Browse
Submit Data
Databases
API
Help

Dataset Information

29 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Draft Genome Sequence of Mesorhizobium sp. Strain SARCC-RB16n, an Effective Nodulating and Nitrogen-Fixing Symbiont of Rooibos [Aspalathus linearis (Burm. f.)] in South Africa.

ABSTRACT: The draft genome sequence of Mesorhizobium sp. strain SARCC-RB16n reveals the presence of major symbiotic (nod and nif) and additional plant growth-promoting (PGPR) genes associated with enhanced growth of Aspalathus linearis (Burm. f.) in South Africa. The genome sequence provides vital information for the development of a commercial inoculant for rooibos cultivation.

SUBMITTER: Hassen AI

PROVIDER: S-EPMC6979297 | biostudies-literature | 2020 Jan

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

Draft Genome Sequence of Mesorhizobium sp. Strain SARCC-RB16n, an Effective Nodulating and Nitrogen-Fixing Symbiont of Rooibos [Aspalathus linearis (Burm. f.)] in South Africa.

Hassen Ahmed Idris AI Swanevelder Z H ZH Bopape Francina L FL Lamprecht Sandra C SC

Microbiology resource announcements 20200123 4

The draft genome sequence of Mesorhizobium sp. strain SARCC-RB16n reveals the presence of major symbiotic (nod and nif) and additional plant growth-promoting (PGPR) genes associated with enhanced growth of Aspalathus linearis (Burm. f.) in South Africa. The genome sequence provides vital information for the development of a commercial inoculant for rooibos cultivation. ...[more]

PMID: 31974148

Similar Datasets

Transcriptomics of the Rooibos (Aspalathus linearis) Species Complex.

Project description:Rooibos (Aspalathus linearis), widely known as a herbal tea, is endemic to the Cape Floristic Region of South Africa (SA). It produces a wide range of phenolic compounds that have been associated with diverse health promoting properties of the plant. The species comprises several growth forms that differ in their morphology and biochemical composition, only one of which is cultivated and used commercially. Here, we established methodologies for non-invasive transcriptome research of wild-growing South African plant species, including (1) harvesting and transport of plant material suitable for RNA sequencing; (2) inexpensive, high-throughput biochemical sample screening; (3) extraction of high-quality RNA from recalcitrant, polysaccharide- and polyphenol rich plant material; and (4) biocomputational analysis of Illumina sequencing data, together with the evaluation of programs for transcriptome assembly (Trinity, IDBA-Trans, SOAPdenovo-Trans, CLC), protein prediction, as well as functional and taxonomic transcript annotation. In the process, we established a biochemically characterized sample pool from 44 distinct rooibos ecotypes (1-5 harvests) and generated four in-depth annotated transcriptomes (each comprising on average ≈86,000 transcripts) from rooibos plants that represent distinct growth forms and differ in their biochemical profiles. These resources will serve future rooibos research and plant breeding endeavours.

| S-EPMC9258316 | biostudies-literature

Rooibos (Aspalathus linearis) Genome Size Estimation Using Flow Cytometry and K-Mer Analyses.

Project description:Plant genomes provide information on biosynthetic pathways involved in the production of industrially relevant compounds. Genome size estimates are essential for the initiation of genome projects. The genome size of rooibos (Aspalathus linearis species complex) was estimated using DAPI flow cytometry and k-mer analyses. For flow cytometry, a suitable nuclei isolation buffer, plant tissue and a transport medium for rooibos ecotype samples collected from distant locations were identified. When using radicles from commercial rooibos seedlings, Woody Plant Buffer and Vicia faba as an internal standard, the flow cytometry-estimated genome size of rooibos was 1.24 ± 0.01 Gbp. The estimates for eight wild rooibos growth types did not deviate significantly from this value. K-mer analysis was performed using Illumina paired-end sequencing data from one commercial rooibos genotype. For biocomputational estimation of the genome size, four k-mer analysis methods were investigated: A standard formula and three popular programs (BBNorm, GenomeScope, and FindGSE). GenomeScope estimates were strongly affected by parameter settings, specifically CovMax. When using the complete k-mer frequency histogram (up to 9 × 105), the programs did not deviate significantly, estimating an average rooibos genome size of 1.03 ± 0.04 Gbp. Differences between the flow cytometry and biocomputational estimates are discussed.

| S-EPMC7076435 | biostudies-literature

Effect of Rooibos (Aspalathus linearis) extract on atorvastatin-induced toxicity in C3A liver cells.

