Browse
Submit Data
Databases
API
Help

Dataset Information

13 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Complete chloroplast genome of Dactylicapnos torulosa (Hook. & Thoms.) Hutch., a medicinal plant from southwest China and its phylogeny.

ABSTRACT: Dactylicapnos torulosa (Hook. & Thoms.) Hutch. is a commonly used medicinal plant in southwest China. In this study, we sequenced the complete chloroplast genome of D. torulosa and explored phylogenetic relationship of the species and its related species. The genome size is 166,238 bp with typical quadripartite structure. A pair of inverted repeats (IRs) of 37,115 bp are separated by a small single copy (SSC) region of 18,627 bp and a large single copy (LSC) region of 73,381 bp. In total, 107 genes are annotated, including 76 protein coding genes, 27 transport RNA, four ribosomal RNA. Moreover, 13 genes are found to contain introns. Phylogenetic analysis showed that Dactylicapnos torulosa formed a basal branch instead of gathering together with Corydalis, which was inconsistent with the traditional treatment on Fumarioideae. This study provides useful information for phylogeny and conservation of the species and its relatives.

SUBMITTER: Hu H

PROVIDER: S-EPMC8604533 | biostudies-literature |

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Similar Datasets

Characterization of the complete chloroplast genome of Ajuga forrestii (Lamiaceae), a medicinal plant in southwest of China.

Project description:Ajuga forrestii is a medicinal plant commonly used in southwest of China. In this study, we sequenced the complete chloroplast (cp) genome sequence of A. forrestii to investigate its phylogenetic relationship in the family Lamiaceae. The chloroplast genome of A. forrestii was 150,492 bp in length with 38.3% overall GC content, including a large single copy (LSC) region of 82,148 bp, a small single copy (SSC) region of 17,160 bp and a pair of inverted repeats (IRs) of 25,592 bp. The cp genome contained 112 genes, including 79 protein coding genes, 29 tRNA genes, and 4 rRNA genes. The phylogenetic analysis indicated Ajuga was closely related to Scutellaria.

| S-EPMC7707673 | biostudies-literature

Characterization of the complete chloroplast genome of Leycesteria formosa wall. (Caprifoliaceae), a medicinal plant in southwest China.

Project description:Leycesteria formosa is a frequently used medicinal plant (namely, 'Yi yao') in Southwest China. In this study, we sequenced the complete chloroplast (cp) genome sequence of L. formosa to investigate its phylogenetic relationship in the family Caprifoliaceae. The chloroplast genome of L. formosa was 156,261 bp in length with 38.1% overall GC content, including a large single-copy (LSC) region of 90,353 bp, a small single-copy (SSC) region of 19,299 bp and a pair of inverted repeats (IRs) of 23,287 bp. The cp genome contained 112 genes, including 79 protein-coding genes, 29 tRNA genes, and 4 rRNA genes. The phylogenetic analysis indicated Leycesteria was closely related to the genus Triosteum or Heptacodium.

| S-EPMC7748767 | 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 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 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 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 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