Browse
Submit Data
Databases
API
Help

Dataset Information

73 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

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

ABSTRACT: 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.

SUBMITTER: Mu J

PROVIDER: S-EPMC7819125 | biostudies-literature |

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Similar Datasets

The complete chloroplast genome sequence of Prunus glandulosa Thunb. (Rosaceae).

Project description:Prunus glandulosa Thunb. is an ornamental species in the genus Prunus (Rosaceae) mainly distributed in eastern China. It is often cultivated in gardens, roadsides, or shrub clusters. It looks like a cherry but resembles to prunes as well. We obtained the complete chloroplast genome of P. glandulosa using next-generation sequencing technology. The chloroplast genome is 158.078 bp in length with typical tetrad structure. It includes two copies of inverted repeats (IRs, 26.385 bp), a large single copy (LSC, 86.269 bp) and a small single copy (SSC, 19.039 bp). The total GC content is 36.7%, including 85 protein-coding genes (PCGs), 36 transfer RNA genes (tRNA), and eight ribosomal RNA genes (rRNA). The maximum-likelihood phylogeny using the full length of chloroplast genomes indicates that P. glandulosa is closer to prunes than to cherries.

| S-EPMC8491658 | 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 sequence of Prunus discadenia (Rosaceae), a species with great ornamental value.

Project description:Prunus discadenia is a Cerasus species with great ornamental value and endemic to China. Here, the complete chloroplast (cp) genome of P. discadenia was assembled based on the Illumina reads. The cp genome is 157,915 bp in length, which contains two inverted repeat regions (26,415 bp) separated by the small single copy (19,119 bp) and the large single copy (85,966 bp) regions. The plastome contains 131 genes, and the overall GC content is 36.7%. Complete chloroplast genome of P. discadenia is of great significance to rebuilt the phylogeny of Cerasus.

| S-EPMC7971230 | biostudies-literature

The complete chloroplast genome of a Chinese medicinal plant, Peristrophe japonica (Thunb.) Bremek. (Lamiales: Acanthaceae) from Nanjing, China.

Project description:Peristrophe japonica (Thunb.) Bremek. is a widely distributed medicinal plant species in China and Japan. In this study, the complete chloroplast genome sequence of P. japonica was assembled and characterized from high-throughput sequencing data. The chloroplast genome is 151,374 bp in length, consisting of a large single-copy (LSC) and a small single-copy (SSC) regions of 83,395 bp and 17,073 bp, respectively, which were separated by a pair of 25,453 bp inverted repeat (IR) regions. The overall GC content of the genome is 38.07%. The genome contains 133 genes, including 88 protein-coding, 37 tRNA, and eight rRNA genes. A phylogenetic tree reconstructed using 23 chloroplast genomes reveals that Peristrophe form a separate group which is a sister of the genus Dicliptera. The work reported here is the first complete chloroplast genome of P. japonica which will provide useful information to the evolutionary studies on the genus of Peristrophe.

| S-EPMC8189061 | biostudies-literature

The complete chloroplast genome sequence of Malus halliana (Rosaceae), an important ornamental plant.

Project description:Malus halliana is an important ornamental plant resource. Herein, we determined the complete chloroplast (cp) genome sequence of M. halliana using Illumina sequencing data. The whole cp genome is 160,089 bp in size, consisting of a pair of inverted repeats (IR 52,706 bp), a large single-copy region (LSC 88,189 bp), and a small single-copy region (SSC 19,194 bp). The plastid genome contains 129 genes, 84 protein-coding genes, 37 tRNA genes, and eight rRNA genes. In addition, a maximum-likelihood phylogenetic analysis demonstrated that M. halliana was most closely related to Malus hupehensis. The complete plastome sequence will provide useful genetic information for phylogenetic studies, the resolution of taxonomic discrepancies, and molecular breeding.

| S-EPMC7510752 | biostudies-literature

Complete Chloroplast Genome Sequence Of Prunus Davidiana (Rosaceae).

Project description:Prunus davidiana is a Chinese wild peach species belonging to the family Rosaceae. In this study, we first assembled the complete chloroplast (cp) genome of P. davidiana by Illumina paired-end reads data, then carried out phylogenetic analysis. The P. davidiana cp genome was 158,055 bp, containing a large single copy region (LSC) of 86,248 bp and a small single copy region (SSC) of 19,047 bp separated by a pair of inverted repeats (IRs) of 26,380 bp. The cp genome contained 131 genes, including 86 protein-coding genes, 37 transfer RNA (tRNA) genes and 8 ribosomal RNA (rRNA) genes. The result of the phylogenetic analysis showed that P. davidiana is closely related to P. mongolica.

| S-EPMC7801015 | 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 a Chinese endemic ornamental plant Sorbus unguiculata Koehne (Rosaceae).

Project description:Sorbus unguiculata is a pinnate-leaved deciduous shrub growing in mixed forests in Sichuan province, China. It is one of the least known species in the genus with high ornamental value. In this study, we firstly assembled and annotated the complete chloroplast genome of the species using the next-generation sequencing method. The results showed that the chloroplast genome size is 159,900?bp, comprising of a large single-copy (LSC) region of 87,888?bp, a small single-copy (SSC) region of 19,256?bp, and a pair of IR regions of 26,378?bp. The whole cp genome predicted 109 genes in total, including 76 protein-coding genes, 29 tRNAs, and 4 tRNAs. The overall GC content of the chloroplast genome is 36.6%. The phylogenetic relationship exhibited that S. unguiculata is closely clustered with S. helenae in Sorbus.

| S-EPMC7687415 | 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 Agapanthus praecox (Agapanthaceae), an ornamental and medicinal plant.

Project description: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

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