Browse
Submit Data
Databases
API
Help

Dataset Information

17 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Characterization of the complete chloroplast genome of Salix variegata (Salicaceae).

ABSTRACT: The complete chloroplast genome sequence of Salix variegata, a native shrub willow species in the south of China, is reported. The plastome is 155,743 bp in length, with one large single copy region of 84,950 bp, one small single copy region of 16,219 bp, and two inverted repeat (IR) regions of 27,287 bp. It contains 130 genes, including 83 protein-coding genes, eight ribosomal RNA, and 38 transfer RNA. Phylogenetic tree shows that this species is a sister to S. purpurea. The published plastome within Salix provides significant insight for elucidating the phylogenetic relationship of taxa within Salicaceae.

SUBMITTER: Chen J

PROVIDER: S-EPMC7748512 | biostudies-literature |

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Similar Datasets

Characterization of the complete chloroplast genome of Salix maizhokunggarensis (Salicaceae).

Project description:The complete chloroplast genome sequence of Salix maizhokunggarensis, a native shrub willow species in the south of China, has been characterized using Illumina pair-end sequencing. The plastome is 155,093 bp in length, with one large single copy region of 83,956 bp, one small single copy region of 16,221 bp, and two inverted repeat (IR) regions of 27,458 bp. It contains 116 genes, including 79 protein-coding genes, 8 ribosomal RNA, and 36 transfer RNA. Phylogenetic tree shows that this species is a sister species to S. suchowensis. The plastome of Salix can provide significant insight for elucidating the phylogenetic relationship of taxa within Salicaceae.

| S-EPMC7748764 | biostudies-literature

Characterization of the complete chloroplast genome of Salix gordejevii (Salicaceae).

Project description:Salix gordejevii is an endemic species in northern China. The analysis of the complete chloroplast genome of S. gordejevii can offer a referential basis for identifying and utilizing Salix germplasm resources. In this study, we obtained chloroplast DNA from S. gordejevii and characterized it. The complete chloroplast genome of S. gordejevii is 155,491 bp in length, comprising a pair of inverted repeats (IR, 27,408 bp), a large single-copy region (LSC, 84,367 bp), and a small single-copy region (SSC, 16,309 bp). We annotated 117 genes in total, including 80 protein-coding genes, 32 tRNA genes, four rRNA genes, and one pseudogene (ycf1). A maximum-likelihood phylogenetic tree was built with MEGA-X and showed that the chloroplast of S. gordejevii has the closest relationship with that of S. magnifica compared to the other reported Salix genomes.

| S-EPMC8330744 | 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

Characterization of the complete chloroplast genome of Salix koreensis Anderss (Salicaceae) 1868.

Project description:Salix koreensis Anderss 1868 is a grey-barked, arboreal willow with high economic value. This study reports the S. koreensis chloroplast (cp) genome. A phylogenetic tree has also been constructed to illustrate the relationship between S. koreensis and 25 other species within the Salicaceae family. The total length of the chloroplast genome is 155,865 bp, which can be divided into four parts: one large single-copy (LSC) length of 84,477 bp, one small single-copy (SSC) length of 16,316 bp, and two inverted repeat (IRA and IRB) lengths of 27,446 bp. The cp genome of S. koreensis is composed of 133 genes, including 86 protein-coding genes, 38 tRNA genes, and 8 rRNA genes. According to the phylogenetic tree, S. koreensis and S. chienii are closely related.

| S-EPMC9246011 | 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 of Salix lindleyana (salicaceae), a plateau plant species

Project description:Abstract Salix lindleyana Wallich ex Andersson 1851 is a species of genus Salix which mainly grows on mountains above 3000 m at sea level in Qinghai–Tibetan Plateau (including the Himalayas and Hengduan Mountains). To determine its phylogenetic position within Salix, we reconstructed S. lindleyana complete chloroplast (cp) genome sequence by de novo assembly using whole-genome sequencing data. The completed chloroplast genome was 155,304 bp, with a total GC content of 36.7%. It had a very typical tetrad structure, including a large single-copy (LSC) region of 84,539 bp, a small single-copy (SSC) region of 16,161 bp, and two inverted repeats (IR) regions of 27,302 bp. A total of 132 functional genes were distributed in the chloroplast genome, including 87 protein-coding genes, 37 tRNA genes, and 8 rRNA genes. Phylogenetic analysis showed that S. lindleyana was clustered with Salix dasyclados Wimmer 1849 and Salix variegata Franchet 1887. The complete chloroplast genome of S. lindleyana provides potential genetic resources for further phylogenetic studies.

| S-EPMC10443960 | biostudies-literature

Characterization of the complete chloroplast genome of Salix chienii W.C. Cheng (Salicaceae) from Southern China.

Project description:Salix chienii W.C. Cheng (Salicaceae) is a dioecious small tree with high economic and medicinal value. In this study, we reported the complete chloroplast DNA (cpDNA) of S. chienii by employing HiSeq sequencing and de novo assembly. The chloroplast genome of S. chienii is 155,672 bp in length, with a 36.60% GC content; it contains one large single copy (LSC), one small single copy (SSC) and two inverted repeat (IR) regions with lengths of 84,494, 16,330, and 27,424 bp, respectively. A total of 132 genes were predicted, including 85 protein-coding genes, 37 tRNA genes, 8 rRNA genes and 2 pseudogenes. A maximum-likelihood phylogenetic tree showed that S. chienii is closely related to S. wilsonii and S. triandra.

| S-EPMC8477920 | biostudies-literature

The complete chloroplast genome sequence of rose-gold pussy willow, Salix gracilistyla Miq. (Salicaceae).

Project description:To understand genetic background of Salix gracilistyla Miq., we presented its complete chloroplast genome which is 155,557?bp and has four sub regions: 84,530?bp of large single copy (LSC) and 16,218?bp of small single copy (SSC) regions are separated by 27,405?bp of inverted repeat (IR) regions including 130 genes (84 protein-coding gene, eight rRNAs, and 38 tRNAs). The overall GC content of the chloroplast genome is 36.7% and those in the LSC, SSC, and IR regions are 34.5%, 31.0%, and 41.9%, respectively. Phylogenetic trees show phylogenetic position of S. gracilistyla with low level of inter-species sequence variations.

| S-EPMC7687643 | 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

Characterization of the complete chloroplast genome of Salix linearistipularis (Franch.) Hao 1936.

Project description:We characterized the complete chloroplast genome of a perennial woody plant species, Salix linearistipularis, based on high-throughput sequencing and de novo assembly technology for the first time. The complete chloroplast genome of S. linearistipularis is 155,564 bp in length, comprising one large single-copy region (LSC, 84,460 bp), one small single-copy region (SSC, 16,182 bp), and two inverted repeat regions (IRA and IRB, 27,461 bp). The GC content of the whole chloroplast genome was 36.69%. This chloroplast genome encodes a total of 132 genes, including 86 protein-coding genes, eight ribosomal RNA genes, and 37 tRNA genes. Phylogenetic analysis reveals that S. linearistipularis is grouped with 13 other Salix species in Salicaceae.

| S-EPMC8386700 | 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