Browse
Submit Data
Databases
API
Help

Dataset Information

14 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

The complete chloroplast genome sequence of an economic plant Salix wilsonii.

ABSTRACT: In this study, we report the first complete chloroplast (cp) genome sequence of Salix wilsonii. The cp genome is 155,026 bp in length, exhibiting a typical quadripartite structure of a large single copy (LSC) region of 83,917 bp, a small single copy (SSC) region of 16,285 bp and a pair of inverted repeats (IRs) region of 27,412 bp. The overall base composition of the cp genome in asymmetric order is A: 32.09%, C: 17.94%, G: 18.65%, and T: 31.31%, and the AT content is 63.4%, whereas the proportions of AT contents in LSC, SSC, and IR regions are 66.53%, 68.99%, and 58.27%, respectively. Further, phylogenetic analysis of 46 species shows that S. wilsonii is evolutionarily closest to Sailx tetrasperma, and both of them belong to the genus Salix.

SUBMITTER: Wu D

PROVIDER: S-EPMC7707237 | biostudies-literature |

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Similar Datasets

Analyzing and Characterizing the Chloroplast Genome of Salix wilsonii.

Project description:Salix wilsonii is an important ornamental willow tree widely distributed in China. In this study, an integrated circular chloroplast genome was reconstructed for S. wilsonii based on the chloroplast reads screened from the whole-genome sequencing data generated with the PacBio RSII platform. The obtained pseudomolecule was 155,750 bp long and had a typical quadripartite structure, comprising a large single copy region (LSC, 84,638 bp) and a small single copy region (SSC, 16,282 bp) separated by two inverted repeat regions (IR, 27,415 bp). The S. wilsonii chloroplast genome encoded 115 unique genes, including four rRNA genes, 30 tRNA genes, 78 protein-coding genes, and three pseudogenes. Repetitive sequence analysis identified 32 tandem repeats, 22 forward repeats, two reverse repeats, and five palindromic repeats. Additionally, a total of 118 perfect microsatellites were detected, with mononucleotide repeats being the most common (89.83%). By comparing the S. wilsonii chloroplast genome with those of other rosid plant species, significant contractions or expansions were identified at the IR-LSC/SSC borders. Phylogenetic analysis of 17 willow species confirmed that S. wilsonii was most closely related to S. chaenomeloides and revealed the monophyly of the genus Salix. The complete S. wilsonii chloroplast genome provides an additional sequence-based resource for studying the evolution of organelle genomes in woody plants.

| S-EPMC6662467 | 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 an economic plant Coffea canephora.

Project description:Coffea canephora is a paramount economic plant with great economic value. The complete chloroplast (cp) genome is 154,751?bp in length, including a large single copy (LSC) region of 84,850?bp, a small single copy (SSC) region of 18,131?bp and a pair of inverted repeats (IRs) of 25,885bp. This cp genome contains 131 genes, comprising of 86 protein-coding genes, 37 tRNAs and 8 rRNAs. The majority of these genes were single copy genes, while 18 genes existed as double copies, including 6 protein-coding genes (ndhB, rpl2, rpl23, rps12, rps7 and ycf2), 8 tRNA genes (trnA-UGC, trnG-GCC, trnI-CAU, trnI-GAU, trnL-CAA, trnN-GUU, trnR-ACG and trnV-GAC) and 4 rRNA genes (rrn4.5, rrn5, rrn16 and rrn23). A neighbour-joining phylogenetic tree was reconstructed to indicate that Coffea canephora is evolutionarily close to Olea europaea within Asterids. The complete cp genome will provide intragenic information for molecular phylogeny and biological studies of the Rubiales.

| S-EPMC7800382 | 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

Assembly and comparative analysis of complete mitochondrial genome sequence of an economic plant Salix suchowensis.

Project description:Willow is a widely used dioecious woody plant of Salicaceae family in China. Due to their high biomass yields, willows are promising sources for bioenergy crops. In this study, we assembled the complete mitochondrial (mt) genome sequence of S. suchowensis with the length of 644,437 bp using Roche-454 GS FLX Titanium sequencing technologies. Base composition of the S. suchowensis mt genome is A (27.43%), T (27.59%), C (22.34%), and G (22.64%), which shows a prevalent GC content with that of other angiosperms. This long circular mt genome encodes 58 unique genes (32 protein-coding genes, 23 tRNA genes and 3 rRNA genes), and 9 of the 32 protein-coding genes contain 17 introns. Through the phylogenetic analysis of 35 species based on 23 protein-coding genes, it is supported that Salix as a sister to Populus. With the detailed phylogenetic information and the identification of phylogenetic position, some ribosomal protein genes and succinate dehydrogenase genes are found usually lost during evolution. As a native shrub willow species, this worthwhile research of S. suchowensis mt genome will provide more desirable information for better understanding the genomic breeding and missing pieces of sex determination evolution in the future.

| S-EPMC5374973 | biostudies-literature

The complete chloroplast genome sequence of Populus wilsonii and its phylogenetic analysis.

