Browse
Submit Data
Databases
API
Help

Dataset Information

33 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

The complete chloroplast genome of Prunus domestica L. (Rosaceae) and its phylogenetic implication.

ABSTRACT: Prunus domestica commonly known as European plum is one of the most important wild fruit tree resources, and up to date, its wild community has only been found to be distributed in wild fruit forest area of the Tianshan Mountainsin Ili region of Xinjiang, China. Despite its agricultural importance and long history of cultivation, many questions remain about the origin of this species, due to absence of genome data. In this study, the complete chloroplast (cp) genome sequence of P. domestica was determined using next-generation sequencing. The entire cp genome was determined to be 157,395 bp in length. It contained large single-copy (LSC) and small single-copy (SSC) regions of 85,744 and 18,949 bp, respectively, which were separated by a pair of 26,351 bp inverted repeat (IR) regions. The genome contained 130 genes, including 85 protein-coding genes, 37 tRNA genes, and eight rRNA genes. The overall GC content of the genome is 36.8%. A phylogenetic tree reconstructed by 39 chloroplast genomes reveals that P. domestica is most closely related to Prunus salicina.

SUBMITTER: Geng W

PROVIDER: S-EPMC7782716 | biostudies-literature |

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Similar Datasets

The complete plastid genome of cherry plants Prunus discoidea (Rosaceae) and its phylogenetic implication.

Project description:Prunus discoidea is an endemic cherry species with ornamental value, spread in eastern China (Anhui, Jiangxi, Zhejiang provinces). Little information is available regarding its genomic, with limited phylogenetic relationship study performed on P. discoidea until now. The plastid genome was 158,024?bp in length consisting of four regions: large single-copy region (85,953?bp), small single-copy region (19,113?bp), and a pair of inverted repeat regions (26,469?bp each). The plastid genome contained a total of 129 genes, including 84 coding genes, 8 rRNA genes, and 37 tRNA genes. Phylogenetic analysis for 20 reported genomes within the Prunus sensu lato showed three main clades of Prunus s.l. with strong supports.

| S-EPMC7707402 | biostudies-literature

The complete plastid genome of cherry plants Prunus sargentii (Rosaceae) and its phylogenetic implication.

Project description:Prunus sargentii is an ornamental flowering cherry species, spread in Japan, Korea, Russia, and Northeast China. Little information is available regarding its genomic, with limited phylogenetic relationship study performed on P. sargentii until now. In this research, we reported the complete plastid genome of P. sargentii. The complete chloroplast of this species is 158,138 bp in length, including a pair of invert repeat regions (IR) (26,463bp) that is divided by a large single-copy region (LSC) (85,959bp) and a small single-copy region (SSC) (19,253bp). The plastid genome contained a total of 128 genes, including 84 coding genes, eight rRNA genes, and 36 tRNA genes. Phylogenetic analysis indicates that P. sargentii has a closer relationship with P. kumanoensis.

| S-EPMC8381913 | 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 Prunus campanulata 'Fugui' (Rosaceae).

Project description:Prunus campanulata 'Fugui' is newly bred cultivar. Here, we report its complete chloroplast genome. The length of the P. campanulata 'Fugui' chloroplast genome is 157,948 bp, with a large single-copy region of 85,948 bp, a small single-copy region of 19,128 bp and a pair of inverted repeat regions of 26,436 bp each. The genome contains 90 protein-coding genes, 65 transfer RNA genes and 9 ribosomal RNA genes. In addition, the genome contains 67 simple sequence repeats. Phylogenetic analysis revealed that P. campanulata 'Fugui' is genetically related to previously reported P. campanulata.

| S-EPMC9423843 | biostudies-literature

Complete chloroplast genome of Prunus fruticosa and its implications for the phylogenetic position within Prunus sensulato (Rosaceae).

