Browse
Submit Data
Databases
API
Help

Dataset Information

22 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Characterization of the complete chloroplast genome of an endangered ornamental and medicinal plant Lilium pumilum.

ABSTRACT: Lilium pumilum DC. is a useful plant species not only for its showy flowers but also for its edible and medicinal values. Here we report on the complete chloroplast genome sequence of L. pumilum. The chloroplast genome is 152,573 bp in size and includes two inverted repeat regions of 52,984 bp, which is separated by a large single-copy region of 82,009 bp and a small single copy region of 17,580 bp. A total of 130 genes were predicted, including 38 tRNA, 8 rRNA, and 84 protein-coding genes. Phylogenetic analysis placed L. pumilum under the family Liliaceae.

SUBMITTER: Jin J

PROVIDER: S-EPMC7748673 | biostudies-literature |

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Similar Datasets

The complete chloroplast genome of Agapanthus praecox (Agapanthaceae), an ornamental and medicinal plant

Project description:Abstract Agapanthus praecox is a monocotyledonous, herbaceous, and perennial plant, which has been used as an ornamental and medicinal plant. Here, we assembled and characterized the complete chloroplast (cp) genome of A. praecox by de novo high throughput sequencing. The results revealed that the cp genome of A. praecox was 157,038 bp in total length, including a large single-copy (LSC) region of 85,195 bp, a small single-copy (SSC) region of 18,113 bp, and two invert repeats (IR) regions of 26,865 bp. The total plastid genome of A. praecox included 132 genes comprising 86 protein-coding genes, 38 tRNA genes, and eight rRNA genes. The phylogenetic analysis was conducted based on the complete cp genomes of 17 species and it indicated that A. praecox is closely related to A. coddi in Agapanthaceae family.

| S-EPMC8567867 | biostudies-literature

The complete chloroplast genome of Ophiopogon japonicus, an ornamental and medicinal plant.

Project description:Ophiopogon japonicus, extensively distributed in East Asia, is widely used in landscaping, the tuber of which also play a vital role in Oriental Medicine. Here, we reported the complete chloroplast genome which exhibited a typical quadripartite structure, 156,679?bp in length with 37.7% overall GC content, including 131 protein-coding genes, 37 transfer RNA genes, eight ribosomal RNA genes, and one pseudogene. Phylogenetic analysis suggested that O. japonicus has a close relationship to Liriope spicata.

| S-EPMC7706634 | biostudies-literature

The complete chloroplast genome of Hemerocallis citrina (Asphodelaceae), an ornamental and medicinal plant.

Project description:Hemerocallis citrina (Asphodelaceae) has been wildly cultivated as ornamental and medicinal plant. Here, we reported the first chloroplast genome sequence of H. citrina. The chloroplast genome size is 156,088 bp with GC content of 37.3%, including a large single-copy (LSC) of 84,843 bp, a small single-copy (SSC) of 18,507 bp, and a pair of 26,369 bp IR(inverted repeat) regions. A total of 133 genes were annotated including 87 protein-coding genes, 38 tRNA genes, and 8 rRNA genes. The phylogenetic analysis revealed that H. citrina belongs to the Hemerocallis genus in Asphodelaceae family.

| S-EPMC7748551 | biostudies-literature

The complete chloroplast genome of Rubus rosifolius (Rosaceae), an ornamental and medicinal plant.

Project description:Rubus rosifolius belongs to the genus Rubus in the family Rosaceae and is widely distributed globally. It has white flowers and red fruits. Moreover, it has medicinal value for diseases of the stomach and other areas. However, the complete chloroplast (cp) genome of R. rosifolius remains unclear. In the present study, we sequenced the complete cp genome of R. rosifolius (GenBank accession no. OL435124), which had a typical quadripartite structure and a size of 155,650 bp. Fifteen genes (trnK-UUU, rps16, trnG-UCC, atpF, rpoC1, trnL-UAA, trnV-UAC, petB, petD, rpl16, rpl2, ndhB, trnI-GAU, trnA-UGC, and ndhA) contained an intron, and two genes (clpP and ycf3) contained two introns. The gene rps12 showed trans-splicing. Phylogenetic analysis showed that R. rosifolius was closely related to Rubus taiwanicola, Rubus rubroangustifolius, and Rubus glandulosopunctatus.

| S-EPMC9297712 | biostudies-literature

The complete chloroplast genome of Prunus japonica thunb.(Rosaceae), an ornamental and medicinal plant.

Project description:Prunus japonica is an ornamental and medicinal plant that is widely cultivated. The complete chloroplast genome of P. japonica was sequenced using Illumina Hiseq X Ten platform. The chloroplast genome was 158,080 bp in length, containing two short inverted repeat (IRa and IRb) regions of 26,385 bp, which was separated by a large single copy (LSC) region of 86,270 bp and a small single copy (SSC) region of 19,040 bp. The GC content of the whole chloroplast genome was 36.8%. The chloroplast DNA of P. japonica comprised 112 distinct genes, including 78 protein-coding genes, 4 ribosomal RNA genes and 30 transfer RNA genes. Phylogenetic analysis indicated that all species of Prunus formed a monophyletic group, P. japonica was closely related to P. hulimis.

| S-EPMC7819125 | biostudies-literature

The complete chloroplast genome of Hedychium flavum Roxb., an ornamental, edible and medicinal plant.

