Browse
Submit Data
Databases
API
Help

Dataset Information

25 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

The complete chloroplast genome sequence of Polygonum chinense L.

ABSTRACT: Polygonum chinense is a traditional natural plant pharmaceutical with antimicrobial, antioxidant, and antidiarrheal effects and mainly distributed in China and Southeast Asian countries. The complete chloroplast sequence of P. chinense has been determined in this study. The cpDNA was 158,981 bp in length, containing a pair of inverted repeats of 30,872 bp each separated by a large and small single-copy region of 84,347 and 12,890 bp, respectively. The genome contained 86 protein-coding genes, eight rRNA genes, and 37 tRNA genes. The overall GC content of the chloroplast genome was 38%. Phylogenetic tree demonstrated that P. chinense closely related to Rheum palmatum and Rheum wittrockii.

SUBMITTER: Yu B

PROVIDER: S-EPMC7782515 | biostudies-literature |

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Similar Datasets

The complete chloroplast genome sequence of Bupleurum chinense DC. (Apiaceae).

Project description:Bupleurum chinense DC. is a traditional medicinal herb species widely distributed in most provinces of China. In this study, we constructed and annotated a complete circular chloroplast (cp) genome of B. chinense. The cp genome of B. chinense is 155,545?bp in length, including two inverted repeat (IR) regions of 26,305?bp, separated by a large single-copy (LSC) region of 85,430?bp and a small single-copy (SSC) region of 17,505?bp. The GC content of whole cp genome is 37.68%. The genome contains 113 different genes, including 79 protein-coding genes, 30 tRNA genes, and 4 rRNA genes. A maximum-likelihood phylogenomic analysis showed that Bupleurum formed a monophyletic group, and was sister to other groups of Apiaceae.

| S-EPMC7707502 | biostudies-literature

The complete chloroplast genome sequence of Capsicum chinense Jacq. (Solanaceae).

Project description:Capsicum chinense is one of the domesticated pepper species and well known for its distinctive pungency. The complete chloroplast genome sequence of C. chinense was generated by de novo assembly using next generation sequencing data. The chloroplast genome is 156 807 bp long, containing large single-copy region of 87 290 bp and small single-copy region of 17 911 bp separated by a pair of inverted repeats of 25 803 bp. A total of 113 genes were predicted including 79 protein-coding genes, 30 tRNA genes and four rRNA genes. Phylogenomic analysis revealed that C. chinense chloroplast genome was most closely related to Capsicum annuum var. glabriusculum (American bird pepper), a wild progenitor of C. annuum.

| S-EPMC7871856 | biostudies-literature

The first complete chloroplast genome sequence from Polemonium chinense (Polemoniaceae).

Project description:In this study, the complete chloroplast genome of Polemonium chinense was determined by next-generation sequencing technology. The plastome is 155,578 bp in length, with a large single-copy region (LSC) of 85,864 bp and a small single-copy region (SSC) of 18,246 bp, separated by a pair of inverted repeat regions (IRs) of 25,734 bp. It contains 135 genes, including 89 protein-coding genes, 37 tRNA genes, 8 rRNA genes, and 1 pseudogene. The overall GC content is 37.1%, while the corresponding values in the LSC, SSC and IR region are 35.1, 30.3, and 42.9%, respectively. The phylogenetic tree shows that Polemoniaceae is sister to Fouquieriaceae.

| S-EPMC7707252 | biostudies-literature

The complete chloroplast genome of Loropetalum chinense var. rubrum yieh (Hamamelidaceae).

Project description:Loropetalum chinense var. rubrum Yieh (L. chinense) is an evergreen shrub or small tree of Hamamelidaceae. In this study, the chloroplast genome sequence of L. chinense is 159,451 bp in length, consisting of a large single-copy region with 88,166 bp (LSC), a small single-copy region with 18,773 bp (SSC), and two inverted repeat regions with 26,256 bp (IRs). The GC content in the chloroplast genome of L. chinense is 38.0%. The chloroplast genome of L. chinense contained 125 genes, including 84 protein-coding genes, 37 tRNA genes, and 4 rRNA genes. The phylogenetic tree showed that L. chinense was closely related to L. subcordatum.

| S-EPMC8667894 | biostudies-literature

The complete chloroplast genome of Verbascum chinense (L.) Santapau.

