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Substantial Reprogramming of the Thellungiella salsuginea Transcriptome in Response to UV and Silver Nitrate Challenge

ABSTRACT: The transcriptional response of T. salsuginea to UV irradiation and AgNO3 was monitored by microarray analysis. Most transcripts (respectively 70% and 78%) were significantly differentially regulated and a large overlap between the two treatments was observed (54% of total). While core genes of the biosynthesis of aliphatic glucosinolates were repressed, tryptophan and indole glucosinolate biosynthetic genes, as well as defence-related WRKY transcription factors, were consistently upregulated.

ORGANISM(S): Eutrema salsugineum

PROVIDER: GSE62651 | GEO | 2015/10/01

SECONDARY ACCESSION(S): PRJNA264721

REPOSITORIES: GEO

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Substantial reprogramming of the Eutrema salsugineum (Thellungiella salsuginea) transcriptome in response to UV and silver nitrate challenge.

Project description:BackgroundCruciferous plants synthesize a large variety of tryptophan-derived phytoalexins in response to pathogen infection, UV irradiation, or high dosages of heavy metals. The major phytoalexins of Eutrema salsugineum (Thellungiella salsuginea), which has recently been established as an extremophile model plant, are probably derivatives of indole glucosinolates, in contrast to Arabidopsis, which synthesizes characteristic camalexin from the glucosinolate precursor indole-3-acetaldoxime.ResultsThe transcriptional response of E. salsugineum to UV irradiation and AgNO3 was monitored by RNAseq and microarray analysis. Most transcripts (respectively 70% and 78%) were significantly differentially regulated and a large overlap between the two treatments was observed (54% of total). While core genes of the biosynthesis of aliphatic glucosinolates were repressed, tryptophan and indole glucosinolate biosynthetic genes, as well as defence-related WRKY transcription factors, were consistently upregulated. The putative Eutrema WRKY33 ortholog was functionally tested and shown to complement camalexin deficiency in Atwrky33 mutant.ConclusionsIn E. salsugineum, UV irradiation or heavy metal application resulted in substantial transcriptional reprogramming. Consistently induced genes of indole glucosinolate biosynthesis and modification will serve as candidate genes for the biosynthesis of Eutrema-specific phytoalexins.

| S-EPMC4464140 | biostudies-literature

Whole genome transcriptome profiling of Thellungiella salsuginea guard cells under saline growth conditions

Project description:The overall objective was to document transcriptomic changes in the guard cells of Thellungiella salsuginea under short (1x) - and long-term (3x) saline growth conditions. For that. microarray analysis was performed using a 60-mer oligonucleotide probe array from Agilent (44 K, design number 031554, Santa Clara, CA, USA). It was clearly observed that salt salinity alters the transcriptomic landscape of Thellungiella guard cells. However, changes in gene expression were evident under 3x saline growth conditions compared to non-saline conditions. Similarly, more GO terms were significantly enriched in differentially expressed guard cell genes of 3x salt than 1x salt treated plants.

2021-03-23 | GSE169311 | GEO

Transcriptome sequencing and microarray design for functional genomics in the extremophile Arabidopsis relative Thellungiella salsuginea

2013-11-19 | GSE42156 | GEO

Dual-transcriptome of post-germinating Arabidopsis thaliana mutant lines infected by Alternaria brassicicola

Project description:We analyzed transcriptome changes from germinating cyp79B2 cyp79B3, qko, and pad3 mutant Arabidopsis seeds. Here were used mutant lines in Col-0 genetic background: a cyp79B2 cyp79B3 double mutant defective in indolic glucosinolate (cyp79B2/B3), a cyp79B2 cyp79B3 myb28 myb29 quadruple mutant defective in indolic and aliphatic glucosinolates (qko), and a camalexin deficient mutant (pad3). Differentially expressed genes were identified at 3, 6 and 10 days after sowing from both the mutant line seeds and from Alternaria brassicicola when inoculated seeds were analyzed.