Project description:Prunus fruticosa is a wild species of Prunus distributed across the central Eurasia. Here, we reported the complete chloroplast (cp) genome of P. fruticosa (GenBank accession number: MT916286). The cp genome was 158,217 bp long, with a large single-copy region (LSC) of 86,322 bp and a small single-copy region (SSC) of 19,153 bp separated by a pair of inverted repeats (IRs) of 26,371 bp. It encodes 129 genes, including 84 protein-coding genes, 37 tRNA genes, and 8 ribosomal RNA genes. We also reconstructed the phylogeny of Prunus sensu lato using maximum likelihood (ML) method, including our data and previously reported cp genomes of related taxa. The phylogenetic analysis indicated that P. fruticosa is closely related with Prunus avium.

| S-EPMC7594838 | biostudies-literature

Complete chloroplast genome of Prunus emarginata and its implications for the phylogenetic position within Prunus sensu lato (Rosaceae).

Project description:Prunus emarginata is a species of Prunus native to western North America.We determined the first complete chloroplast genome of P. emarginata using genome skimming approach. The cp genome was 157,458?bp long, with a large single-copy region (LSC) of 85,567?bp and a small single-copy region (SSC) of 19,121?bp separated by a pair of inverted repeats (IRs) of 26,385?bp. It encodes 129 genes, including 84 protein-coding genes, 37 tRNA genes, and 8 ribosomal RNA genes. We also reconstructed the phylogeny of Prunus sensu lato using maximum likelihood (ML) method, including our data and previously reported cp genomes of related taxa. The phylogenetic analysis indicated that P. emarginata is closely related with Prunus subhirtella var. subhirtella and Prunus yedoensis.

| S-EPMC7707383 | biostudies-literature

Complete chloroplast genome of Prunus pensylvanica and its implications for the phylogenetic position within Prunus sensu lato (Rosaceae).

Project description:Prunus pensylvanica is one of the two native cherry species of North America. We determined the first complete chloroplast genome of P. pensylvanica using genome-skimming approach. The cp genome was 157,953 bp long, with a large single-copy region (LSC) of 86,030 bp and a small single-copy region (SSC) of 19,135 bp separated by a pair of inverted repeats (IRs) of 26,394 bp. It encodes 129 genes, including 84 protein-coding genes, 37 tRNA genes, and 8 ribosomal RNA genes. We also reconstructed the phylogeny of Prunus sensu lato using maximum likelihood (ML) method, including our data and previously reported cp genomes of related taxa. The phylogenetic analysis indicated that P. pensylvanica is closely related to P. emarginata.

| S-EPMC7707365 | biostudies-literature

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 sequence of Prunus Cerasifera Ehrh. 'Pissardii' (Rosaceae).

Project description:Prunus cerasifera Ehrh. 'Pissardii', is a widespread ornamental and fruit tree. Here, we reported the complete chloroplast (cp) genome of P. cerasifera 'Pissardii' (GenBank accession number: MN418903). The total cp genome is 157,952?bp in length, displayed a typical quadripartite structure, including a large single copy region (LSC) of 86,286?bp and a small single copy region (SSC) of 18,926?bp, which are separated by a pair of inverted repeat (IR) regions of 26,370?bp. The overall guanine-cytosine (GC) content of the genome sequence is 36.7%. The cp genome encodes 134 unique genes, including 84 protein-coding genes, 42 tRNA genes, and 8 rRNA genes. Phylogenetic analysis of 27 chloroplast genomes showed that P. cerasifera 'Pissardii' was closely related to P. humilis in Rosaceae.

| S-EPMC7707454 | biostudies-literature

Complete chloroplast genome of the wild Japanese Mountain cherry (Prunus jamasakura, Rosaceae).

Project description:Prunus jamasakura is a species of Prunus native to eastern Asia. We determined the first complete chloroplast genome of Prunus jamasakura using genome skimming approach. The cp genome was 157,905 bp long, with a large single-copy region (LSC) of 85,910 bp and a small single-copy region (SSC) of 19,123 bp separated by a pair of inverted repeats (IRs) of 26,436 bp. It encodes 129 genes, including 84 protein-coding genes, 37 tRNA genes, and 8 ribosomal RNA genes. We also reconstructed the phylogeny of Prunus sensu lato using maximum likelihood (ML) method, including our data and previously reported cp genomes of related taxa. The phylogenetic analysis indicated that P. jamasakura is closely related with Prunus speciosa.

| S-EPMC7748705 | 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