Browse
Submit Data
Databases
API
Help

Dataset Information

36 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

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

ABSTRACT: 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.

SUBMITTER: Ang L

PROVIDER: S-EPMC7748676 | biostudies-literature |

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Similar Datasets

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 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 chloroplast genome sequence and phylogenetic analysis of Populus maximowiczii Henry 1913 (Salicaceae Mirb.).

Project description:The classification and identification of species in Populus has remained a formidable challenge due to widespread interspecies hybridization. The complete chloroplast genome of Populus maximowiczii was obtained by Illumina high-throughput sequencing technology, with a typical quadripartite structure and 37.0% GC content. The chloroplast genome of P. maximowiczii was 156,892 in length, including a large single-copy region (LSC: 84,988 bp), a small single-copy region (SSC: 16,630 bp), and a pair of inverted repeats (IRs: each 27,637 bp in length). A total of 131 genes were annotated, including 86 protein-coding genes, 37 tRNAs, and 8 rRNAs. The phylogenetic analysis indicated that 43 species belonging to Populus were classified into monophyly, with P. cathayana being the closest relatives to P. maximowiczii. In conclusion, this study provides valuable insights into understanding the phylogeny of Populus.

| S-EPMC11342814 | biostudies-literature

Complete chloroplast genome sequence of Homalium hainanense (Salicaceae).

Project description:Homalium hainanense is a large evergreen tree species belonging to Salicaceae family, and its wood is tough, fine-grained, which makes it a good source of commercial use for building construction and furniture manufacturing. In this study, we sequenced the complete chloroplast genome of H. hainanense based on next generation sequencing and used these data to assess genomic resources. The size of the H. hainanense chloroplast genome was 157,852 bp, including a large single-copy region (85,888 bp), a small single-copy region (16,592 bp), and a pair of inverted repeats regions (27,686 bp). The overall GC content of the H. hainanense chloroplast genome was 36.6%. The plastome of H. hainanense was predicted to contain 112 unique genes, including 78 protein coding genes, 30 tRNA genes and 4 rRNA genes. The reconstructed phylogeny revealed that Homalium was monophyletic and H. hainanense was sister to H. stenophyllum, H. paniculiflorum and H. racemosum.

| S-EPMC7782329 | biostudies-literature

Complete chloroplast genome sequence of Salix sinopurpurea (Salicaceae).

Project description:Salix sinopurpurea is a morphologically special shrubby willow characterizing opposite leaves. Here, we reported the complete chloroplast (cp) genome sequence of Salix sinopurpurea. The cp genome is 155,546 bp in length, including a large single-copy (LSC) region of 84,412 bp, a small single-copy (SSC) region of 16,216 bp, and a pair of inverted repeated regions of 27,459 bp. The cp genome of Salix sinopurpurea encodes 130 genes, including 85 protein-coding genes, 37 tRNA genes, and eight rRNA genes. Phylogenetic tree showed that Salix sinopurpurea is closely related to Salix psammophila and Salix suchowensis.

| S-EPMC7954483 | biostudies-literature

The complete chloroplast genome sequence of Salix viminalis (Salicaceae).

Project description:Here, the complete chloroplast (cp) genome of Salix viminalis was reported. The genome is 155,531?bp long, with a GC content of 36.71%, and contains four sub-regions: 84,395?bp of large single copy (LSC) and 16,218?bp of small single copy (SSC) regions, separated by 27,459?bp of inverted repeat (IR) regions. A total of 129 genes were annotated, including 83 protein-coding genes, 38 tRNA genes, and 8 rRNA genes. The Phylogenetic analyses based on the whole cp genome sequence placed S. viminalis into a clade containing Salix rehderiana, Salix taoensis, Salix koriyanagi, and Salix suchowensis. This is the first complete cp genome for S. viminalis that would be useful for phylogenetic and population genetic studies of this species.

| S-EPMC7706889 | 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 Xylosma racemosa (Siebold & Zucc.) Miq. (Salicaceae).

Project description:Xylosma racemosa (Siebold & Zucc.) Miq. which plays an important role in ecology, medicine and economy, is a deciduous species of Salicaceae. In this paper, we sequenced, assembled, and annotated the chloroplast (cp) genome of X. racemosa (Siebold & Zucc.) Miq. by using the sequencing data from Illumina Novaseq platform. The complete cp genome of X. racemosa is 157,262 bp in length, containing a large single-copy (LSC) region of 84,289 bp, and a small single-copy (SSC) region of 17,817 bp. It contains 131 genes, including 8 rRNA genes, 37 tRNAs genes and 86 protein-coding genes. The GC content of X. racemosa cp genome is 36.74%. The phylogenetic analysis suggests that X. racemosa is a sister species to Xylosma congesta in Salicaceae.

| S-EPMC8451645 | 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