Browse
Submit Data
Databases
API
Help

Dataset Information

44 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Complete chloroplast genome of Prunus rufa (Rosaceae), a wild flowering cherry endemic to the Himalayan region.

ABSTRACT: Prunus rufa is a species of Prunus native to the Himalayan region. We determined the first complete chloroplast genome of P. rufa using a genome skimming approach. The cp genome was 157,723 bp long, with a large single-copy region (LSC) of 85,860 bp and a small single-copy region (SSC) of 19,081 bp separated by a pair of inverted repeats (IRs) of 26,391 bp each. 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. rufa is closely related to Prunus cerasoides.

SUBMITTER: Li YL

PROVIDER: S-EPMC7720985 | biostudies-literature | 2019 Dec

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

Complete chloroplast genome of Prunus rufa (Rosaceae), a wild flowering cherry endemic to the Himalayan region.

Li Yue-Ling YL Clarke Barry B Li Jian-Hui JH Sun Zhong-Shuai ZS

Mitochondrial DNA. Part B, Resources 20191213 1

Prunus rufa is a species of Prunus native to the Himalayan region. We determined the first complete chloroplast genome of P. rufa using a genome skimming approach. The cp genome was 157,723 bp long, with a large single-copy region (LSC) of 85,860 bp and a small single-copy region (SSC) of 19,081 bp separated by a pair of inverted repeats (IRs) of 26,391 bp each. It encodes 129 genes, including 84 protein-coding genes, 37 tRNA genes, and 8 ribosomal RNA genes. We also reconstructed ...[more]

PMID: 33366467

Similar Datasets

Complete chloroplast genome of Prunus itosakura (Rosaceae), a wild flowering cherry from Japan.

Project description:Prunus itosakura is a flowering tree species with high ornamental and economic values. We determined the first complete chloroplast genome of P. itosakura using genome skimming approach. The cp genome was 157,813 bp long, with a large single-copy region (LSC) of 85,931 bp and a small single-copy region (SSC) of 19,120 bp separated by a pair of inverted repeats (IRs) of 26,381 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. itosakura is closely related with Prunus subhirtella var. subhirtella.

| S-EPMC7748579 | biostudies-literature

Complete chloroplast genome of Ulleung Island endemic flowering cherry, Prunus takesimensis (Rosaceae), in Korea.

Project description:Prunus takesimensis is an endemic flowering cherry on Ulleung Island, Korea. The complete chloroplast (cp) genome of P. takesimensis was generated by de novo assembly using whole-genome next-generation sequencing approach. The cp genome size was 157,948 bp in length consisting of four regions; large single copy region (85,959 bp), small single copy region (19,117 bp), and a pair of inverted repeat regions (26,436 bp). The genome contained a total of 128 genes, including 83 coding genes, 8 rRNA genes, and 37 tRNA genes. Phylogenetic analysis for 20 reported genomes within the family Rosaceae showed the monophyly of the genus Prunus including newly sequenced P. takesimensis.

| S-EPMC7800873 | biostudies-literature

The complete chloroplast genome of Prunus conradinae (Rosaceae), a wild flowering cherry from China.

Project description:Prunus conradinae is a flowering cherry species with high ornamental value. In this study, the complete chloroplast (cp) genome of P. conradinae was obtained using a genome skimming approach. The cp genome was 158,019 bp long, with a large single-copy region of 85,910 bp and a small single-copy region of 19,247 bp separated by two inverted repeats of 26,431 bp. It encodes 130 genes, including 85 protein-coding genes, 37 tRNA genes, and eight ribosomal RNA genes. The phylogenetic analysis indicated that P. conradinae is closely related to the congeners P. maximowiczii, P. takesimensis, P. speciosa, P. serrulata var. spontanea, P. discoidea, and P. matuurai.

| S-EPMC7782140 | biostudies-literature

The complete chloroplast genome of Prunus clarofolia (Rosaceae), a wild cherry endemic to China.

Project description:Prunus clarofolia (Schneid.) Yu et Li is a very attractive wild flowering cherry endemic to China. In this study, the complete chloroplast genome of P. clarofolia was assembled. The total length of the chloroplast genome was 157,899 bp, containing a pair of inverted repeat regions of 26,393 bp each, separated by a small single-copy region of 19,142 bp, and a large single-copy region of 85,971 bp. The overall GC content of the chloroplast genome was 36.71%. The genome contained 131 genes, including 85 protein-coding genes, 37 tRNA genes, eight rRNA genes, and one pseudogene. Phylogenetic analysis revealed that P. clarofolia and P. pseudocerasus showed the closest relationship.

| S-EPMC8741222 | biostudies-literature

Complete chloroplast genome of Cerasus fengyangshanica (Rosaceae), a wild flowering cherry endemic to China.