Project description:Rooibos (Aspalathus linearis) has various health benefits. Two case studies have associated chronic Rooibos consumption with conventional prescription medications, including atorvastatin (ATV), with hepatotoxicity. Statins act by inhibiting hydroxymethylglutaryl-coenzyme A reductase, a rate-limiting enzyme in cholesterol synthesis. Although rare, statins are potentially hepatotoxic. The aim was to investigate interactions between aspalathin-rich Rooibos extract GRT™ and ATV-induced hepatotoxicity in C3A liver cells cultured with and without palmitate. Effects of co-treatment of GRT?+?ATV on cell viability, oxidative stress, apoptosis, mitochondrial integrity, and cellular reactive oxygen species (ROS) production were assessed. Significantly increased ROS production was observed in cells exposed to ATV and palmitate. Combination therapy of GRT?+?ATV also showed significant increases in ROS production. Under palmitate-treated conditions, ATV-induced significant apoptosis which was not ameliorated by GRT?+?ATV co-treatment. Despite studies purporting hepatoprotection from Rooibos, our study showed that GRT was unable to modulate ATV-induced hepatotoxic effects in this model.

| S-EPMC7586973 | biostudies-literature

Characterisation of Phomopsis spp. associated with die-back of rooibos (Aspalathus linearis) in South Africa.

Project description:Die-back of rooibos (Aspalathus linearis) causes substantial losses in commercial Aspalathus plantations in South Africa. In the past, the disease has been attributed to Phomopsis phaseoli (teleomorph: Diaporthe phaseolorum). Isolates obtained from diseased plants, however, were highly variable with regard to morphology and pathogenicity. The aim of the present study was thus to identify the Phomopsis species associated with die-back of rooibos. Isolates were subjected to DNA sequence comparisons of the internal transcribed spacer region (ITS1, 5.8S, ITS2) and partial sequences of the translation elongation factor-1 alpha gene. Furthermore, isolates were also compared in glasshouse inoculation trials on 8-mo-old potted plants to evaluate their pathogenicity. Five species were identified, of which D. aspalathi (formerly identified as D. phaseolorum or D. phaseolorum var. meridionalis) proved to be the most virulent, followed by D. ambigua, Phomopsis theicola, one species of Libertella and Phomopsis, respectively, and a newly described species, P. cuppatea. A description is also provided for D. ambigua based on a newly designated epitype specimen.

| S-EPMC2104715 | biostudies-literature

Rooibos (Aspalathus linearis) extract enhances boar sperm velocity up to 96 hours of semen storage.

Project description:Rooibos (Aspalathus linearis) is a native shrub from South African fynbos and has become very popular in the last decades for its antioxidant and medicinal attributes. Several studies have shown its beneficial properties in numerous cell lines, but to date, the in vitro effects of rooibos extract on sperm cells are still unknown. In this study, boar semen was supplemented with four concentrations both of fermented and unfermented rooibos extracts during 96 h of liquid storage at 17°C. The effects of rooibos extracts on sperm velocity, membrane integrity, and acrosomal status were evaluated at 2 h, 48 h, and 96 h of semen storage. Overall our results indicate that rooibos extract enhances sperm velocity, protects the acrosome structure, and tends to preserve the membrane integrity during semen storage. Although the unfermented rooibos showed higher total polyphenol content and total antioxidant capacity than the fermented one, the latter had better effects on sperm velocity leading to, for instance, an increase of 30% in the rectilinear velocity (VSL) at 48 h compared to the control group. Taking into account the different storage times, we established a suitable range of extracts concentrations to be used in boar semen. The rooibos extract ought to be considered as a powerful and natural source of antioxidants for the preservation of boar semen.

| S-EPMC5570286 | biostudies-literature

Cytotoxic Effects of Phytomediated Silver and Gold Nanoparticles Synthesised from Rooibos (Aspalathus linearis), and Aspalathin.

Project description:The green chemistry approach has continuously been applied for the synthesis of functional nanomaterials to reduce waste, environmental hazards, and the use of toxic chemicals among other reasons. Bioactive natural compounds have been found great potential in this regard and are used to improve the stability, activity, and biodistribution of metal nanoparticles (MNPs). Aspalathin (ASP) from Aspalathus linearis (rooibos) has a well-defined pharmacological profile and functional groups capable of both reducing and capping agents in the synthesis of metallic nanoparticles (NP). This study provides the first report of the phytomediated synthesis of gold and silver nanoparticles (AuNPs/AgNPs) via ASP and the green rooibos (GR) extract. The study demonstrated a green chemistry approach to the biosynthesis of nanoparticles of GR-AuNPs, ASP-AuNPs, GR-AgNPs, and ASP-AgNPs. The results showed that GR and ASP could act both as reducing and stabilising agents in the formation of crystalline, with different shapes and dispersity of NPs in the ranges of 1.6-6.7 nm for AgNPs and 7.5-12.5 nm for the AuNPs. However, the ASP NPs were less stable in selected biogenic media compared to GR NPs and were later stabilised with polyethene glycol. The cytotoxicity studies showed that GR-AgNPs were the most cytotoxic against SH-SY5Y and HepG2 with IC50 108.8 and 183.4 μg/mL, respectively. The cellular uptake analysis showed a high uptake of AuNPs and indicated that AgNPs of rooibos at a lower dose (1.3-1.5 μg/mL) is favourable for its anticancer potential. This study is a contribution to plant-mediated metallic nanoparticles using a pure single compound that can be further developed for targeted drug delivery for cancer cells treatments in the coming years.

| S-EPMC8620073 | biostudies-literature

Inhibition of Browning in Apples Using Betacyclodextrin-Assisted Extracts of Green Rooibos (Aspalathus linearis).

