Browse
Submit Data
Databases
API
Help

Dataset Information

30 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Complete chloroplast genome of Lycium ferocissimum (Solanaceae), a species native to South Africa.

ABSTRACT: Lycium ferocissimum, known as African boxthorn or boxthorn, is a shrub in the Solanaceae family. In this study, we characterized the complete chloroplast (cp) genome sequence of L. ferocissimum using genome skimming data. It had a circular mapping molecular with the length of 155,894 bp, with a large single-copy region (LSC, 86,536 bp) and a small single-copy region (SSC, 18,406 bp) separated by a pair of inverted repeats (IRs, 25,476 bp). The cp genome encodes 113 unique genes, consisting of 79 protein-coding genes, 30 tRNA genes, and 4 rRNA genes, with 20 duplicated genes in the IR regions. The phylogenetic analysis indicated that L. ferocissimum is sister to the other three Lycium species.

SUBMITTER: Li Z

PROVIDER: S-EPMC7748727 | biostudies-literature |

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Similar Datasets

Characterization of the complete chloroplast genome of Lycium ruthenicum (Solanaceae).

Project description:Lycium ruthenicum is a precious desert plant with high medicinal and ecological values. It contains rich anthocyanins, which are safe natural pigments and could be used for natural food colorants. In this study, the complete chloroplast (cp) genome of L. ruthenicum was assembled on the basis of next generation sequencing. The whole genome is 154,996?bp in length, including two single copy regions (LSC: 85,993?bp and SSC: 18,213?bp) and two inverted repeat regions (IR: 25,395?bp). The overall G?+?C content of the genome is 37.9%. The cp genome consists of 111 unique genes, including 30 tRNA genes, 4 rRNA genes and 77 protein-coding genes. Phylogenetic analysis indicates that L. ruthenicum is closely clustered with Atropa belladonna, Przewalskia tangutica, and Scopolia parviflora.

| S-EPMC7800349 | biostudies-literature

Phylogenetic analyses of Lycium chinense (Solanaceae) and its coordinal species applying chloroplast genome.

Project description:Lycium chinense is an important edible and medicinal plant. Now, the complete chloroplast (cp) genome of L. chinense was assembled based on the Illumina sequencing reads. The cp genome of L. chinense was 155,736 bp long and contained two short inverted repeat regions (25,469 bp), which were separated by a small single-copy region (18,206 bp) and a large single-copy region (86,592 bp). The cp genome encodes 113 unique genes, including 79 protein-coding genes, 30 transfer RNA genes, and 4 ribosomal RNA genes. The topology of the phylogenetic tree showed that L. chinense is closely clustered with species Lycium ruthenicum and Lycium barbarum.

| S-EPMC7510570 | biostudies-literature

The complete chloroplast genome sequence of Lycium ruthenicum (Solanaceae), a traditional medicinal plant in China.

Project description:Lycium ruthenicum, Known as a traditional medicinal plant in China, is distributed in the arid and semiarid areas of northwest China. In this study, we assembled the complete chloroplast (cp) genome of L. ruthenicum using data from high-throughput Illumina sequencing. The L. ruthenicum cp genome is 154,979?bp in size and includes two inverted repeat regions of 25,395?bp each, which is separated by a large single copy region of 85,984?bp and a small single copy region of 18,205?bp. A total of 132 genes were predicted, including 37 tRNA, 8 rRNA, and 86 protein-coding genes. In addition, 9 PCG genes possess a single intron, 74 PCG genes no intron, and 3 other genes harbor two introns. 6 tRNA genes harbor a single intron. Phylogenetic analysis placed L. ruthenicum within the Solanaceae.

| S-EPMC7687596 | biostudies-literature

Characterization of the complete chloroplast genome of Lycium barbarum (Solanales: Solanaceae), a unique economic plant to China.

Project description:Lycium barbarum (Solanaceae) is a unique economic plant to China. The complete chloroplast (cp)genome was sequenced and assembled by using Illumina paired-end reads data. The circular cp genome is 155,656 bp in size, including a pair of inverted repeat (IR) regions of 25,451 bp, a large single copy (LSC) region of 86,554 bp and a small single copy (SSC) region of 18,200 bp. Besides, 15 genes possess a single intron, while another three genes (clpP, rps12 and ycf3) have a couple of introns. The GC content of entire L. barbarum cp genome, LSC, SSC and IR regions are 37.8%, 35.9%, 32.3%, and 43.2%, respectively. Phylogenetic analysis based on the concatenated coding sequences of cp PCGs showed that L. barbarum and Atropa belladonna are closely related with each other within the family Solanaceae.

| S-EPMC7799892 | biostudies-literature

The complete chloroplast genome of Mentha spicata, an endangered species native to South Europe.

Project description:Mentha spicata, also known as mint, is the best known source of aromatic essential oil. It was widespread in Europe and Asia. But due to human activity, it has been classified as Least Concern (LC) species in the IUCN Red List of Threatened Species. Here, we presented the complete chloroplast genome of M. spicata. The circular genome is 16,430?bp in length and contains 132 genes, including 87 protein-coding genes (PCG), 37 transfer RNA genes (tRNA) and eight ribosomal RNA genes (rRNA). The overall nucleotide composition is: 30.7% A, 19.2% C, 18.6% G, 31.5% T, with a total G?+?C content of 37.85%. The phylogenetic tree was constructed to explore the taxonomic status of M. spicata, which contributes to phylogenetic studies and further conservation strategies for this species.

| S-EPMC7800456 | biostudies-literature

The complete chloroplast genome of Capsicum frutescens (Solanaceae).

