Browse
Submit Data
Databases
API
Help

Dataset Information

24 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

The complete mitochondrial genome of Panax ginseng (Apiales, Araliaceae): an important medicinal plant.

ABSTRACT: Ginseng (Panax ginseng C. A. Meyer) is a multifunctional medicinal herb used worldwide and is an economically important high-value crop in Korea. Here, we presented the mitochondrial genome of P. ginseng landrace 'Jakyung', which is one of the most common cultivars cultivated in Korean farms. The complete mitochondrial genome sequence was 464,661 bp in length and had a single circular form. The ginseng mitochondrial genome encoded 72 unique genes, including 45 protein-coding genes, 24 tRNA genes, and three rRNA genes. Nucleotide composition analysis revealed a GC content of 45.1%, with a slightly higher A + T bias (A, 27.1%; T, 27.8%; G, 22.5%; C, 22.6%). Phylogenetic analysis showed that P. ginseng was closely related to Daucus carota in the Apiales. This complete mitochondrial genome sequence of P. ginseng provides valuable genetic information for further studies of this important medicinal plant.

SUBMITTER: Jang W

PROVIDER: S-EPMC8477949 | biostudies-literature |

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Similar Datasets

The complete chloroplast genome sequence of Hydrocotyle sibthorpioides (Apiales: araliaceae).

Project description:Hydrocotyle sibthorpioides Lam. is a widespread and important Chinese medicinal plant. In this study, we have sequenced the complete chloroplast genome of H. sibthorpioides, which is 152,880 bp in length with large (LSC 84,064 bp) and small (SSC 18,690 bp) single-copy regions separated by a pair of inverted repeats (IRs 25,063 bp) and contains 113 unique genes with 17 genes duplicated in the IR making a total of 130 genes. The phylogenetic analysis strongly supports the position of H. sibthorpioides and indicates it belongs to the Araliaceae family, potential to facilitate a better understanding of population and phylogenetic studies in Apiales.

| S-EPMC7800476 | biostudies-literature

Development of highly transferable microsatellites for Panax ginseng (Araliaceae) using whole-genome data.

Project description:Highly transferable expressed sequence tag (EST) microsatellites were developed for Panax ginseng (Araliaceae), one of the most celebrated traditional Chinese medicines and an endangered species in East Asia, using whole-genome data. Twenty-one EST microsatellites were characterized from next-generation sequencing and were composed of di- and trinucleotide repeats. Polymorphisms and genetic diversity were evaluated for 45 accessions of three ginseng landraces. The number of alleles for each locus ranged from one to five among the landraces, and the polymorphism information content varied from 0.0000 to 0.6450. These microsatellites were also tested for congeneric amplification with P. notoginseng, P. stipuleanatus, P. quinquefolius, P. bipinnatifidus, and the closely related species Aralia elata. These novel EST-derived microsatellite markers will facilitate further population genetic studies of the genera Panax and Aralia.

| S-EPMC5104526 | biostudies-literature

Positive Selection Driving Cytoplasmic Genome Evolution of the Medicinally Important Ginseng Plant Genus Panax.

Project description:Panax L. (the ginseng genus) is a shade-demanding group within the family Araliaceae and all of its species are of crucial significance in traditional Chinese medicine. Phylogenetic and biogeographic analyses demonstrated that two rounds of whole genome duplications accompanying with geographic and ecological isolations promoted the diversification of Panax species. However, contributions of the cytoplasmic genomes to the adaptive evolution of Panax species remained largely uninvestigated. In this study, we sequenced the chloroplast and mitochondrial genomes of 11 accessions belonging to seven Panax species. Our results show that heterogeneity in nucleotide substitution rate is abundant in both of the two cytoplasmic genomes, with the mitochondrial genome possessing more variants at the total level but the chloroplast showing higher sequence polymorphisms at the genic regions. Genome-wide scanning of positive selection identified five and 12 genes from the chloroplast and mitochondrial genomes, respectively. Functional analyses further revealed that these selected genes play important roles in plant development, cellular metabolism and adaptation. We therefore conclude that positive selection might be one of the potential evolutionary forces that shaped nucleotide variation pattern of these Panax species. In particular, the mitochondrial genes evolved under stronger selective pressure compared to the chloroplast genes.

| S-EPMC5893753 | 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

Genome and evolution of the shade-requiring medicinal herb Panax ginseng.

