Browse
Submit Data
Databases
API
Help
Login

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

The complete chloroplast genome sequence of Hippophae rhamnoides subsp. sinensis.

ABSTRACT: The complete chloroplast genome sequence of Hippophae rahmnoides subsp. sinensis was characterized from Illumina pair-end sequencing. The chloroplast genome of H. rahmnoides subsp. sinensis was 156,355?bp in length, containing a large single-copy region (LSC) of 84,002?bp, a small single-copy region (SSC) of 19,055?bp, and two inverted repeat (IR) regions of 26,649?bp. The overall GC content is 36.6%, while the corresponding values of the LSC, SSC, and IR regions are 64.5%, 69.2%, and 60.1%, respectively. The genome contains 131 complete genes, including 88 protein-coding genes, 38 tRNA genes (29 tRNA species), and 8 rRNA genes (4 rRNA species). The neighbour-joining phylogenetic analysis showed that H. rahmnoides subsp. sinensis and H. rahmnoides clustered together as sisters to other H. rahmnoides species.

SUBMITTER: Diao S

PROVIDER: S-EPMC7748493 | BioStudies | 2020-01-01

REPOSITORIES: biostudies

ACCESS DATA

Json Xml

Similar Datasets

Characterization of the complete chloroplast genome of Festuca sinensis (Gramineae).

Project description:The complete chloroplast genome from Festuca sinensis, an important perennial bunchgrass of the Gramineae, is determined in this study. The whole chloroplast genome sequence of F. sinensis has been characterized by Illumina pair-end sequencing. The circular genome is 134,177?bp long, containing a large single-copy region (LSC) of 79,367?bp and a small single-copy region (SSC) of 12,510?bp, which are separated by a pair of 21,150?bp inverted repeat regions (IRs). It encodes a total of 150 genes, including 93 protein-coding genes (75 PCG species), 49 tRNA genes (30 tRNA species) and eight ribosomal RNA genes (4 rRNA species). The most of gene species occur as a single copy, while 30 gene species occur in double copies. The overall A?+?T content of is 61.6%, while the corresponding values of the LSC, SSC, and IR regions are 63.7, 67.4, and 56.0%, respectively. Phylogenetic analysis suggested that Festuca sinensis was relatively close to Festuca ovina compared with other species of Festuca genera in Gramineae among the species analyzed. This complete chloroplast genome will provide valuable insight into conservation and exploitation efforts for this species as well as useful resources for studying the Gramineae phylogeny.

2019-01-01 | S-EPMC7748645 | BioStudies

The complete chloroplast genome of Sycopsis sinensis Oliver.

Project description:Sycopsis sinensis is a species of the genus Sycopsis Oliv in the Hamamelidaceae, and it is a native broadleaved evergreen woody plant species in China. Here, we sequenced, assembled, and analyzed the complete chloroplast (cp) genome of S. sinensis. The chloroplast genome of S. sinensis was 159,093?bp with 38.02% GC content, including a large single-copy (LSC) region of 87,841?bp, a small single-copy (SSC) region of 18,792?bp and two equal length inverted repeat (IR) regions of 26,230?bp. And, it contained 131 genes, including 37 tRNA genes, 8 rRNA genes, and 86 mRNA genes. Phylogenetic analysis strongly shows that S. sinensis has a close relationship with Distylium macrophyllum, whose posterior probability is 1.0.

2020-01-01 | S-EPMC7782631 | BioStudies

The complete chloroplast genome sequence of economical standard tea plant, Camellia sinensis L. cultivar Sangmok, in Korea.

Project description:The complete chloroplast genome sequence of Camellia sinensis L. cultivar Sangmok was determined using high-throughput sequencing technology. We sequenced Sangmok chloroplast genome and performed comparative with 21 published other Camellia and species from different genus for phylogenetic analysis. Chloroplast genome was 153,044?bp in length, containing a pair of 24,627?bp inverted repeat (IR) regions, which were separated by small and large single-copy regions (SSC and LSC) of 19,155 and 64,665?bp, respectively. The chloroplast genome contained 97 genes (63 protein-coding genes, 29 tRNA genes, and 5 rRNA genes). The overall GC content of the chloroplast genome was 37.2%. The phylogenetic analysis among species in number of the genus Camellia provided that C. sinensis L. cultivar Sangmok is closely related to KJ806277 Camellia pubicosta.

2020-01-01 | S-EPMC7782013 | BioStudies

Chloroplast genome structure and phylogeny of Spiranthes sinensis, an endangered medicinal orchid plant.

Project description:Spiranthes sinensis is an important medicinal plant of Spiranthes family and is currently in an endangered state. To better guide the systematic classification of S. sinensis, the complete genome of its chloroplast was sequenced and characterized. The complete chloroplast genome is 152,786?bp in length and contains a large single copy (LSC) region of 83,446?bp, a small single copy (SSC) region of 17,938?bp, and two inverted repeat (IRA and IRB) regions of 25,701?bp. The genome encodes 132 genes (112 unique genes), including 86 protein-coding genes (78 unique genes), 8 rRNA genes (4 unique genes), and 38 tRNA genes (30 unique genes). The total GC content of plasmid genome is 36.18%. Phylogenetic results indicated that S. sinensis is more closely related to Ludisia discolor, Goodyera schlechtendaliana, Goodyera fumata, and Goodyera procera. The study enriches the plasmid genomic information of S. sinensis and is of great significance for the genetic protection of this species.

2019-01-01 | S-EPMC7706474 | BioStudies

The complete chloroplast genome sequence of Tapiscia sinensis (Staphyleaceae).