Project description:PREMISE OF THE STUDY:We report the complete sequence of the chloroplast genome of Capsicum frutescens (Solanaceae), a species of chili pepper. METHODS AND RESULTS:Using an Illumina platform, we sequenced the chloroplast genome of C. frutescens. The total length of the genome is 156,817 bp, and the overall GC content is 37.7%. A pair of 25,792-bp inverted repeats is separated by small (17,853 bp) and large (87,380 bp) single-copy regions. The C. frutescens chloroplast genome encodes 132 unique genes, including 87 protein-coding genes, 37 transfer RNA (tRNA) genes, and eight ribosomal RNA (rRNA) genes. Of these, seven genes are duplicated in the inverted repeats and 12 genes contain one or two introns. Comparative analysis with the reference chloroplast genome revealed 125 simple sequence repeat motifs and 34 variants, mostly located in the noncoding regions. CONCLUSIONS:The complete chloroplast genome sequence of C. frutescens reported here is a valuable genetic resource for Capsicum species.

| S-EPMC4873274 | biostudies-literature

The complete chloroplast genome of Petunia exserta (Solanaceae: Petunioideae), an endangered ornamental species.

Project description:Petunia exserta is an ornamental species on the brink of extinction in the wild. We report here the complete chloroplast genome of P. exserta, which is 156,598 bp in size consisting of a large single-copy region (87,095 bp), a small single-copy region (18,643 bp), and a pair of inverted repeats (25,430 bp for each). The chloroplast (used 'cp' hereafter) genome contains 132 genes, including 8 rRNA genes, 37 tRNA genes, and 87 protein-coding genes. Phylogenetic analysis demonstrated that P. exserta was most closely related to P. hybrida, and they together were closer to Calibrachoa hybrida than other taxa in the Solanaceae family.

| S-EPMC8366615 | biostudies-literature

Complete chloroplast genome of Physalis chenopodifolia Lam. (Solanaceae).

Project description:Physalis chenopodifolia is a perennial wild tomatillo with traditional use in central Mexico because of its edible fruits. Due to their agronomic potential and nutraceutical properties, this species is a resource that can be a candidate to plant breeding programs to be included in the Mexican diet. Here, we report the complete chloroplast genome of P. chenopodifolia. Its full size is 156,888 bp, includes a large single-copy (LSC) region of 87,117 bp, a small single-copy (SSC) region of 18,451 bp, and two invert repeat (IR) regions of 25,660 bp each. The plastome contains 113 genes, 79 protein-coding genes, 4 rRNA genes and 30 tRNA genes. The phylogenetic hypothesis supports P. chenopodifolia as a member of Physalis genus. Although relationships within the genus have moderated bootstrap support, the utility of the complete plastome sequence to solve infrageneric phylogenetic relationships is confirmed.

| S-EPMC7720949 | biostudies-literature

The complete chloroplast genome of Solanum betacea (Solanaceae, Solaneae).

Project description:Solanum betacea is a sub-tropical tree, and the fruit has high nutritional value, unique flavor and color. It is used as a functional ingredient in health care, food, cosmetic and pharmaceutical applications. The complete chloroplast(Cp) genome of S. betacea has been assembled and annotated in this paper. Its length was 155,937 bp, containing a large single-copy region of 86,731 bp, a small single-copy region of 18,450 bp, and a pair of IR regions of 25,378 bp in each. The complete chloroplast genome of S. betacea contained 134 genes, including 90 protein-coding genes, 36 transfer RNA genes (tRNAs), and 8 ribosome RNA genes (rRNAs). The overall GC content was 37.7% and the GC contents of the LSC, SSC, and IR regions were 35.7%, 31.8%, and 43.1%, respectively. Phylogenetic analysis with the reported chloroplast genomes revealed that S. betacea has been most closely related to Solanum torvum. These findings will provide useful information for further investigation of chloroplast genome evolution in Solanum betacea.

| S-EPMC8143614 | biostudies-literature

The complete chloroplast genome sequence of Nicotiana debneyi (Solanaceae).

Project description:In present study, we report the complete chloroplast genome of Nicotiana debneyi, a species endemic to eastern coast of Australia. The total genome size of N.debneyi is 156,073 bp in length, containing a large single-copy region of 86,672 bp, a small single-copy region of 18,581 bp, and two inverted repeat regions of 25,410 bp. The all GC content of N.debneyi chloroplast genome is 38.4%. It encodes a total of 129 unique genes, including 84 protein-coding genes, 37 tRNA genes, and eight rRNA genes, of which seven tRNA, four rRNA and seven protein-coding genes are duplicated in the IR. Sixteen genes contain a single intron, and only two genes have two introns. Phylogenetic analysis results strongly supported that N.debneyi was closely related to Nicotiana sylvestris and Nicotiana tabacum.

| S-EPMC7995905 | 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