Browse
Submit Data
Databases
API
Help

Dataset Information

26 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

The complete chloroplast genome sequence of Populus deltoides 'Siyang-2'.

ABSTRACT: Populus deltoides 'Siyang-2' is an improved variety of forest trees that have been identified recently. It shows superior growth performance compared to other local cultivars in the region of Yangtze-Huaihe in China. In this study, the whole chloroplast (cp) genome sequence of 'Siyang-2' was assembled and characterized by high-throughput sequencing data. The complete cp genome was 156,957 bp in length, containing a large single-copy region (LSC) of 85,096 bp, and a small single-copy region (SSC) of 16,563 bp, which were separated by a pair of 27,649 bp inverted repeat regions (IRs). The cp genome contained 131 genes, including 86 protein-coding genes, 37 tRNA genes, and 8 ribosomal RNA genes. Most of the gene species occur as a single copy, while 20 gene species occur in double copies. The overall GC content of 'Siyang-2' cp genome is 34.6%, while the corresponding values of the LSC, SSC, and IR regions are 34.5%, 30.6%, 41.9%, respectively. The complete cp genome provides valuable phylogenetic and cp genetic engineering studies of this important improved poplar species P. deltoides 'Siyang-2'.

SUBMITTER: Su T

PROVIDER: S-EPMC7748702 | biostudies-literature |

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Similar Datasets

Complete chloroplast genome sequence and phylogenetic analysis of Populus deltoides Caihong.

Project description:Colored-leaf plants are increasingly popular, which has higher ecological, economic and social benefits. Caihong poplar, one of colored-leaf plants from Populus deltoides, has been widely used in courtyard embellishment, road greening, garden set King and so on. In this study, the complete chloroplast genome of Caihong poplar was evaluated, and the total chloroplast genome size of which is 156,957 bp in length with 36.69% GC content, including large single-copy region (LSC) of 85,096 bp, a pair of inverted repeat regions (IRs) of 27,649 bp each, and a small single-copy region (SSC) of 16,563 bp. There were 22 tRNA genes, 83 protein-coding genes, and four rRNA genes. The phylogenetic analysis with 22 species indicated that Caihong poplar was closely clustered with Populus deltoides Zhonglin 2025. In conclusion, the complete chloroplast genomes of Caihong poplar in this study provided valuable genomic resources for further phylogeny and species identification in the Populus family.

| S-EPMC7872566 | biostudies-literature

Characterization of the complete chloroplast genome of Populus deltoides Zhonglin 2025.

Project description:The complete chloroplast genome of Populus deltoides was characterized by reference-based assembly using whole-genome sequencing data. The total chloroplast genome size of Populus deltoides included a pair of inverted repeat regions (IRs) of 27,649 bp each, a small single-copy region (SSC) of 16,563 bp, and large single-copy region (LSC) of 85,096 bp, which was 156,957 bp in length. A total of 109 genes were predicted from the chloroplast genome, including 83 protein-coding genes, 22 tRNA genes, and four rRNA genes. The GC content of chloroplast genome for Populus deltoides was 36.68%. The phylogenetic analysis based on the reported chloroplast genomes of Populus showed that the chloroplast of the Populus deltoides is most closely related to the Populus fremontii. The complete chloroplast genome of Populus deltoides provides new insights into Populus evolutionary and genomic studies.

| S-EPMC7671709 | biostudies-literature

Complete Genome Sequence of Terriglobus albidus Strain ORNL, an Acidobacterium Isolated from the Populus deltoides Rhizosphere.

Project description:Terriglobus albidus strain ORNL is a heterotrophic soil acidobacterium isolated from the rhizosphere of an Eastern cottonwood tree (Populus deltoides) in Tennessee. Its 6.4-Mb chromosome was completely sequenced using PacBio long reads, and it encodes 5,010 proteins and 53 RNAs.

| S-EPMC6856270 | biostudies-literature

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

Project description:The complete chloroplast genome sequence of Populus koreana was characterized using Illumina pair-end sequencing. The chloroplast genome of P. koreana 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%, whereas the corresponding 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 eight rRNA genes (four rRNA species). The neighbour-joining phylogenetic analysis showed that P. koreana and Populus fremontii clustered together as sisters to other Populus species.

| S-EPMC7748676 | biostudies-literature

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.

| S-EPMC7707770 | biostudies-literature

The complete chloroplast genome sequence of Populus davidiana Dode.

Project description:The complete chloroplast genome sequence of Populus davidiana Dode was determined in this study. The cpDNA was 155,853 bp in length, containing a pair of inverted repeats (IRs) of 27,571 bp each separated by a large and small single copy (LSC and SSC) regions of 84,127 bp and 16,584 bp, respectively. The cpDNA contained 130 genes, including 85 protein-coding genes, 8 ribosomal RNA genes and 37 transfer RNA genes. Phylogenetic analysis indicated P. davidiana was mostly close to Populus tremula, widely distributed in Europe and Populus tremula × alba.

| S-EPMC7800723 | biostudies-literature

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

Project description:The complete chloroplast genome sequence of Populus mexicana was characterized from Illumina pair-end sequencing. The chloroplast genome of P. mexicana was 156,188 bp in length, containing a large single-copy region (LSC) of 86,871 bp, a small single-copy region (SSC) of 16,559 bp, and 2 inverted repeat (IR) regions of 26,377 bp. The overall GC content is 36.74%, while the corresponding values of the LSC, SSC, and IR regions are 64.8, 69.3, and 60.3, respectively. The genome contains 111 complete genes, including 72 protein-coding genes (62 protein-coding gene species), 31 tRNA genes (29 tRNA species), and 8 rRNA genes (4 rRNA species). The neighbor-joining phylogenetic analysis showed that P. mexicana and Populus fremontii clustered together as sisters to other Populus species.

| S-EPMC7748492 | biostudies-literature

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.

| S-EPMC7510576 | biostudies-literature

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.

| S-EPMC7510596 | biostudies-literature

Complete Genome Sequence of the Novel Roseimicrobium sp. Strain ORNL1, a Verrucomicrobium Isolated from the Populus deltoides Rhizosphere.

Project description:Roseimicrobium sp. strain ORNL1 is a soil bacterium that belongs to the phylum Verrucomicrobia and was isolated from the rhizosphere of a forest Eastern cottonwood tree, Populus deltoides, in Tennessee. Its 7.9-Mb chromosome was completely sequenced using PacBio long reads and is predicted to encode 6,288 proteins and 76 RNAs.

| S-EPMC7330248 | 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