Browse
Submit Data
Databases
API
Help

Dataset Information

47 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Complete chloroplast genome of Prunus fasciculata (Rosaceae), a species native to western North America.

ABSTRACT: Prunus fasciculata is a wild species of Prunus native to western North America. Here, we reported the complete chloroplast (cp) genome of P. fasciculata (GenBank accession number: MW160273). The cp genome was 157,986 bp long, with a large single-copy (LSC) region of 86,068 bp and a small single-copy (SSC) region of 19,166 bp separated by a pair of inverted repeats (IRs) of 26,376 bp. It encodes 129 genes, including 84 protein-coding genes, 37 tRNA genes, and eight 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 confirmed the sister group relationship between P. fasciculata and the remaining subg. Prunus.

SUBMITTER: Li YL

PROVIDER: S-EPMC7889079 | biostudies-literature | 2021 Feb

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

Complete chloroplast genome of Prunus fasciculata (Rosaceae), a species native to western North America.

Li Yue-Ling YL Reed James J Xu Yu-Qian YQ Qu Da-Hao DH Sun Zhong-Shuai ZS

Mitochondrial DNA. Part B, Resources 20210209 2

Prunus fasciculata is a wild species of Prunus native to western North America. Here, we reported the complete chloroplast (cp) genome of P. fasciculata (GenBank accession number: MW160273). The cp genome was 157,986 bp long, with a large single-copy (LSC) region of 86,068 bp and a small single-copy (SSC) region of 19,166 bp separated by a pair of inverted repeats (IRs) of 26,376 bp. It encodes 129 genes, including 84 protein-coding genes, 37 tRNA genes, and eight ribosomal ...[more]

PMID: 33628896

Similar Datasets

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

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 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

The complete chloroplast genome sequence of Prunus salicina cultivar 'Zuili' (Rosaceae).

Project description:'Zuili' is a distinguished plum (Prunus salicina Lindley 1830) originating from Tongxiang City, Zhejiang Province, China, and a nationally recognized geographical indication product. In this study, we reported the complete chloroplast genome of P. salicina cultivar 'Zuili'. The genome has a circular structure of 157,935 bp containing a large single-copy (LSC) region of 86,133 bp, a small single-copy (SSC) region of 19,028 bp, and two inverted repeats (IRs) of 26,387 by each. It harbors 130 genes (111 unique genes), including 85 protein-coding genes (78 are unique), eight ribosomal RNA genes (four are unique), and 37 transfer genes (29 are unique). The phylogenetic analysis based on whole chloroplast genomes showed 'Zuili' was clustered with Prunus salicina cultivar 'Wuyuecui' (MW406461.1) and 'No. 2 Guofeng' (MW406472.1). This study provides valuable information that can contribute to the identification and further evolutionary analysis of Prunus salicina cultivar 'Zuili'.

| S-EPMC10863533 | 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

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

Project description: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.

| S-EPMC7782716 | biostudies-literature

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

Past climate change and plant evolution in Western North America: a case study in Rosaceae.

Project description:Species in the ivesioid clade of Potentilla (Rosaceae) are endemic to western North America, an area that underwent widespread aridification during the global temperature decrease following the Mid-Miocene Climatic Optimum. Several morphological features interpreted as adaptations to drought are found in the clade, and many species occupy extremely dry habitats. Recent phylogenetic analyses have shown that the sister group of this clade is Potentilla section Rivales, a group with distinct moist habitat preferences. This has led to the hypothesis that the ivesioids (genera Ivesia, Horkelia and Horkeliella) diversified in response to the late Tertiary aridification of western North America. We used phyloclimatic modeling and a fossil-calibrated dated phylogeny of the family Rosaceae to investigate the evolution of the ivesioid clade. We have combined occurrence- and climate data from extant species, and used ancestral state reconstruction to model past climate preferences. These models have been projected into paleo-climatic scenarios in order to identify areas where the ivesioids may have occurred. Our analysis suggests a split between the ivesioids and Potentilla sect. Rivales around Late Oligocene/Early Miocene (?23 million years ago, Ma), and that the ivesioids then diversified at a time when summer drought started to appear in the region. The clade is inferred to have originated on the western slopes of the Rocky Mountains from where a westward range expansion to the Sierra Nevada and the coast of California took place between ?12-2 Ma. Our results support the idea that climatic changes in southwestern North America have played an important role in the evolution of the local flora, by means of in situ adaptation followed by diversification.

| S-EPMC3517582 | biostudies-literature