Browse
Submit Data
Databases
API
Help

Dataset Information

18 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

The complete chloroplast genome sequence of Heracleum millefolium Diels (Apiaceae).

ABSTRACT: We assembled the complete chloroplast genome of Heracleum millefolium which is a traditional widely used medicinal plant in China. The whole genome is 150,025 bp in length which was divided into four subregions: a large single-copy region (93,645 bp), a pair of 19,458 bp inverted repeats regions, and a small single-copy region (17,464 bp), respectively. Additionally, the chloroplast genome of H. millefolium detected 128 genes, including 85 protein coding genes, 36 transfer RNAs, and eight ribosomal RNAs. The overall GC content of this chloroplast genome is 37.5% and the mean coverage value is 1752.4x. Phylogenetic analysis based on 17 chloroplast genomes dataset was conducted to clarify the relationships of the major clades in Apiaceae. The results strongly supported the monophyly of Heracleum and the closer relationship of H. millefolium and H. candicans.

SUBMITTER: Ciren D

PROVIDER: S-EPMC9255025 | biostudies-literature |

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Similar Datasets

The complete chloroplast genome sequence of Libanotis buchtormensis (Apiaceae).

Project description:Libanotis buchtormensis (Fisch.) DC. is one of the traditional Chinese herbal medicines in the Qinling District, while the genetic information is limited. In the study, we reported the complete chloroplast genome of L. buchtormensis using BGISEQ-500 sequencing data. The complete chloroplast genome was 147,036 bp in length with a GC content of 37.6%, consisting of four parts, namely LSC (91,969 bp), SSC (17,469 bp), and two IRs (18,799 bp in each). The cp genome contained 127 genes, including 83 CDS genes, 36 tRNA genes, and 8 rRNA genes. The phylogenetic analysis showed that L. buchtormensis was sister to Ledebouriella seseloides.

| S-EPMC8725980 | biostudies-literature

The complete chloroplast genome sequence of Ostericum koreanum (Apiaceae).

Project description:Ostericum koreanum Kitagawa is an important herbal medicine, whose taxonomic status has been changed to Angelica reflexa as a new species. This study generated the complete chloroplast genome sequence of O. koreanum, and reconsidered its molecular taxonomic status in Angelica by comparing it with related species. The length of the complete chloroplast genome was 147,282 bp, and there were four structures that included the large single copy region (93,185 bp), the small single copy region (17,663 bp) and the duplicated inverted regions (18,217 bp of each). Based on its phylogenetic trees, O. koreanum was grouped by high bootstrap value with the Angelica species. This result proved that O. koreanum is included in Angelica. Therefore, this chloroplast genome data generated for the first time a valuable genetic resource for the discrimination of herbal materials, phylogeny, and evolution.

| S-EPMC7800663 | biostudies-literature

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 the medicinal plant, Angelica gigas (Apiaceae).

Project description:The complete chloroplast genome sequence of Angelica gigas, a traditional herbal plant used in treating diseases, was obtained by de novo assembly using illumina sequencing data (Illumina Inc., San Diego, CA). The circular molecule of the genome was constructed of four parts, with a size of 146,916 bp in total - a large single copy (LSC) region of 93,118 bp, a small single copy (SSC) region of 17,582 bp and two inverted repeat (IRa and IRb) regions of 18,108 bp each. There were a total of 113 annotated genes, including 80 protein-coding genes, 29 tRNA genes and four rRNA genes. The phylogenetic result acquired through maximum parsimony analysis showed that A. gigas is closely related with A. decursiva and Seseli montanum.

| S-EPMC7870150 | biostudies-literature

The complete chloroplast genome sequence of Sinolimprichtia alpina var. dissecta (Apiaceae).

Project description:Sinolimprichtia alpina var. dissecta is a plant variety which is characterized from S. alpina var. alpina in possessing characteristic, highly dissected bracteoles. In the current study, we have sequenced the complete chloroplast genome of S. alpina var. dissecta using the Illumina sequencing platform. The chloroplast genome is 156,719 bp in length, consisting of a LSC region of 95,625 bp, a SSC region of 10,500 bp, and a pair of inverted repeats (IR) regions of 25,297 bp. The GC content was 37.7%. A total of 126 unique genes were identified, including 81 protein-coding genes, 37 tRNA genes and 8 rRNA genes. Phylogenetic analysis based on 28 chloroplast genomes indicates that S. alpina var. dissecta is most closely related to Pterygopleurum neurophyllum.

| S-EPMC8018366 | biostudies-literature

The complete chloroplast genome of Torilis scabra (Apiaceae).