Project description:The complete chloroplast genome of Populus wilsonii was reconstructed by reference-based assembly using whole-genome sequencing data. The total chloroplast genome size of P. wilsonii was 158,080?bp in length, including a pair of inverted repeat regions (IRs) of 27,749?bp each, a large single-copy region (LSC) of 85,949?bp and a small single-copy region (SSC) of 16,633?bp. A total of 133 genes were predicted from the chloroplast genome, including 86 protein-coding genes, 39 tRNA genes and eight rRNA genes. Among these genes, 20 genes occurred in IRs, containing nine protein-coding genes, seven tRNA genes and four rRNA genes. The GC content of P. wilsonii chloroplast genome was 36.6%. The phylogenetic analysis with 15 other species showed that P. wilsonii was closely clustered with Populus cathayana. The complete chloroplast genome of P. wilsonii provides new insights into Populus evolutionary and genomic studies.

| S-EPMC7799498 | biostudies-literature

The complete chloroplast genome sequence of Michelia wilsonii: an endangered species in China.

Project description:The first complete chloroplast genome (cpDNA) sequence of Michelia wilsonii was determined from Illumina HiSeq pair-end sequencing data in this study. The cpDNA is 160,100 bp in length, contains a large single-copy region (LSC) of 88,162 bp and a small single-copy region (SSC) of 18,786 bp, which were separated by a pair of inverted repeats (IR) regions of 26,576 bp. The genome contains 132 genes, including 87 protein-coding genes, 8 ribosomal RNA genes, and 37 transfer RNA genes. Further phylogenomic analysis showed that M. wilsonii closed to Michelia odora and Michelia yunnanensis in Michelieae tribe of the Magnoliaceae family.

| S-EPMC7748524 | biostudies-literature

The complete chloroplast genome sequence of the medicinal and economic plant woad Isatis indigotica (Brassicaceae).

Project description:Chloroplast (cp) genome sequences provide a valuable source for phylogenetic analysis. It becomes a popular useful tool for population and phylogeny in recently report. Here, the complete chloroplast genome of the Isatis indigotica has been reconstructed from the whole-genome Illumina sequencing data. The circular genome is 156,670 bp in size and comprises a pair of inverted repeat (IR) regions of 26,995 bp each, a large single-copy (LSC) region of 84,907 bp and a small single-copy (SSC) region of 17,773 bp. The total GC content is 36.5%, while the corresponding values of the LSC, SSC and IR region are 34.2%, 29.7% and 42.3%, respectively. The chloroplast genome contains 140 genes, including 94 protein-coding genes. The phylogenetic analysis showed a strong sister relationship with Raphanus sativus in Brassicaceae. These findings provide a foundation for further investigation of cp genome evolution in I. indigotica and other higher plants.

| S-EPMC7799964 | biostudies-literature

The complete chloroplast genome sequence of Salix kochiana Trautv. and its phylogenetic analysis.

Project description:Salix kochiana Trautvetter 1837 is one of the highest value shrubs present in northern China with important economic and ecological benefits. This study revealed the structural characteristics and phylogenetic relationships of chloroplast genes in S. kochiana Trautv. The results showed that the length of the complete chloroplast genome was 155,657 bp, which was a typical circular double-stranded structure, including an 84,458 bp large single-copy region (LSC), a 16,221 bp small single-copy region (SSC) and a 27,489 bp pair of inverted repeat regions (IRA and IRB). The chloroplast genome contains 48,757 A bases, 28,017 G bases, 49,843 T bases, and 29,040 C bases, with a GC content of 36.66%. Through bioinformatics annotation, a total of 126 genes were found in the chloroplast genome, including 81 protein-coding genes, 37 tRNA genes, and eight rRNA genes. Phylogenetic analysis showed that S. kochiana Trautv. was closely related to S. triandroides.

| S-EPMC9245976 | biostudies-literature

Characterization of the complete chloroplast genome of Magnolia wilsonii (Magnoliaceae).

Project description:The complete chloroplast (cp) genome of Magnolia wilsonii, an endangered and endemic species in China, was first reported in this study. The M. wilsonii cp genome was 157,434?bp in length, including two inverted repeat (IR) regions of 26,868?bp, a large single copy (LSC) region of 85,387?bp, and a small single copy (SSC) region of 18,311?bp. A total of 113 unique genes, including 79 protein-coding genes, 4 ribosomal RNA genes, and 30 transfer RNA genes, were annotated. The overall GC content was 38.8%. Phylogenetic analysis of 34 representative cp genomes within the genus Magnolia suggests that M. wilsonii was sister to M. sieboldii.

| S-EPMC7707560 | biostudies-literature

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