Browse
Submit Data
Databases
API
Help

Dataset Information

30 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Characterization of the complete chloroplast genome of Aconitum pendulum (Ranunculaceae), an endemic medicinal herb.

ABSTRACT: Aconitum pendulum is an endemic medicinal herb, which has effects of relieving pains and is widely used to treat frostbite, rheumatoid arthritis, and so on. In this study, we sequenced the complete chloroplast genome with Illumina sequencing technology. The complete chloroplast genome length is 155,597 bp, shows a typical tetrad structure, which manifests as one large and one small single copy (LSC and SSC) regions of 86,336 and 16,961 bp, isolated by two inverted repeat regions (IRs) of 26,150 bp. This study annotated altogether 131 unique genes, consisting of 86 protein-encoding genes, 8 rRNA, and 37 tRNA. According to the maximum likelihood phylogenetic tree based on 20 complete chloroplast genomes, A. pendulum shows close association with additional Aconitum subgenus. The chloroplast genome-wide for A. pendulum would help to conserving the precious natural populations.

SUBMITTER: Wang ZH

PROVIDER: S-EPMC7748560 | biostudies-literature |

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Similar Datasets

The complete chloroplast genome sequence of Aconitum austroyunnanense W. T. Wang (Ranunculaceae): a medicinal plant endemic to China.

Project description:The complete chloroplast (cp) genome of Aconitum austroyunnanense W. T. Wang, a rare and endangered medicinal plant endemic to southwestern China, was sequenced to be 155,818 bp in length, including two inverted repeat (IR, 26,128 bp) regions, one large single-copy region (LSC) and one small single-copy region (SSC) of 86,555 bp and 17,007 bp, respectively. The cp genome has 131 annotated genes, including 85 protein-coding genes, 37 tRNA genes, 8 rRNA genes, and a pseudogene (ycf1). The overall GC content of it is 38.1%. Phylogenetic analysis revealed that the cp genome of A. austroyunnanense is closely related to that of Aconitum hemsleyanum.

| S-EPMC7748539 | biostudies-literature

Characterization of the complete chloroplast genome of Aconitum flavum (Ranunculaceae).

Project description:Aconitum flavum, a traditional Chinese medicine. The complete chloroplast genome sequence is 155,654 bp in length, with one large single copy region of 86,390 bp, one small single copy region of 16,968 bp, and two inverted repeat (IR) regions of 26,148 bp. It contains 129 genes, including 83 protein-coding genes, 8 ribosomal RNA, and 37 transfer RNA. Phylogenetic tree shows that this species is a sister to A. brachypodum.

| S-EPMC7781867 | biostudies-literature

The complete chloroplast genome of Aconitum austrokoreense Koidz. (Ranunculaceae), an endangered endemic species in Korea.

Project description:We determined the complete chloroplast genome sequences of Aconitum austrokoreense Koidz., an endangered endemic species in Korea. The chloroplast DNA is 155,682?bp in length and encodes 37 tRNAs, 8 rRNAs, and 86 protein-coding genes. Phylogenetic analysis and sequence comparison of protein-coding genes with those in other Ranunculaceae chloroplast DNAs showed that the chloroplast genome of A. austrokoreense is closely related to that of A. chiisanense and large sequence variations identified in rps16, matK, and rpl20 are specific to these two species.

| S-EPMC7800541 | 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

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

A comparison of chloroplast genome sequences in Aconitum (Ranunculaceae): a traditional herbal medicinal genus.

