Browse
Submit Data
Databases
API
Help

Dataset Information

8 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

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

ABSTRACT: 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.

SUBMITTER: Ren R

PROVIDER: S-EPMC8386700 | biostudies-literature |

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Similar Datasets

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

Project description: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.

| S-EPMC7748512 | 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

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

The complete chloroplast genome of Epimedium sutchuenense Franch. (Berberidaceae)

Project description:Abstract Epimedium L. is the largest herbaceous genus in the family Berberidaceae which comprises more than 60 species. Epimedium sutchuenense Franch. is narrowly inhabited in the Daba Mountains of China. In the current study, we assembled the first complete chloroplast genome of E. sutchuenense through Illumina paired-end sequencing. The complete chloroplast genome of E. sutchuenense was 157,218 bp in length and the total GC content was 38.78%. A total of 112 unique genes were identified, including 78 protein-coding genes, 30 tRNA genes and 4 rRNA genes. The phylogenetic analysis demonstrated that E. sutchuenense was sister to Epimedium wushanense T. S. Ying. Our results provided valuable information for further phylogenetic research and germplasm exploration of Epimedium genus.

| S-EPMC8547808 | 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 of Epimedium davidii Franch. (Berberidaceae).

Project description:Epimedium davidii, which belongs to Berberidaceae, is mainly distributed in the southwest of China. In this study, the complete chloroplast genome of E. davidii was sequenced and assembled. The circular genome is 159,715 bp in length, which comprises a large single-copy region (LSC, 85,862 bp), a small single-copy region (SSC, 17,081 bp), and a pair of inverted repeat regions (IRa and IRb, 28,386 bp). The chloroplast genome of E. davidii contains 112 unique genes, of which 78 protein-coding genes, 30 tRNA genes, and 4 rRNA genes. Phylogenetic analysis indicated that E. davidii was closely related to Epimedium acuminatum.

| S-EPMC7748688 | 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

Complete Chloroplast Genome Sequence of Coptis chinensis Franch. and Its Evolutionary History.

Project description:The Coptis chinensis Franch. is an important medicinal plant from the Ranunculales. We used next generation sequencing technology to determine the complete chloroplast genome of C. chinensis. This genome is 155,484?bp long with 38.17% GC content. Two 26,758?bp long inverted repeats separated the genome into a typical quadripartite structure. The C. chinensis chloroplast genome consists of 128 gene loci, including eight rRNA gene loci, 28 tRNA gene loci, and 92 protein-coding gene loci. Most of the SSRs in C. chinensis are poly-A/T. The numbers of mononucleotide SSRs in C. chinensis and other Ranunculaceae species are fewer than those in Berberidaceae species, while the number of dinucleotide SSRs is greater than that in the Berberidaceae. C. chinensis diverged from other Ranunculaceae species an estimated 81 million years ago (Mya). The divergence between Ranunculaceae and Berberidaceae was ~111 Mya, while the Ranunculales and Magnoliaceae shared a common ancestor during the Jurassic, ~153 Mya. Position 104 of the C. chinensis ndhG protein was identified as a positively selected site, indicating possible selection for the photosystem-chlororespiration system in C. chinensis. In summary, the complete sequencing and annotation of the C. chinensis chloroplast genome will facilitate future studies on this important medicinal species.

| S-EPMC5494076 | biostudies-literature

The complete chloroplast genome of Pseudostellaria davidii (franch.) Pax, 1934.

Project description:Pseudostellaria davidii (Franch.) Pax belongs to subseries distancs of Pseudostellaria (Caryophyllaceae), and is mainly distributed in north-eastern Asia. The complete chloroplast (cp) genome of P. davidii was assembled and annotated for the first time in this study. The cp genome of P. davidii is 149,732 bp in length with the GC content of 36.57%, and it consists of four subregions: a large single-copy (LSC) region of 81,156 bp, a small single-copy (SSC) region of 16,894 bp and two inverted repeats (IR) regions of 25,841 bp each. The cp genome of P. davidii encodes a total of 111 unique genes, which are 77 protein-coding genes, four rRNA genes, and 30 tRNA genes. The results of phylogenetic analysis strongly suggested that Pseudostellaria was a monophyletic group and P. davidii forms an independent sister clade to other species of Pseudostellaria.

| S-EPMC10071897 | 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

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