Browse
Submit Data
Databases
API
Help

Dataset Information

24 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

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

ABSTRACT: 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.

SUBMITTER: Huang W

PROVIDER: S-EPMC8491697 | biostudies-literature |

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Similar Datasets

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 sequence of Rubus peltatus Maxim. (Rosaceae).

Project description:Rubus peltatus Maxim. (Bull. Acad. Imp. 1871) is a wild species endemic to East and Southeast China. However, genetic resources were unavailable for this species. It holds great potential for domestication or other breeding purposes with the extraordinary large yellow fruits. The complete chloroplast genome sequence of R. peltatus, assembled with Illumina Hiseq X Ten platform sequencing data, was reported. The chloroplast genome was 155,582 bp in length. The large single-copy (LSC) and small single-copy (SSC) of 85,329 bp and 18,779 bp were separated by two inverted repeats (IRs) of 25,737 bp. The chloroplast genome of R. peltatus contains 130 genes, including eight transfer RNA genes, 36 ribosomal RNA genes, and 86 protein-coding genes. Phylogenetic analysis supports R. peltatus has a close relationship with the R. cochinchinensis and R. takesimensis.

| S-EPMC9248939 | biostudies-literature

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

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

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

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 sequence of Gillenia trifoliata (Rosaceae).

Project description:Gillenia trifoliata (L.) Moench is an ornamental and medicinal species endemic to North America. In this study, a complete circular chloroplast genome of G. trifoliata was assembled and annotated. The chloroplast genome of G. trifoliata is 159,496?bp in size and consists of two IR (26,394?bp) regions separated by LSC (87,647?bp) and SSC (19,061?bp) regions. The GC content of the chloroplast genome is 36.5%. The chloroplast genome comprised of 112 different genes, including 78 protein-coding genes. The phylogenetic analysis revealed that G. trifoliata lies within subfamily Amygdaloideae and forms the progenitor lineage of the pome-bearing Maleae.

| S-EPMC7687496 | biostudies-literature

The complete chloroplast genome sequence of Sorbus amabilis (Rosaceae).

Project description:Sorbus amabilis Cheng ex Yü, a small excellent ornamental tree species, is only distributed in Eastern China. In this study, we assembled and annotated the complete chloroplast (cp) genome of the species using the next-generation sequencing for the first time. The cp genome was 160,006 bp in size, consisting of two copies of invert repeat (IR) regions of 26,405 bp, one large single-copy (LSC) region of 87,870bp, and one small single-copy (SSC) region of 19,326 bp. The overall GC content of the genome was 36.55%. The genome was predicted to contain 128 genes, including 88 protein-coding genes, 37 tRNA genes, and eight rRNA genes. Phylogenetic analysis of 25 chloroplast genomes in Rosaceae indicated that S. amabilis is most closely related to S. commixta. These findings may provide useful information to the phylogeny of the genus Sorbus.

| S-EPMC7510610 | biostudies-literature

The complete chloroplast genome sequence of Malus toringo (Rosaceae).

Project description:Malus toringo (Siebold) Siebold ex de Vriese is a worthy species in the genus Malus (family Rosaceae) distributing from North America and Asia, especially in China. In addition to its ornamental value, the medicinal value of its fruits has also been developed to treat food stagnation diseases. Herein, we obtained the complete chloroplast genome of M. toringo using next-generation sequencing technology. The complete chloroplast genome is 160,039 base pair (bp) in length, including a large single copy (LSC) region of 88,142 bp, a small single copy (SSC) region of 19,183 bp, and a pair of inverted repeat regions (IRs, 26,357 bp). And, the overall GC content of the chloroplast genome was 36.6%. Besides, a total of 128 unique genes were found in the chloroplast genome, namely 83 protein-coding genes (PCGs), 37 tRNA genes (tRNA), and eight rRNA genes (rRNA). A maximum-likelihood phylogenetic tree was reconstructed using the full length of chloroplast genome to show the phylogenetic relationships among species in genus Malus. It was concluded that M. toringo was phylogenetically close to M. angustifolia.

| S-EPMC7782744 | 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