Project description:Tapiscia sinensis, belong to Tapisciaceae, is endangered tree endemic to China. Here, we provide the complete plastid genomic data of T. sinensis with the aim of providing data for future conservation efforts research and revealing its phylogenetic position. The complete chloroplast sequence is 161,093?bp, including a large single-copy (LSC) region of 87,782?bp, a small single-copy (SSC) region of 18,517?bp, a pair of invert repeats (IR) regions of 27,387?bp. Plastid genome contains 131 genes, 85 protein-coding genes, 38 tRNA genes, and eight rRNA genes. Phylogenetic analysis base on 19 plastid genomes indicates that T. sinensis located Malvids branch, and is more closely related to the species of the order Sapindales than those of the order Malvales.

2020-01-01 | S-EPMC7781918 | BioStudies

Characterization of the complete chloroplast genome of Carya hunanensis W. C. Cheng & R. H. Chang.

Project description:Carya hunanensis W. C. Cheng & R. H. Chang is a tree of great economic importance in China. In this study, the complete chloroplast genome of C. hunanensis was determined and analyzed phylogenetically. The whole genome was determined to be 159,892?bp in length, presenting a typical quadripartite structure with a large single copy (LSC) region (89,466?bp), a small single copy (SSC) region (18,714?bp), and a pair of inverted repeat (IR) regions (25,856?bp each). There were 132 genes annotated in the genome, including 84 protein-coding genes, 40 tRNA genes, and eight rRNA genes. The overall GC content of C. hunanensis chloroplast genome was 36.24%. Phylogenetic analysis indicated that C. hunanensis was closely related to C. kweichowensis and Annamocarya sinensis.

2021-01-01 | S-EPMC7832538 | BioStudies

The complete chloroplast genome sequence of medicinal plant, Artemisia Montana.

Project description:The complete chloroplast genome sequence of Artemisia montana was characterized from Illumina pair-end sequencing. The chloroplast genome of A. montana was 151,130?bp in length, containing a large single-copy region (LSC) of 80,975?bp, a small single-copy region (SSC) of 16,011?bp, and two inverted repeat (IR) regions of 27,162?bp. The overall GC content is 30.70%, while the correponding values of the LSC, SSC, and IR regions are 64.6%, 69.2%, and 60.1%, respectively. The genome contains 131 complete genes, including 86 protein-coding genes (62 protein-coding gene species), 37 tRNA genes (29 tRNA species) and 8 rRNA genes (4 rRNA species). The Neighbour-joining phylogenetic analysis showed that A. montana and Artemisia lavandulaefolia YC clustered together as sisters to other Artemisia species.

2020-01-01 | S-EPMC7510612 | BioStudies

The complete chloroplast genome sequence of Populus davidiana (Salicaceae).

Project description:The complete chloroplast genome sequence of Populus davidiana was characterized from Illumina pair-end sequencing. The chloroplast genome of P. davidiana was 156,868?bp in length, containing a large single-copy region (LSC) of 84,976?bp, a small single-copy region (SSC) of 16,606?bp, and two inverted repeat (IR) regions of 27,643?bp. The overall GC content is 30.70%, while the correponding values of the LSC, SSC, and IR regions are 64.6%, 69.2%, and 60.1%, respectively. The genome contains 131 complete genes, including 86 protein-coding genes (62 protein-coding gene species), 37 tRNA genes (29 tRNA species) and 8 rRNA genes (4 rRNA species). The Neighbour-joining phylogenetic analysis showed that P. davidiana and Populus rotundifolia clustered together as sisters to other Populus species.

2020-01-01 | S-EPMC7510576 | BioStudies

The complete chloroplast genome sequence of Populus tremuloides (Salicaceae).

Project description:The complete chloroplast genome sequence of Populus tremuloides was characterized from Illumina pair-end sequencing. The chloroplast genome of P. tremuloides was 155,816?bp in length, containing a large single-copy region (LSC) of 85,804?bp, a small single-copy region (SSC) of 16,489?bp, and two inverted repeat (IR) regions of 26,962?bp. The overall GC content is 36.71%, while the correponding values of the LSC, SSC, and IR regions are 64.9%, 69.2%, and 60.3%, respectively. The genome contains 167 complete genes, including 86 protein-coding genes (77 protein-coding gene species), 73 tRNA genes (29 tRNA species) and 8 rRNA genes(4 rRNA species). The Neighbour-joining phylogenetic analysis showed that P. tremuloides and Populus tremula clustered together as sisters to other Populus species.

2019-01-01 | S-EPMC7707770 | BioStudies

The complete chloroplast genome sequence of Populus tremula (Salicaceae).

Project description:The complete chloroplast genome sequence of Populus tremula was characterized from Illumina pair-end sequencing. The chloroplast genome of P. tremula was 156,862?bp in length, containing a large single-copy region (LSC) of 84,971?bp, a small single-copy region (SSC) of 16,605?bp, and two inverted repeat (IR) regions of 27,640?bp. The overall GC content is 30.69%, while the correponding values of the LSC, SSC, and IR regions are 64.5%, 69.3%, and 60.1%, respectively. The genome contains 131 complete genes, including 86 protein-coding genes (62 protein-coding gene species), 37 tRNA genes (29 tRNA species) and 8 rRNA genes (4 rRNA species). The Neighbour-joining phylogenetic analysis showed that P. tremula and Populus davidiana clustered together as sisters to other Populus species.

2020-01-01 | S-EPMC7510596 | BioStudies

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

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