Project description:Panax ginseng C. A. Meyer, reputed as the king of medicinal herbs, has slow growth, long generation time, low seed production and complicated genome structure that hamper its study. Here, we unveil the genomic architecture of tetraploid P. ginseng by de novo genome assembly, representing 2.98 Gbp with 59 352 annotated genes. Resequencing data indicated that diploid Panax species diverged in association with global warming in Southern Asia, and two North American species evolved via two intercontinental migrations. Two whole genome duplications (WGD) occurred in the family Araliaceae (including Panax) after divergence with the Apiaceae, the more recent one contributing to the ability of P. ginseng to overwinter, enabling it to spread broadly through the Northern Hemisphere. Functional and evolutionary analyses suggest that production of pharmacologically important dammarane-type ginsenosides originated in Panax and are produced largely in shoot tissues and transported to roots; that newly evolved P. ginseng fatty acid desaturases increase freezing tolerance; and that unprecedented retention of chlorophyll a/b binding protein genes enables efficient photosynthesis under low light. A genome-scale metabolic network provides a holistic view of Panax ginsenoside biosynthesis. This study provides valuable resources for improving medicinal values of ginseng either through genomics-assisted breeding or metabolic engineering.

| S-EPMC6181221 | biostudies-literature

The complete mitochondrial genome sequences of Bupleurum falcatum (Apiales: Apiaceae).

Project description:Bupleurum falcatum has a long history of use in traditional oriental medicine. The first complete mitochondrial genome sequences of B. falcatum were 463,792 bp based on 494,582 aligned reads. A total of 51 genes was annotated including 32 protein-coding genes, 16 tRNA genes, and three rRNA genes. In a comparison of B. falcatum and carrot (Daucus carota) revealed that the former species has four exclusive genes, but lacks six genes present in the latter. The compositional structure and phylogenetic relationships indicated that the mitochondrial genome of B. falcatum is similar to that of D. carota.

| S-EPMC7782287 | biostudies-literature

Complete chloroplast genome sequence of Peganum harmala, an important medicinal plant.

Project description:Peganum harmala is a perennial herbaceous plant belonging to the genus Peganum, Nitrariaceae and is mainly distributed in dry areas in the Mediterranean and many Asia countries. This plant species has high medicinal value and considerable ecological value. This article reports the first chloroplast genome of species in Peganum. The size of the P. harmala chloroplast genome is 160,070 bp, including a large single-copy (LSC) region (88,279 bp), a small single-copy (SSC) region (26,468 bp), and two reverse (IR) regions (18,856 bp). The P. harmala chloroplast genome consists of 132 genes, including 83 protein-coding genes, 38 transfer RNA (tRNA) genes, and 8 ribosomal RNA (rRNA) genes. The GC content of P. harmala chloroplast genome is 36.44%. Phylogenetic analysis showed that P. harmala and another Nitrariaceaeis species formed a single blade in the phylogenetic tree.

| S-EPMC7748625 | biostudies-literature

The complete plastome of Panax stipuleanatus: Comparative and phylogenetic analyses of the genus Panax (Araliaceae).

Project description:Panax stipuleanatus (Araliaceae) is an endangered and medicinally important plant endemic to China. However, phylogenetic relationships within the genus Panax have remained unclear. In this study, we sequenced the complete plastome of P. stipuleanatus and included previously reported Panax plastomes to better understand the relationships between species and plastome evolution within the genus Panax. The plastome of P. stipuleanatus is 156,069 base pairs (bp) in length, consisting of a pair of inverted repeats (IRs, each 25,887 bp) that divide the plastome into a large single copy region (LSC, 86,126 bp) and a small single copy region (SSC, 8169 bp). The plastome contains 114 unigenes (80 protein-coding genes, 30 tRNA genes, and 4 rRNA genes). Comparative analyses indicated that the plastome gene content and order, as well as the expansion/contraction of the IR regions, are all highly conserved within Panax. No significant positive selection in the plastid protein-coding genes was observed across the eight Panax species, suggesting the Panax plastomes may have undergone a strong purifying selection. Our phylogenomic analyses resulted in a phylogeny with high resolution and supports for Panax. Nine protein-coding genes and 10 non-coding regions presented high sequence divergence, which could be useful for identifying different Panax species.

| S-EPMC6317490 | biostudies-literature

Panaxsiamensis J. Wen, a new species of the ginseng genus (Panax, Araliaceae) from northern Thailand

Project description: Not available

| S-EPMC10576250 | biostudies-literature

The complete chloroplast genome of Physochlaina physaloides (Solanaceae), an important medicinal plant.

Project description:Physochlaina is an important perennial herbaceous genus with significant medicinal value, while the phylogeny of Physochlaina and tribe Hyoscyameae is not well resolved yet. In this study, we report the complete chloroplast genome sequences of Ph. physaloides, its complete chloroplast genome is 156,413 bp in length, which is a typical quadripartite structure that includes a large single-copy region of 86,659 bp, a small single-copy region of 18,012 bp, and its GC content was 37.7%. A total of 132 genes were identified, including 87 protein-coding genes, 37 tRNA genes, and 8 rRNA genes. Furthermore, a phylogenetic tree of the tribe Hyoscyameae was constructed based the complete chloroplast genome sequence, and a new topology of the tribe was obtained. This study provides valuable genetic information for the conservation and utilization of Ph. physaloides and also provide the potential for better understanding of the phylogeny of Hyoscyameae and Solanaceae.

| S-EPMC7707380 | 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