Project description:Verbascum chinense is a perennial plant in the Scrophulariaceae family that is traditionally used as sedative, astringent, febrifuge, and for skin eruptions. Here, we determined the complete chloroplast(cp) genome sequence for V. chinense using genome skimming sequencing. The cp genome was 153,618 bp and consisted of a large single copy (LSC) region (84,834 bp), a small single copy (SSC) region (17,884 bp), and two inverted repeats (IRs) (25,450 bp). It encodes 114 unique genes, including 80 protein-coding genes, four rRNAs, and 30 tRNAs. Phylogenetic analysis indicates that V. chinense exhibits a closer relationship with V. phoeniceum rather than Scrophularia.

| S-EPMC7782814 | biostudies-literature

Complete chloroplast genome of the wild-type Monimopetalum chinense (Celastraceae).

Project description:Monimopetalum chinense (Celastraceae), belonging to the monotypic genus, is an endangered species endemic to eastern China. The complete chloroplast (cp) genome sequence of M. chinense was determined using next-generation sequencing technology. Total length of the cp genome is 159,208 bp, which contained a large single-copy (LSC) of 88,024 bp in length and a small single copy (SSC) of 18,662 bp, separated by two inverted repeats (IRs) of 26,261 bp. The cp DNA is structured with 133 genes, comprising 88 protein-coding genes, 37 tRNA genes, and eight rRNA genes. Phylogenetic analysis suggested that Monimopetalum is closely related to the genus Catha and Euonymus with in the Celastraceae.

| S-EPMC7687622 | biostudies-literature

Complete chloroplast genome sequence of Amomum villosum.

Project description:The first complete chloroplast genome of Amomum villosum (Zingiberaceae) was reported in this study. The A. villosum genome was 163,608 bp in length, and comprised a pair of inverted repeat (IR) regions of 29,820 bp each, a large single-copy (LSC) region of 88,680 bp, and a small single-copy (SSC) region of 15,288 bp. It encoded 141 genes, including 87 protein-coding genes (79 PCG species), 46 tRNA genes (28 tRNA species), and 8 rRNA genes (4 rRNA species). The overall AT content was 63.92%. Phylogenetic analysis showed that A. villosum was closely related to two species Amomum kravanh and Amomum compactum within the genus Amomum in family Zingiberaceae.

| S-EPMC7706907 | biostudies-literature

Complete chloroplast genome sequence of Hedychium coronarium.

Project description:The first complete chloroplast genome of Hedychium coronarium (Zingiberaceae) was reported in this study. The H. coronarium chloroplast genome was 163,949 bp in length and comprised a pair of inverted repeat (IR) regions of 29,780 bp each, a large single-copy (LSC) region of 88,581 bp and a small single-copy (SSC) region of 15,808 bp. It encoded 141 genes, including 87 protein-coding genes (79 PCG species), 46 tRNA genes (28 tRNA species), and eight rRNA genes (four rRNA species). The nucleotide composition was asymmetric (31.68% A, 18.35% C, 17.74% G, 32.23% T) with an overall AT content of 63.92%. Phylogenetic analysis showed that H. coronarium was classified into a monophyletic group within the genus Hedychium in family Zingiberaceae.

| S-EPMC7706620 | biostudies-literature

The complete chloroplast genome sequence of Calanthe sieboldii (orchidaceae)

Project description: Not available

| S-EPMC10913714 | biostudies-literature

Complete chloroplast genome sequence of Kosteletzkya pentacarpos.

Project description:Kosteletzkya pentacarpos is a promising plant being developed as a salt-tolerant biofuel crop that also the ability to fix heavy metals. Here, high-throughput sequencing technology was used to sequence and assemble the chloroplast genome of K. pentacarpos. The full length of the chloroplast genome is 161,777 bp, comprising a large single-copy region of 90,019 bp, a small single-copy region of 18,978 bp, and a pair of inverted repeats of 26,390 bp. A total of 113 genes were annotated, including 79 protein-coding, 30 transfer RNA, and 4 ribosomal RNA genes. Phylogenetic analysis based on whole chloroplast genome sequences showed that K. pentacarpos has a close relationship with Abelmoschus in Malvaceae. This study increases the available genomic information on K. pentacarpos, and provides a basis for the rational exploitation and utilization of germplasm resources.

| S-EPMC9262370 | 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