Project description:Torilis scabra (Thunb.) DC. is widely distributed in China and Japan and has been introduced to North America. In this study, the complete chloroplast genome sequence of the T. scabra was obtained by de novo assembly using the NGS data. The chloroplast genome of T. scabra was 157,855 bp in length and divided into four distinct regions, such as large single-copy region (85,362 bp), small single-copy region (17,993 bp), and a pair of inverted repeat regions (27,250 bp). The genome annotation predicted a total of 127 genes, including 82 protein-coding genes, 37 tRNA genes, and 8 rRNA genes. Phylogenetic analysis with reported chloroplast genomes showed that T. scabra has a close genetic relationship with Anthriscus cerefolium.

| S-EPMC7706797 | biostudies-literature

The complete chloroplast genome of Meeboldia yunnanensis (Apiaceae).

Project description:Meeboldia yunnanensis Wolff (Apiaceae) is a perennial species naturally distributed in Yunnan and Xizang. The complete chloroplast genome sequence of M. yunnanensis was generated by de novo assembly using whole-genome next-generation sequencing data. The complete chloroplast genome of M. yunnanensis was 154,865 bp in total sequence length and divided into four distinct regions: small single-copy region (17,370 bp), large single-copy region (84,641 bp), and a pair of inverted repeat regions (26,427 bp). The genome annotation displayed a total of 130 genes, including 85 protein-coding genes, 37 tRNA genes, and 8 rRNA genes. Phylogenetic analysis with the reported chloroplast genomes revealed that M. yunnanensis has close relationship to Pterygopleurum neurophyllum.

| S-EPMC7706806 | biostudies-literature

The complete chloroplast genome of Heteromorpha arborescens (Apiaceae).

Project description:Heteromorpha arborescens has long been recognized and cultivated as an important medicinal plant. We reported its complete plastid genome for the first time and reconstructed its phylogenetic position. The complete plastid genome was 157,172 bp in length with a typical quadripartite organization: a large single-copy (LSC) region of 86,436 bp, a small single-copy (SSC) region of 18,222 bp, and two inverted repeat regions (IRa and IRb), each of 26,257 bp. A total of 130 functional genes were recovered, consisting of 85 protein-coding genes, 37 tRNA genes, and 8 rRNA genes. The phylogenetic analysis suggested that H. arborescens is sister to other species except Cetella arborescens in Apiaceae with strong ultrafast support.

| S-EPMC7781938 | biostudies-literature

Characterization of the complete chloroplast genome sequence of Elaeagnus henryi Warb. ex Diels (Elaeagnaceae).

Project description:Elaeagnus henryi Warb. ex Diels belongs to the Elaeagnaceae. Here, we reveal the complete chloroplast genome of Elaeagnus henryi. The complete chloroplast genome is 152,244 bp in length and contains a large single-copy (LSC) region of 82,235 bp, a small single-copy (SSC) region of 18,279 bp and a pair of inverted repeats (IRs) of 25,865 bp. There are 126 genes, including 81 protein-coding, 37 transfer RNA (tRNA), and eight ribosomal RNA (rRNA) genes. The total GC content of the chloroplast genome sequence is 37.1%. The maximum-likelihood phylogenetic analysis indicated that E. henryi was sister to Elaeagnus pungens (MW145133). The result may be because the species are advanced and developed from the same ancestor.

| S-EPMC9621288 | biostudies-literature

Complete chloroplast genome of Angelica hirsutiflora Liu et al. 1961 (Apiaceae).

Project description:Angelica hirsutiflora Liu et al.1961, is a perennial herb in the Apiaceae family that is endemic to Taiwan. In this study, the complete circular chloroplast genome of A. hirsutiflora was reconstructed and annotated using Illumina sequencing. The size of the chloroplast genome is 154,266 bp, consisting of two inverted repeats (IRs, 25,075 bp) separated by a large single-copy region (LSC, 86,569 bp) and a small single-copy region (SSC, 17,547 bp). The GC content of the chloroplast genome is 37.6%. There are 114 different genes in the chloroplast genome of A. hirsutiflora, including 80 protein-coding genes, 30 tRNA genes and four rRNA genes. A maximum-likelihood phylogenetic analysis showed that A. hirsutiflora forms a distinct clade, and separated from other species within the genus Angelica. This study provided insights into the evolutionary relationships among different species of Angelica.

| S-EPMC11000599 | 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