Browse
Submit Data
Databases
API
Help

Dataset Information

69 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

The complete chloroplast genome of ornamental plant Ruellia simplex C.Wright (Acanthaceae).

ABSTRACT: Ruellia simplex C.Wright is a perennial plant of the Acanthaceae, which has significant ornamental value. Because of its strong adaptability, it is widely planted in Chinese rural areas. Based on sequencing data from Illumina, the first complete chloroplast (cp) genome of Ruellia simplex C.Wright is reported in this paper. This cp genome was 143,016bp in length, including a large single-copy region (LSC) of 91,857bp, a small single-copy (SSC) of 17,591bp and two inverted repeat regions (IRs) of 16,784bp. It contained 128 genes, 35 transfer RNA genes, 8 ribosomal RNA genes, with an overall GC content of 38.41%. Additionally, the phylogenetic analysis showed that Ruellia simplex is closely related to Strobilanthes cusia (NC_037485), Strobilanthes bantonensis (MT576695) and Echinacanthus attenuatus (NC_039762). The results of this study provide valuable information for the continued study of its species evolution, genetic engineering and germplasm resource utilization.

SUBMITTER: Siyi F

PROVIDER: S-EPMC8344733 | 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 the ornamental plant Primula violaris (Primulaceae).

Project description:Primula violaris is a perennial herb distributed throughout the western part of Hubei Province and the southern part of Shaanxi Province, China. We present on of the first reports of the complete chloroplast genome sequence for P. violaris. The complete chloroplast genome was 153,630 bp in size, including a large single-copy (LSC) region of 84,526 bp, a small single-copy (SSC) region of 17,812 bp, and a pair of inverted repeat (IR) regions of 25,646 bp. There were 130 genes in the chloroplast genome, including 86 CDSs, 36 transfer RNA (tRNA) genes, and eight rRNA genes. Phylogenetic analysis showed that P. violaris is closely related to P. oreodoxa. (NC_050848).

| S-EPMC8635539 | biostudies-literature

The complete chloroplast genome of Symphoricarpos orbiculatus (Caprifoliaceae), an important ornamental plant.

Project description:Symphoricarpos orbiculatus is an important landscape and ornamental plant. In this study, we report the complete chloroplast genome sequences of S. orbiculatus. The complete chloroplast genome of S. orbiculatus was 156,044?bp in length. The genome has a typical quadripartite structure, including a large single-copy (LSC) region of 88,756?bp, a small single-copy (SSC) region of 19,130?bp, and two inverted repeat (IR) regions of 24,079?bp each. Overall, the GC content was 38.4%. In the genome, it was identified to comprise130 genes, including 85 protein-coding genes, 37 tRNA genes, and 8 rRNA genes. This study provides valuable information for molecular phylogenetic study of Caprifoliaceae and is significant for variety development of Symphoricarpos.

| S-EPMC7707196 | 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

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

The complete chloroplast genome of the Buddleja alternifolia (Buddleiaceae), an ornamental plant.

Project description:Buddleja alternifolia is China's specialty, and scattered in northwest China. Here, we assembled and characterized the complete chloroplast (cp) genome of B. alternifolia using Illumina sequencing data for the first time. The complete cp genome was 154,280 bp in length, consisting of a pair of inverted repeats of 25,440 bp, a large single-copy (LSC) region of 85,330 bp, and a small single-copy (SSC) region of 18,070 bp. The genome encoded 115 unique genes, including 80 protein-coding genes, 31 tRNA genes, and four rRNA genes. Phylogenetic analysis based on 16 complete cp genome sequences indicated that B. alternifolia is closely related to Buddleja colvilei.

| S-EPMC7748639 | biostudies-literature

The complete chloroplast genome of the Lonicera maackii (Caprifoliaceae), an ornamental plant.

Project description:Lonicera maackii, is scattered in west and northeast China as well as adjacent Korea, Japan and the Soviet union. Here, we assembled and characterized the complete chloroplast (cp) genome of L. maackii using Illumina sequencing data for the first time. The complete cp genome was 155,337 bp in length, consisting of a pair of inverted repeats of 23,718 bp, a large single-copy region of 89,221 bp and a small single-copy region of 18,680 bp. The genome encoded 113 unique genes, including 79 protein-coding genes, 30 tRNA genes and four rRNA genes. Phylogenetic analysis based on 25 complete cp genome sequences indicated that L. maackii is closely related to Lonicera sachalinensis and Lonicera insularis.

| S-EPMC7748521 | biostudies-literature

The complete chloroplast genome of Cerasus dictyoneura, an ornamental plant of China.

Project description:The complete cp genome of Cerasus dictyoneura was 158,084 bp in length, consisting of a LSC of 86,275 bp and a SSC of 19,039 bp, which were separated by a pair of 26,385 bp IRs. The genome contained 131 genes, including 86 proteincoding genes, 37 tRNA genes, and 8 rRNA genes. The overall GC content is 36.7%, while the corresponding values of the LSC, SSC, and IR regions are 34.6, 29.5, and 42.6%, respectively. Furthermore, phylogenetic analysis based on 16 complete cp genome sequences indicated that C. dictyoneura is within Eurosids I.

| S-EPMC7707308 | biostudies-literature

The draft genome of Ruellia speciosa (Beautiful Wild Petunia: Acanthaceae).

Project description:The genus Ruellia (Wild Petunias; Acanthaceae) is characterized by an enormous diversity of floral shapes and colours manifested among closely related species. Using Illumina platform, we reconstructed the draft genome of Ruellia speciosa, with a scaffold size of 1,021?Mb (or ?1.02?Gb) and an N50 size of 17,908?bp, spanning ?93% of the estimated genome (?1.1?Gb). The draft assembly predicted 40,124 gene models and phylogenetic analyses of four key enzymes involved in anthocyanin colour production [flavanone 3-hydroxylase (F3H), flavonoid 3'-hydroxylase (F3'H), flavonoid 3',5'-hydroxylase (F3'5'H), and dihydroflavonol 4-reductase (DFR)] found that most angiosperms here sampled harboured at least one copy of F3H, F3'H, and DFR. In contrast, fewer than one-half (but including R. speciosa) harboured a copy of F3'5'H, supporting observations that blue flowers and/or fruits, which this enzyme is required for, are less common among flowering plants. Ka/Ks analyses of duplicated copies of F3'H and DFR in R. speciosa suggested purifying selection in the former but detected evidence of positive selection in the latter. The genome sequence and annotation of R. speciosa represents only one of only four families sequenced in the large and important Asterid clade of flowering plants and, as such, will facilitate extensive future research on this diverse group, particularly with respect to floral evolution.

| S-EPMC5397612 | 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