Browse
Submit Data
Databases
API
Help

Dataset Information

35 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

The complete nucleotide sequence of chloroplast genome of Gentiana apiata (Gentianaceae), an endemic medicinal herb in China.

ABSTRACT: Gentiana apiata N. E. Brown (Gentianaceae) is a perennial herb plant and only grows in Qinba Mountains in China. Here, we first characterized the complete nucleotide sequence of chloroplast (cp) genome of G. apiata via Illumina next generation sequencing platform. The complete chloroplast genome of G. apiata was 144,274 bp in length, comprising of a large single copy (LSC) region of 77,353 bp, a small single copy (SSC) region of 17,009 bp, and two inverted repeat regions (IRs) of 24,956 bp. The cp genome contains 127 genes, including 82 protein-coding genes, 35 tRNA, eight rRNA genes, and two pseudogenes. Phylogenetic analysis based on 18 cp genome sequences showed that G. apiata closely related to congeneric species.

SUBMITTER: Huang CX

PROVIDER: S-EPMC7706864 | biostudies-literature |

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Similar Datasets

Complete chloroplast genome sequence of Swertia mileensis (Gentianaceae): a medicinal species endemic to China.

Project description:Swertia mileensis is an important medicinal plant endemic to South-east Yunnan, China, which has been widely used to treat icteric hepatitis. The complete chloroplast genome sequence of S. mileensis is presented in this study, the total size is 153,015 bp in length with a typical quadripartite structure including a pair of inverted repeat (IRs, 25,786 bp) regions separated by a large single copy (LSC, 83,048 bp) region and a small single copy (SSC, 18,395 bp) region. The overall GC content of it is 38.2%. The cp genome has 134 annotated genes, including 85 protein-coding genes, 37 tRNA genes and 8 rRNA genes. Among these genes, nine genes have one intron and two genes contain two introns. The phylogenetic tree based on 16 complete plastomes of support close relationships among two species of Swertia with 100% bootstrap value.

| S-EPMC7707743 | biostudies-literature

Characterisation of the complete chloroplast genome of Gentiana delavayi Franch. (gentianaceae), a medicinal plant in southwest of China.

Project description:Gentiana delavayi is a medicinal plant commonly used in southwest of China. In this study, we sequenced the complete chloroplast (cp) genome sequence of G. delavayi to investigate its phylogenetic relationship in the family Gentianaceae. The chloroplast genome of G. delavayi was 151,569 bp in length with 37.8% overall GC content, including a large single copy (LSC) region of 81,177 bp, a small single copy (SSC) region of 16,921 bp and a pair of inverted repeats (IRs) of 25,471 bp. The cp genome contained 114 genes, including 78 protein coding genes, 30 tRNA genes, and 4 rRNA genes. The phylogenetic analysis indicated G. delavayi was closely related to G. stipitata.

| S-EPMC7707525 | biostudies-literature

The complete nucleotide sequence of chloroplast genome of Euphorbia kansui (Euphorbiaceae), an endemic herb in China.

Project description:Euphorbia kansui T.N. Liou ex S.B. Ho (Euphorbiaceae) is a perennial herb plant endemic to China. This species has important economic and medicinal values. In this study, we first characterized the complete nucleotide sequence of chloroplast (cp) genome of E. kansui using the Illumina Hiseq platform. The cp genome was 161,061?bp in length, comprising of a large single copy (LSC) region of 91,288?bp, a small single copy (SSC) region of 17,086?bp, and two inverted repeat regions of 26,343?bp each. The cp genome contains 130 genes, including 86 protein-coding genes, 8 ribosomal RNAs (rRNAs), and 36 transfer RNAs (tRNAs). The phylogenetic analysis indicated that E. kansui was placed as a sister to the congeneric Euphorbia esula.

| S-EPMC7800493 | biostudies-literature

The complete chloroplast genome and phylogenetic analysis of Gentiana arethusae Burkill (Gentianaceae) from China

Project description:Abstract Gentiana arethusae Burkill is a perennial herb classified in the Gentianaceae. In this study, the complete chloroplast genome of G. arethusae was sequenced and analyzed. The chloroplast genome is 137,458 bp in length and encodes a total of 116 genes, including 71 protein-coding, 37 tRNA, and eight rRNA genes. The genome has a low GC content of 38.0%. Phylogenetic analysis of the genome of G. arethusae resolved it in a clade with Gentiana obconica and Gentiana veitchiorum. The complete chloroplast genome of G. arethusae will be helpful to study the genetic diversity and phylogenetics of the Gentianaceae.

| S-EPMC8510589 | biostudies-literature

Characterization of the complete chloroplast genome of Gentiana rhodantha (Gentianaceae).