Project description:Cerasus fengyangshanica is a wild flowering cherry endemic to Mount Fengyang, China. Here, we reported the complete chloroplast (cp) genome of C. fengyangshanica (GenBank accession number: MW160272). The cp genome was 157,964 bp long, with a large single-copy region (LSC) of 85,972 bp and a small single-copy region (SSC) of 19,086 bp separated by a pair of inverted repeats (IRs) of 26,453 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 C. fengyangshanica is closely related with Prunus maximowiczii.

| S-EPMC7832537 | biostudies-literature

Complete chloroplast genome of Cerasus kumanoensis (Rosaceae), a wild flowering cherry endemic to Kii Peninsula, Japan.

Project description:Cerasus kumanoensis is a recently described wild cherry species from the Kii Peninsula, Japan. Here we determined the first complete chloroplast genome of C. kumanoensis using genome skimming approach. The cp genome was 157,898 bp long, with a large single-copy region (LSC) of 85,926 bp and a small single-copy region (SSC) of 19,070 bp separated by a pair of inverted repeats (IRs) of 26,451 bp. It encodes 129 genes, including 84 protein-coding genes, 37 tRNA genes, and 8 ribosomal RNA genes. Besides, we reconstructed the phylogeny of Prunus using maximum likelihood (ML) method, including our data and previously reported cp genomes of related taxa. The phylogenetic analysis indicated that C. kumanoensis is close related with a group including Prunus takesimensis and P. speciosa.

| S-EPMC7706986 | 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

Multiple Lines of Evidence for Independent Origin of Wild and Cultivated Flowering Cherry (Prunus yedoensis).

Project description:As with many other ornamental and cultivated plants that have been under human selection and cultivation for a long time, it has been a major challenge to trace back the complex evolutionary history of flowering cherry, Prunus yedoensis. This challenge has been further amplified by great morphological similarities, little molecular divergence, frequent natural and artificial hybridization, and poor documentation of breeding history among cultivated and wild flowering cherries. The origin and taxonomic distinction between wild P. yedoensis from Jeju Island, Korea, and one of the most popular cultivated flowering cherries, P. × yedoensis "Somei-yoshino" has been a controversy for the past few decades. We sampled many areas extensively, and using four different molecular markers we provided evidence for their independent origin. Wild P. yedoensis in Korea originated from multiple bidirectional hybridization events between two sympatric species, P. spachiana f. ascendens as the maternal species and P. serrulata var. spontanea/P. serrulata var. quelpaertensis as the most probable paternal species. On the contrary, our results supported a single artificial hybrid origin of P. × yedoensis "Somei-yoshino" from cultivated P. spachiana f. ascendens as the maternal species and P. speciosa, a species endemic to Izu Islands, as the paternal species. Based on extensive sampling, we provided strong evidence that wild and cultivated P. yedoensis are distinct taxonomic entities that have originated from different evolutionary processes. A potential for the development of new cultivars from wild P. yedoensis and conservation of diverse germplasms in situ insular setting and ex situ should be explored in the future.

| S-EPMC6930925 | biostudies-literature

The complete chloroplast genome of Prunus apetala, a native deciduous flowering cherry of Japan.

Project description:The complete chloroplast (cp) genome of Prunus apetala was determined. The length of the cp genome of P. apetala is 157,987 bp. A total of 129 genes are comprised of 84 protein-coding genes, 37 tRNA genes, and 8 rRNA ribosomal genes. The overall GC content of cp genome is 36.7%. The phylogenetic position of P. apetala is sister to Prunus serrulata var. spontanea.

| S-EPMC7707193 | biostudies-literature

The complete chloroplast genome of Prunus takasagomontana, a deciduous flowering cherry native to Taiwan island.

Project description:Prunus takasagomontana Sasaki 1931 is a deciduous flowering cherry endemic to Taiwan island, China. Here, we first report the complete chloroplast genome of P. takasagomontana. The complete chloroplast genome of P. takasagomontana is 157,946 bp in length, which is comprised of a pair of inverted repeat (IR) regions of 26,437 bp, a small single-copy (SSC) region of 19,145 bp, and a large single-copy (LSC) region of 85,927 bp. A total of 129 genes are annotated, including 84 protein-coding genes, 37 tRNA genes, and eight rRNA ribosomal genes. The phylogenetic analysis showed that P. takasagomontana is sister to P. serrulata var. spontanea.

| S-EPMC9341366 | biostudies-literature