast genome is 151,374 bp in length, consisting of a large single-copy (LSC) and a small single-copy (SSC) regions of 83,395 bp and 17,073 bp, respectively, which were separated by a pair of 25,453 bp inverted repeat (IR) regions. The overall GC content of the genome is 38.07%. The genome contains 133 genes, including 88 protein-coding, 37 tRNA, and eight rRNA genes. A phylogenetic tree reconstructed using 23 chloroplast genomes reveals that Peristrophe form a separate group which is a sister of the genus Dicliptera. The work reported here is the first complete chloroplast genome of P. japonica which will provide useful information to the evolutionary studies on the genus of Peristrophe.

| S-EPMC8189061 | biostudies-literature

The complete chloroplast genome of Prunus japonica thunb.(Rosaceae), an ornamental and medicinal plant.

Project description:Prunus japonica is an ornamental and medicinal plant that is widely cultivated. The complete chloroplast genome of P. japonica was sequenced using Illumina Hiseq X Ten platform. The chloroplast genome was 158,080 bp in length, containing two short inverted repeat (IRa and IRb) regions of 26,385 bp, which was separated by a large single copy (LSC) region of 86,270 bp and a small single copy (SSC) region of 19,040 bp. The GC content of the whole chloroplast genome was 36.8%. The chloroplast DNA of P. japonica comprised 112 distinct genes, including 78 protein-coding genes, 4 ribosomal RNA genes and 30 transfer RNA genes. Phylogenetic analysis indicated that all species of Prunus formed a monophyletic group, P. japonica was closely related to P. hulimis.

| S-EPMC7819125 | biostudies-literature

Complete Chloroplast Genome of Medicinal Plant Lonicera japonica: Genome Rearrangement, Intron Gain and Loss, and Implications for Phylogenetic Studies.

Project description:The complete chloroplast (cp) genome of Lonicera japonica, a common ornamental and medicinal plant in North America and East Asia, was sequenced and analyzed. The length of the L. japonica cp genome is 155,078 bp, contains a pair of inverted repeat regions (IRa and IRb), of 23,774 bp each, as well as large (LSC, 88,858 bp) and small (SSC, 18,672 bp) single-copy regions. A total of 129 genes were identified in the cp genome, 16 of which were duplicated within the IR regions. Relative to other plant cp genomes, the L. japonica cp genome had a unique rearrangement between trnI-CAU and trnN-GUU. In L. japonica cpDNA, rps19, rpl2, and rpl23 move to the LSC region, from the IR region. The ycf1 pesudogene in the IR region is lost, and only one copy locates in the SSC region. Comparative cp DNA sequence analyses of L. japonica with other cp genomes reveal that the gene order, and the gene and intron contents, are slightly different. The introns in ycf2 and rps18 genes are found for the first time. Four genes (clpP, petB, petD, and rpl16) lost introns. However, its genome structure, GC content, and codon usage were similar to those of typical angiosperm cp genomes. All preferred synonymous codons were found to use codons ending with A/T. The AT-rich sequences were less abundant in the coding regions than in the non-coding ones. A phylogenetic analysis based on 71 protein-coding genes supported the idea that L. japonica is a sister of the Araliaceae species. This study identified unique characteristics of the L. japonica cp genome that contribute to our understanding of the cpDNA evolution. It offers valuable information for the phylogenetic and specific barcoding of this medicinal plant.

| S-EPMC6155926 | 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 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 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 of Acanthopanax brachypus (Araliaceae), a famous medicinal plant in China.

Project description: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.

| S-EPMC7781937 | biostudies-literature

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

Project description: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.

| S-EPMC7748881 | 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

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

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