Project description:Green rooibos' bioactive compounds contribute greatly towards its antioxidant activity. The anti-browning activity of aqueous (GRE) and beta-cyclodextrin (β-GRE)-assisted extracts of green rooibos was investigated in canned apples. Freeze-dried extracts (GRE and β-GRE) obtained at 40 °C for 60 min were added in canned apples at 0.25 and 0.5% prior to heat processing and stored at 23 and 37 °C for 24 weeks. Lightness (L*), colour difference (DE*), furfural and hydroxymethyl furfural (HMF) were determined to establish the effect of extracts against non-enzymatic browning (NEB) development. The L* value decreased, whereas DE*, HMF and furfural increased with increased storage time and temperature. A higher inhibition was observed for samples stored at 23 °C, and storage at 37 °C reduced (p < 0.05) the inhibitory capacity of extracts. Greater inhibition against NEB development was reported for β-GRE 0.25 and 0.5 via the L* value (40.93-46.67%), β-GRE 0.25 for DE* (46.67%) and β-GRE 0.25 and 0.5 for HMF (59.55-67.33%). No differences (p > 0.05) were observed in furfural inhibition between all extracts, although inhibition was reported at 62.69-72.29%. Browning inhibition correlated with the reaction rate constant (k0) and activation energy (Ea), exhibiting a correlation coefficient of 0.925, 0.964, 0.932 and 0.754 for L*, DE*, HMF and furfural, respectively.

| S-EPMC9914553 | biostudies-literature

Visualization of Aspalathin in Rooibos (Aspalathus linearis) Plant and Herbal Tea Extracts Using Thin-Layer Chromatography.

Project description:Aspalathin, the main polyphenol of rooibos (Aspalathus linearis), is associated with diverse health promoting properties of the tea. During fermentation, aspalathin is oxidized and concentrations are significantly reduced. Standardized methods for quality control of rooibos products do not investigate aspalathin, since current techniques of aspalathin detection require expensive equipment and expertise. Here, we describe a simple and fast thin-layer chromatography (TLC) method that can reproducibly visualize aspalathin in rooibos herbal tea and plant extracts at a limit of detection (LOD) equal to 178.7 ng and a limit of quantification (LOQ) equal to 541.6 ng. Aspalathin is a rare compound, so far only found in A. linearis and its (rare) sister species A. pendula. Therefore, aspalathin could serve as a marker compound for authentication and quality control of rooibos products, and the described TLC method represents a cost-effective approach for high-throughput screening of plant and herbal tea extracts.

| S-EPMC6429207 | biostudies-literature

Impact of Cold versus Hot Brewing on the Phenolic Profile and Antioxidant Capacity of Rooibos (Aspalathus linearis) Herbal Tea.

Project description:Consumption of rooibos (Aspalathus linearis) as herbal tea is growing in popularity worldwide and its health-promoting attributes are mainly ascribed to its phenolic composition, which may be affected by the brewing conditions used. An aspect so far overlooked is the impact of cold brewing vs regular brewing and microwave boiling on the poly(phenolic) profile and in vitro antioxidant capacity of infusions prepared from red ('fermented', oxidized) and green ('unfermented', unoxidized) rooibos, the purpose of the present study. By using an untargeted metabolomics-based approach (UHPLC-QTOF mass spectrometry), 187 phenolic compounds were putatively annotated in both rooibos types, with flavonoids, tyrosols, and phenolic acids the most represented type of phenolic classes. Multivariate statistics (OPLS-DA) highlighted the phenolic classes most affected by the brewing conditions. Similar antioxidant capacities (ORAC and ABTS assays) were observed between cold- and regular-brewed green rooibos and boiled-brewed red rooibos. However, boiling green and red rooibos delivered infusions with the highest antioxidant capacities and total polyphenol content. The polyphenol content strongly correlated with the in vitro antioxidant capacities, especially for flavonoids and phenolic acids. These results contribute to a better understanding of the impact of the preparation method on the potential health benefits of rooibos tea.

| S-EPMC6826389 | biostudies-literature

Draft Genome Sequence of Bradyrhizobium sp. Strain LVM 105, a Nitrogen-Fixing Symbiont of Chamaecrista fasciculata (Michx.) Greene.

Project description:Here, we present the draft genome sequence of Bradyrhizobium sp. strain LVM 105, a soil bacterium that forms nitrogen-fixing nodules on the roots of partridge pea. The genome size was 8,386,213 bp, with a GC content of 63.8%. The draft assembly contained 97 scaffolds with an N50 value of 415,026 bp.

| S-EPMC6449556 | biostudies-literature