Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Sequencing and characterization of the complete chloroplast genome of Sorbaria arborea (Rosaceae).

ABSTRACT: Sorbaria arborea is a species which is endemic to China. We utilized next-generation Illumina sequencing technology to sequence and assemble its chloroplast genome. The 160,137 bp genome contained four main sections, including a pair of inverted repeat regions which were 26,332 bp in length, and a small single-copy region was 19,418 bp, as well as a large single-copy region, which was 88,055 bp. The genome had a GC content of 36.1% and contained 113 unique genes, including 4 rRNAs, 30 tRNAs, and 79 protein-coding genes. The phylogenetic relationship of 25 Rosaceae species was constructed based on their chloroplast genome sequences, which supported a close relationship between S. arborea and Amygdaloideae. This newly sequenced plastid genome provides useful information for assessing the genetic diversity and phylogenetic position of S. arborea.

SUBMITTER: Sun W

PROVIDER: S-EPMC7748509 | biostudies-literature | 2020 Feb

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

Sequencing and characterization of the complete chloroplast genome of Sorbaria arborea (Rosaceae).

Sun Wenguang W Chen Zhe Z Lv Zhenyu Z Li Zhimin Z

Mitochondrial DNA. Part B, Resources 20200206 1

Sorbaria arborea is a species which is endemic to China. We utilized next-generation Illumina sequencing technology to sequence and assemble its chloroplast genome. The 160,137 bp genome contained four main sections, including a pair of inverted repeat regions which were 26,332 bp in length, and a small single-copy region was 19,418 bp, as well as a large single-copy region, which was 88,055 bp. The genome had a GC content of 36.1% and contained 113 unique genes, including 4 rRNAs, 30 tRN ...[more]

PMID: 33366887

Similar Datasets

Characterization of the complete chloroplast genome sequence of Malus toringoides (Rosaceae).

Project description:Malus toringoides belongs to the Malus genus (Rosaceae) and is a precious resource among wild plants. In this study, we report the first complete chloroplast (cp) genome sequence of M. toringoides. The whole cp genome contains 126 genes, 83 protein-coding genes, 35 tRNA genes, and eight rRNA genes. A maximum-likelihood phylogenetic tree analysis based on 12 complete chloroplast genomes indicated that M. toringoides clustered closely with Malus hupehensis. Thus, the chloroplast genome can provide valuable genetic information for the protection and exploitation of M. toringoides.

| S-EPMC7782576 | biostudies-literature

Characterization of the complete chloroplast genome sequence of Malus kansuensis (Rosaceae).

Project description:The Malus kansuensis belongs to the Malus genus of Rosaceae family and it is an important apple rootstock resource native to China. Here, its complete chloroplast genome was sequenced and assembled by high-throughput Illumina sequencing data. The DNA was circular in shape with 160,133 bp length, containing IRA and IRB inverted repeat regions (26,354 bp), large single-copy region (LSC) (88,141 bp), and small single-copy region (SSC)(19,284 bp). In the chloroplast genome, 129 functional genes were predicted, including 85 protein-coding genes, 36 tRNA genes, and 8 rRNA genes. The phylogenetic tree basically accords with the traditional taxonomy of the order Malus genus of Rosaceae family.

| S-EPMC7831360 | biostudies-literature

Characterization of the complete chloroplast genome sequence of Rubus rufus Focke (Rosaceae).

Project description:Rubus rufus Focke is a deciduous shrub species native to subtropical China and is valuable resources for the Raspberry cultivation by virtue of prolific fruits and stout resistances to hash stress. In this study, we assembled and characterized the complete chloroplast genome of R. rufus as resources for the future study. The chloroplast genome was 156,232 bp in length, composing of one large single copy (LSC; 85,840 bp) and one small single copy (SSC; 18,850 bp), separated by two inverted repeats (IRs; 25,771 bp). A total of 130 genes were predicted, including eight rRNAs, 36 tRNAs, and 86 protein-coding genes. The phylogenetic analysis showed a close relationship between R. rufus and Rubus cochinchinensis in the tribe Rubeae.

| S-EPMC8491697 | biostudies-literature

The complete chloroplast genome of the Crataegus kansuensis (Rosaceae): characterization and phylogeny.

