Browse
Submit Data
Databases
API
Help

Dataset Information

24 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

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

ABSTRACT: 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.

SUBMITTER: Dong Y

PROVIDER: S-EPMC8567867 | biostudies-literature |

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Similar Datasets

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 an endangered ornamental and medicinal plant Lilium pumilum.

Project description: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.

| S-EPMC7748673 | biostudies-literature

Characterization of the complete chloroplast genome of Clematis potaninii (Ranunculaceae), a medicinal and ornamental plant.

Project description:Clematis potaninii Maxim. is an important medicinal and ornamental plant. The length of C. potaninii chloroplast genome was 159,691 bp, with a large single-copy region of 79,503 bp, a small single-copy region of 18,106 bp, and two inverted repeat regions of 31,041 bp each. The chloroplast genome contains 138 genes including 94 protein-coding, eight rRNA, and 36 tRNA genes. Phylogenetic analysis showed that C. potaninii is closely related to C. alternata.

| S-EPMC9291703 | biostudies-literature

The complete chloroplast genome of ornamental and medicinal Callerya dielsiana (Fabaceae).

Project description:Callerya dielsiana is a Chinese endemic tropical/subtropical liana. We sequenced the complete chloroplast genome with the Illumina Hiseq X-Ten platform. The genome is obtained with 132,301 bp in length, lacking an inverted repeat (IR) region, contains 4 rRNAs, 30 tRNAs genes, and 76 protein-coding genes. The overall GC content is 33.9%. Based on the whole chloroplast genomes of 14 legume species, a phylogenetic tree is constructed and indicated that C. dielsiana belongs to the well-supported tribe Wisterieae. The tribe is sister to Glycyrrhiza and nested within the IRLC (Inverted Repeat-Lacking Clade) group of the subfamily Papilionoideae (Fabaceae).

| S-EPMC9347464 | biostudies-literature

The complete chloroplast genome of Callicarpa bodinieri (Lamiales, Lamiaceae), an ornamental and medicinal plant from Chongqing, China.

Project description:Plants classified to the genus Callicarpa L. have important medicinal and ornamental value. Here, we report and characterize the complete chloroplast (cp) genome of C. bodinieri to provide molecular basis for the further studies on the phylogeny analysis of this genus. The cp genome is 154,183 bp in length and is organized with a typical quadripartite structure, containing two inverted repeats of 25,701 bp separated by a large single-copy region of 84,956 bp and a small single-copy region of 17,825 bp. The cp genome of C. bodinieri contains 112 distinct genes, including 78 protein-coding, 30 tRNAs and 4 rRNAs genes. The phylogenetic analysis showed that C. bodinieri is fully resolved in a clade with C. nudiflora, sister to the clade of C. formosana and C. longifolia var. floccosa.

| S-EPMC7995876 | 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