Project description:The first complete chloroplast genome (cp) sequences of Gentiana rhodantha were reported in this study. The cp genome of G. rhodantha was 148,967 bp in size, with two inverted repeat (IR) regions of 25,760 bp, the large single copy (LSC) region of 79,831 bp, and the small single copy (SSC) region of 17,616 bp. The cp genome contained 112 genes, including 78 protein-coding genes, 4 ribosomal RNA, and 30 transfer RNA genes. The overall GC content was 36.4%. Phylogenetic analysis of the cp genomes within the tribe Gentianeae suggests that G. rhodantha is in a sister clade of other subtribe Gentianinae.

| S-EPMC7748746 | biostudies-literature

The complete chloroplast genome of Paris polyphylla var. chinensis, an endemic medicinal herb in China.

Project description:Paris polyphylla var. chinensis is a species of flowering herb of the family Liliaceae and widely distributed in 12 provinces in China. It has been used in Chinese traditional medicine for centuries. The chloroplast (cp) genome of P. polyphylla var. chinensis, sequenced based on next-generation platform (NEOSAT), is 164,429?bp in size. The cp genome encodes 133 genes, including eight rRNA genes, 87 protein-coding genes (PCGs), and 38 tRNA genes. Phylogenetic relationship analysis based on complete cp genome sequences exhibited that P. polyphylla var. chinensis was most related to Daiswa forrestii.

| S-EPMC7707722 | biostudies-literature

The complete chloroplast genome of Polygonatum odoratum (Liliaceae), an endemic medicinal herb.

Project description:In this study, we sequenced the complete chloroplast genome of Polygonatum odoratum with Illumina sequencing technology. The complete chloroplast genome length is 156,082bp, shows a typical tetrad structure, which manifests as one large and one small single copy (LSC and SSC) regions of 85,009 and 18,513bp, isolated by two inverted repeat regions (IRs) of 26,280bp. This study annotated altogether 131 unique genes, consisting of 86 protein-encoding genes, 8 rRNA and 38tRNA. According to the maximum likelihood phylogenetic tree based on 8 complete chloroplast genomes, P. odoratum shows close association with additional Maianthemum genus. The chloroplast genome-wide for P. odoratum would help to conserving the precious natural populations.

| S-EPMC7655049 | biostudies-literature

The complete chloroplast genome of Polygonatum odoratum (Liliaceae), an endemic medicinal herb.

Project description:In this study, we sequenced the complete chloroplast genome of Polygonatum odoratum with Illumina sequencing technology. The complete chloroplast genome length is 156,082 bp shows a typical tetrad structure, which manifests as one large and one small single copy (LSC and SSC) regions of 85,009 and 18,513 bp, isolated by two inverted repeat regions (IRs) of 26,280 bp. This study annotated altogether 131 unique genes, consisting of 86 protein-encoding genes, 8 rRNA, and 38 tRNA. According to the maximum likelihood phylogenetic tree based on eight complete chloroplast genomes, P. odoratum shows a close association with additional Maianthemum genus. The chloroplast genome-wide for P. odoratum would help to conserve the precious natural populations.

| S-EPMC7671610 | biostudies-literature

Complete plastid genome sequence of the rare and endangered medicinal herb Psammosilene tunicoides, endemic to China.

Project description:Psammosilene tunicoides W.C. Wu et C.Y. Wu, a monotypic species and endemic to Southwest China, is a rare and endangered traditional medicinal herb with satisfactory effects on multifold pathology. In order to provide crucial data for protection, we reported and analyzed the complete plastid genome of P. tunicoides as the foundation of germplasm conservation. The complete plastid genome is a typical quadripartite circular molecule of 153,957 bp in length, including a large single copy (LSC) region of 83,972 bp and a small single copy (SSC) region of 17,495 bp separated by two inverted repeat (IR) regions of 26,245 bp. In total of 111 unique genes were predicted, including 78 protein-coding genes (PCGs), 29 transfer RNA genes, and four ribosomal RNA genes. The overall GC content of P. tunicoides is 36.5%. The phylogenetic analysis revealed that P. tunicoides and Dianthus caryophyllus formed an independent clade with a 100% bootstrap support.

| S-EPMC7687624 | biostudies-literature

Phylogenetic analysis and characterization of the complete chloroplast genome of Dipsacus asperoides, the endemic medicinal herb in China.

Project description:Dipsacus asperoides is a traditional and endemic medicinal herb in China. Its roots was considered top grade herb as early as in the Shen Nong Herbal Classic. In this study, we assembled and analyzed the complete chloroplast genome of D. asperoides. The complete chloroplast genome is 160,481 bp in length, exhibiting a large single-copy region (88,546 bp), a small single-copy region (19,671 bp), and two inverted-repeat regions (26,132 bp in each one). The chloroplast genome of D. asperoides contains 133 genes, including 89 protein-coding genes (PCGs), 36 transfer RNA (tRNAs), and eight ribosome RNA (rRNAs). The overall nucleotide content of the chloroplast genome is A of 30.2%, T of 31.0%, C of 19.7%, and G of 19.1%, with a total AT content of 61.2% and GC content of 38.8%. However, the phylogenetic Maximum-Likelihood (ML) analysis based on the amino acid sequences of 89 PCGs from 14 species chloroplast genome that D. asperoides is closely related to Dipsacus asper. This study can be used for medicinal herb value research and clinical drug development.

| S-EPMC7706563 | 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