Project description:Crataegus kansuensis Wils. is an important wild eco economical species of the family Rosaceae. The complete chloroplast genome reported here is 159,865 bp in length, including two inverted repeats (IRs) of 26,384 bp, which are separated by a large single-copy (LSC) and a small single-copy (SSC) of 87,815 bp and 19,282 bp, respectively. The whole chloroplast genome of C. kansuensis contains 113 genes, including 79 protein-coding genes, 30 transfer RNA, and 4 ribosome RNA. Phylogenetic analysis indicated that C. kansuensis is closely related to that of C. chungtienensis and C. marshallii, and the genus Crataegus L. was sister to the genus Amelanchier Medik.

| S-EPMC7782147 | biostudies-literature

Characterization of the complete chloroplast genome sequence of medicinal plant: Potentilla bifurca (Rosaceae).

Project description:Potentilla bifurca is a medicinal plant, the root extracts have been applied for the treatment of certain viral infections as folk medicinal herbs. The complete chloroplast genome sequence of is 155,841 bp in length, contains 128 complete genes, including 84 protein-coding genes (84 PCGs), 8 ribosomal RNA genes (4 rRNAs), and 37 tRNA genes (37 tRNAs). The overall GC content of cp DNA is 37.1%, the corresponding values of the LSC, SSC, and IR regions are 35.0%, 31.0%, and 42.8%. Phylogenetic tree shows that P. bifurca was identified as the basal clade of Potentilla.

| S-EPMC7832467 | biostudies-literature

The complete chloroplast genome of Rubus pacificus (Rosaceae).

Project description:The complete chloroplast genome of Rubus pacificus, a representative species of R. sect. Malachobatus subsect. Stipulosi, has been characterized by reference-based assembly using Illumina paired-end data. The complete chloroplast genome is 156,255 bp in length, containing a large single-copy region (LSC) of 85,864 bp and a small single-copy region (SSC) of 18,849 bp, which are separated by a pair of inverted repeat regions (IR) of 25,771 bp. A total of 129 genes were predicted from the chloroplast genome, including 85 protein-coding genes, 36 tRNA genes, and eight rRNA genes. According to the present sampling, phylogenetic analysis reveals that R. pacificus and R. laciniatostipulatus form a strongly supported clade and R. sect. Malachobatus subsect. Stipulosi is not monophyletic.

| S-EPMC9467575 | 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 Laurocerasus zippeliana (Rosaceae).

Project description:Laurocerasus zippeliana is a widely known landscape plant with high adaptability. We report herein the complete chloroplast genome sequence of L. zippeliana assembled from Illumina high-throughput sequencing data. With a total length of 158,940 bp, the complete chloroplast genome was a typical quadripartite circle: two inverted repeats (IRs) of 26,339 bp for each, a large single-copy (LSC) region of 87,339 bp, and a small single-copy (SSC) region of 18,923 bp. A total of 110 unique genes were identified, consisting of 78 protein-coding genes, 28 tRNA genes, and 4 rRNA genes. Phylogenetic analysis confirmed the position of L. zippeliana within the order Rosales.

| S-EPMC7706693 | biostudies-literature

The complete chloroplast genome sequence of Rubus eucalyptus (Rosaceae).

Project description:Rubus eucalyptus Focke belong to genus Rubus in the family Rosaceae, the fresh fruits of which can be used for medicine and cosmetic. The plastome of R. eucalyptus is 155,672 bp in length, with one large single copy region of 85,277 bp, one small single copy region of 18,864 bp, and two inverted repeat (IR) regions of 25,748 bp. It contains 130 genes, including 86 protein-coding genes, 8 ribosomal RNA, and 37 transfer RNA. Phylogenetic tree shows that R. eucalyptus was at the basal of Rosaceae. The published plastome within Rubus provides significant insight for elucidating the phylogenetic relationship of taxa within tribe Rosaceae.

| S-EPMC7706686 | 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