Browse
Submit Data
Databases
API
Help

Dataset Information

20 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

The complete chloroplast genome of Aruncus dioicus var. kamtschaticus (Rosaceae).

ABSTRACT: Aruncus dioicus var. kamtschaticus is an economically important herb in the cold temperate regions of East Asia, and displays highly variable morphological features. Completed chloroplast genome of A. dioicus var. kamtschaticus isolated in Korea is 157,859 bp long with four subregions: 85,972 bp of large single copy and 19,185 bp of small single-copy regions separated by 26,351 bp of inverted repeat regions. The genome includes 131 genes (86 protein-coding genes, eight rRNAs, and 37 tRNAs). Phylogenetic analyses show that our chloroplast genome was clustered with two partial chloroplast genomes of A. dioicus.

SUBMITTER: Suh HJ

PROVIDER: S-EPMC8009126 | biostudies-literature |

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Similar Datasets

The complete chloroplast genome sequence of Spiraea japonica var. acuminata Franch. (Rosaceae).

Project description:Spirea japonica var. acuminata Franch. (Rosaceae) is a Chinese herbal medicine distributed in southwest and east China. The first complete chloroplast genome of Spirea japonica var. acuminata Franch. was assembled and reported in this study. The genome is 153,822 bp in length and contained 125 encoded genes in total, including 80 protein-coding genes, eight ribosomal RNA genes, and 37 transfer RNA genes. The phylogenomic analysis showed that Spirea japonica var. acuminata Franch. was closely related to Spirea blumei, Spirea trilobata, Spirea mongolica and Spirea insularis according to the current sampling extent.

| S-EPMC8797734 | 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 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 of Sibbaldia aphanopetala (Rosaceae: Potentilleae).

Project description:The complete chloroplast genome of Sibbaldia aphanopetala reported herein was a circular DNA molecule of 153,491 bp in length. The genome had a typical quadripartite structure, consisting of a pair of inverted repeats (IRa and IRb: 25,611 bp) separated by a large single-copy region (LSC: 84,244 bp) and a small single-copy region (SSC: 18,025 bp). The cp genome encoded a set of 129 genes, containing 84 protein-coding genes, 37 tRNA genes, and eight rRNA genes. Phylogenetic analysis indicated that S. aphanopetala was sister to S. procumbens.

| S-EPMC7782742 | 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

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

Project description:Malus toringoides belongs to the subfamily Amygdaloideae of Rosaceae, which is an endemic species in China. It has significant ornamental, economic, and ecological value. Herein, we assembled the complete chloroplast genome of Malus toringoides using the next-generation sequencing technology. The total length of the complete chloroplast genome was 160,093 base pair (bp), consisting of one large single-copy (LSC) region with a sequence length of 88,177 bp, one small single-copy (SSC) region which sequence length is 19,194 bp, and a pair of inverted repeat regions (IRs, 26361 bp). Besides, the complete chloroplast genome contained 128 genes, namely 83 protein-coding genes (PCGs), 37 tRNA genes (tRNA), and 8 rRNAgenes (rRNA), the GC content was 36.6%. The phylogenetic relationship among species in genus Malus is closely related, especially the phylogenetic relationship among Malus angustifolia, Malus prattii, Malus micromalus, Malus prunifolia, Malus baccata, Malus hupehensis and Malus toringoides. Furthermore, phylogenetic relationship of Malus toringoides in Malus was closely related to Malus hupehensis. Our study affords important genetic information for further researches on the related species.

| S-EPMC7782016 | biostudies-literature

The complete chloroplast genome of Geum macrophyllum (Rosaceae: Colurieae).

Project description:The complete chloroplast genome of Geum macrophyllum is reported and characterized in this study. The chloroplast genome of G. macrophyllum was a circular form with a size of 155,940 bp in length. The genome presented a typical quadripartite structure composed of a pair of inverted repeats (IRa and IRb) of 26,152 bp separated by a large single copy (LSC) region of 85,307 bp and a small single copy (SSC) region of 18,329 bp. The genome contained a set of 129 genes, including 84 protein-coding genes, 37 tRNA genes, and eight rRNA genes, in which 17 were duplicated and 112 were unique. Phylogenetic analysis placed G. macrophyllum as sister to G. triflorum based on current sampling.

| S-EPMC7872518 | biostudies-literature

The complete chloroplast genome of Drymocallis saviczii (Rosaceae: Potentilleae).

Project description:The complete chloroplast genome of Drymocallis saviczii was reported in the present study. The chloroplast genome of D. saviczii was a circular DNA molecule with a size of 154,487 bp in length. The genome had a typical quadripartite structure composed of a pair of inverted repeats (IRa and IRb) of 25,991 bp separated by a large single-copy (LSC) region of 84,332 bp and a small single-copy (SSC) region of 18,173 bp. The genome encoded a set of 129 genes, comprising 84 protein-coding genes, 37 tRNA genes, and eight rRNA genes. Phylogenetic analysis demonstrated that D. saviczii was closer to D. glandulosa in current sampling.

| S-EPMC7782235 | 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