Project description:Hedychium flavum Roxb. 1820 is a perennial herb mainly distributed in China, India, Myanmar and Thailand with ornamental, edible and medicinal value. It is extensively cultivated as a source of aromatic essential oils, ornamental plant, food flavorings and vegetables, and folk medicine. In this study, we sequence the complete chloroplast genome of H. flavum by de novo assembly. The assembled genome has a typical quadripartite circular structure with 163,909 bp in length, containing a large single-copy region (LSC, 88,589 bp), a small single-copy region (SSC, 15,762 bp), and two inverted repeat regions (IRs, 29,779 bp). The cp genome contains 133 genes, including 87 protein-coding genes, 38 tRNA genes and 8 rRNA genes. Phylogenetic analysis based on the complete cp genome shows a close affinity of H. flavum and H. neocarneum with 100% bootstrap support. This study will provide useful genetic resource for further phylogenetic analysis of the genus Hedychium and Zingiberaceae.

| S-EPMC10653761 | biostudies-literature

Complete chloroplast genome of Callicarpa formosana Rolfe, a famous ornamental plant and traditional medicinal herb.

Project description:Callicarpa formosana is a species of beauty-berry with large medicinal value belonging to the family Verbenaceae. In this study, the complete chloroplast genome of C. formosana was sequenced using Illumina Hiseq X Ten platform. The chloroplast genome was 1,54,210 bp in length, containing two short inverted repeat (IRa and IRb) regions of 25,701 bp, which was separated by a large single copy (LSC) region of 84,938 bp and a small single copy (SSC) region of 17,870 bp. The GC content of the whole chloroplast genome was 38.1%. The chloroplast DNA of C. formosana comprised 113 genes, including 79 protein-coding genes, 4 ribosomal RNA genes, and 30 transfer RNA genes. Phylogenetic analysis indicated that the genus Callicarpa L. was located in the basal position within the family Verbenaceae. The chloroplast genome (cpDNA) of C. formosana was closely related to Callicarpa nudiflora.

| S-EPMC7781935 | biostudies-literature

Characterization of the complete chloroplast genome of the ornamental plant Osmanthus cooperi.

Project description:Osmanthus cooperi is an evergreen ornamental plant belonging to the olive family. In this study, its complete chloroplast genome was assembled from the whole genome Illumina sequencing data. The circular genome is 155,262?bp long, and comprises a pair of inverted repeat regions (IRs, 25,685?bp each), a large single-copy region (LSC, 86,525?bp), and a small single-copy region (SSC, 17,367?bp). It encodes 132 genes, including 8 rRNA genes, 36 tRNAs genes, and 88 protein-coding genes. The GC content of O. cooperi cp genome is 37.8%. Phylogenetic analysis indicates that O. cooperi is close to O. fragrans in Oleaceae.

| S-EPMC7687408 | biostudies-literature

Characterization of the complete chloroplast genome of ornamental plant, Bougainvillea peruviana (Nyctaginaceae).

Project description:Bougainvillea peruviana is a widely domesticated ornamental plant species. However, studies on B. peruviana are limited. In this study, we reported the complete chloroplast (cp) genome of B. peruviana. The cp genome is 154,465 bp in length, containing a large single-copy (LSC) of 85,563 bp and a small single-copy (SSC) of 18,050 bp, which are separated by a pair of inverted repeats (IRs) of 25,426 bp, each. A total of 132 genes, including 86 protein-coding genes, 38 tRNA genes, and eight rRNA genes, were predicted. The overall GC content for the cp genome is 36.5%. The maximum-likelihood tree constructed based on cp genome sequences showed that B. peruviana is placed under Nyctaginaceae and is diverged before Bougainvillea glabra and Bougainvillea spectabilis under strong bootstrap support.

| S-EPMC7782202 | biostudies-literature

Characterization of the complete chloroplast genome of Senna bicapsularis (Leguminosae), an ornamental plant.

Project description:Senna bicapsularis is an important flowering, ornamental plant. The extracts showed antioxidant activity and antibacterial properties. In addition, S. bicapsularis can be used as a model woody plants. In the present study, the complete chloroplast genome was sequenced. The result showed that the length of circular chloroplast genome was 162,744 bp, containing a large single-copy region of 91,176 bp, a small single-copy region of 18,264 bp, and two inverted repeat regions of 26,652 bp. The chloroplast genome contained 128 genes, including 83 protein-coding, eight rRNA, and 37 tRNA genes. Phylogenetic tree analysis showed that S. bicapsularis has closely relationship with Senna occidentalis, Senna tora and Senna siamea.

| S-EPMC7782358 | 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