Project description:The herbal medicinal genus Aconitum L., belonging to the Ranunculaceae family, represents the earliest diverging lineage within the eudicots. It currently comprises of two subgenera, A. subgenus Lycoctonum and A. subg. Aconitum. The complete chloroplast (cp) genome sequences were characterized in three species: A. angustius, A. finetianum, and A. sinomontanum in subg. Lycoctonum and compared to other Aconitum species to clarify their phylogenetic relationship and provide molecular information for utilization of Aconitum species particularly in Eastern Asia. The length of the chloroplast genome sequences were 156,109 bp in A. angustius, 155,625 bp in A. finetianum and 157,215 bp in A. sinomontanum, with each species possessing 126 genes with 84 protein coding genes (PCGs). While genomic rearrangements were absent, structural variation was detected in the LSC/IR/SSC boundaries. Five pseudogenes were identified, among which ?rps19 and ?ycf1 were in the LSC/IR/SSC boundaries, ?rps16 and ?infA in the LSC region, and ?ycf15 in the IRb region. The nucleotide variability (Pi) of Aconitum was estimated to be 0.00549, with comparably higher variations in the LSC and SSC than the IR regions. Eight intergenic regions were revealed to be highly variable and a total of 58-62 simple sequence repeats (SSRs) were detected in all three species. More than 80% of SSRs were present in the LSC region. Altogether, 64.41% and 46.81% of SSRs are mononucleotides in subg. Lycoctonum and subg. Aconitum, respectively, while a higher percentage of di-, tri-, tetra-, and penta- SSRs were present in subg. Aconitum. Most species of subg. Aconitum in Eastern Asia were first used for phylogenetic analyses. The availability of the complete cp genome sequences of these species in subg. Lycoctonum will benefit future phylogenetic analyses and aid in germplasm utilization in Aconitum species.

| S-EPMC5680694 | biostudies-literature

The complete chloroplast genome of Aconitum piepunense (Ranunculaceae) and its phylogenetic analysis

Project description:Abstract Aconitum piepunense belonging to the family Ranunculaceae is an endangered herb species in southwestern China. In this study, the complete chloroplast genome of A. piepunense was sequenced, and the results revealed a typical quadripartite structure with a length of 155,836 bp, including a large single-copy region (LSC, 86,433 bp), a small single-copy region (SSC, 16,945 bp), and a pair of inverted repeat (IR) regions (IRa and IRb, 26,229 bp, respectively). A total of 130 genes were identified in the A. piepunense chloroplast genome, containing 85 protein-coding genes, 37 transfer RNA (tRNA) genes, and 8 ribosomal RNA (rRNA) genes. Phylogenetic analysis based on the maximum likelihood method indicated that A. piepunense formed a monophyletic group, which was sister to A. contortum and A. vilmorinianum.

| S-EPMC8725895 | biostudies-literature

Characterization of the complete chloroplast genome of the Tangut monkshood Aconitum tanguticum (Ranunculales: Ranunculaceae).

Project description:The Tangut monkshood (Aconitum tanguticum) is a perennial herb with high medicinal values. Here, its chloroplast genome was assembled from Illumina sequencing reads. The circular genome is 157,114 bp long with an A + T-biased nucleotide composition, and comprises a pair of inverted repeat (IR) regions (26,255 bp), separated by a large single-copy (LSC) region (87,559 bp) and a small single-copy (SSC) region (17,045 bp). It encodes a total of 112 gene species, with 19 of them being completely or partially duplicated and 18 of them harboring one or two introns. Phylogenetic analysis recovered two major clades of the genus Aconitum.

| S-EPMC7782905 | biostudies-literature

Complete chloroplast genome of medicinal plant Aconitum carmichaelii: genome characterization and phylogenetic analysis.

Project description:The complete chloroplast genome sequence of an important medicinal plant of the family Ranunculaceae, Aconitum carmichaelii Debx., was characterized in this study. The assembled chloroplast genome was 154,776?bp in length, which included a large single-copy (LSC), a small single-copy (SSC), and two inverted repeat (IR) regions of 86,330bp, 15,986?bp, and 26,193?bp, respectively. The GC content of the genome was 38.1%. Phylogenetic analysis with the whole nucleotide sequences of reported Aconitum chloroplast genomes indicated a close relationship of A. carmichaelii with A. kusnezoffii.

| S-EPMC7800505 | biostudies-literature

The complete chloroplast genome of Aconitum coreanum (H. Lev.) Rapaics (Ranunculaceae).

Project description:Aconitum coreanum (H. Lév.) Rapaics listed in the Korean Red List is a medicinal herb. We presented complete chloroplast genome, which is 157,024?bp long and has four subregions: 87,637?bp of large single-copy and 16,901?bp of small single-copy regions, which are separated by two 26,243?bp inverted repeat regions including 132 genes (86 protein-coding genes, 8 rRNAs, and 37 tRNAs). The overall GC content of the chloroplast is 38.0%. Phylogenetic trees show that A. coreanum occupied a basal position at subgenus Aconitum clade and two A. coreanum isolated from midwestern and eastern regions of Korea are clustered together.

| S-EPMC7707295 | 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