2024-03-26 | GSE214602 | GEO

Transcriptome sequencing and microarray design for functional genomics in the extremophile Arabidopsis relative Thellungiella salsuginea

Project description:Arabidopsis thaliana is not particularly stress tolerant and may lack protective mechanisms required to survive extreme environmental conditions. Thellungiella salsuginea has therefore attracted increasing interest as an alternative plant model species that possesses high tolerance of various abiotic stresses. While the T. salsuginea genome has recently been sequenced, its annotation is still far from complete and, due to the low number of ESTs available, evidence for actual transcriptional activity is lacking for most genes. ESTs were generated from a non-normalized and a normalized library synthesized from RNA pooled from plant samples from different developmental stages and grown under abiotic stress conditions. The ESTs of Thellungiella was sequenced by 454 pyrosequencing method. More than 1 million sequence reads were assembled into 42,810 unigenes, approximately 50% of which could be functionally annotated. From this sequence information, we constructed a 44k Agilent oligonucleotide microarray. A comparison of same-species and cross-species hybridization results showed the superior performance of the newly designed array for Thellungiella samples. In addition, the array was validated in a cold acclimation experiment that used the appropriately adapted MapMan software for analysis and visualization. To examine the quality of the Thellungiella array and to assess whether hybridization results from a dedicated array are superior to cross-species hybridization using the Arabidopsis array from the same manufacturer, we performed reciprocal array hybridizations. In this experiment, RNA from the Yukon accession of Thellungiella and RNA from the Col-0 accession of Arabidopsis were both hybridized on the Agilent Thellungiella and Arabidopsis expression arrays. For both species, RNA was extracted from acclimated and non-acclimated plants from three independent biological replicates.

2013-11-19 | E-GEOD-42156 | biostudies-arrayexpress

Eutrema salsugineum cultivar:Thellungiella salsuginea (Pall.) O. E. Schulz

Project description:Eutrema salsugineum cultivar:Thellungiella salsuginea (Pall.) O. E. Schulz Raw sequence reads

| PRJNA377594 | ENA

Transcriptome Analysis of Arabidopsis thaliana and Changes of Glucosinolates Metabolism Pathway Induced by Flg22

Project description:Purpose: The goals of this study are to analyze the transcriptome of Arabidopsis thaliana treated after flg22 and to find changes of glucosinolate metabolism genes after treatment. Methods: Total mRNA of 10 day wild-type Arabidopsis seedlings that were treated with and without flg22( final concentrations 1μmol/L) in 1/2 MS medium for 4h, were extracted respectively. Each sample was harvested in three independent biological replicates with equal weight and mixed ,subsequently sequencing. The sequence reads that passed quality filters were mapped to the Arabidopsis_thaliana genome (TAIR10.18).Then the mapping genes were used for the abundance and functional analysis. Results: We mapped about 45 million and 52 million sequence reads of control sample and treatment sample to the Arabidopsis_thaliana genome (TAIR10.18) and identified total 23,413 genes with Botiw/TopHat workflow. Comparison of the two samples showed 1,200 differentially expressed genes (DEGs), including 290 down-regulated and 910 up-regulated genes. The DEGs were associated with energy metabolism, amino acid metabolism and biosynthesis of secondary metabolites. After flg22 treatment, genes involved in indolic glucosinolate biosynthesis pathway were up-regulated significantly，which is further demonstrated by Real Time RT-PCR, while aliphatic glucosinolate pathway almost had no change, indicating the important role of indolic glucosinolates in plant defense responses. Conclusion: Our study provides the overall genetic resource of Arabidopsis_thaliana after treated by flg22 to date. These data will pave the way for further studies about deeply understand pathogen induced defense and the contribution of indolic glucosinolates.

2017-03-22 | GSE56117 | GEO

Cold acclimation responses of Arabidopsis thaliana and Eutrema salsugineum (Thellungiella salsuginea)

Project description:Cold acclimation responses of Arabidopsis thaliana and Eutrema salsugineum (Thellungiella salsuginea)

| PRJNA390727 | ENA

Salt stress responses of Arabidopsis thaliana and Eutrema salsugineum (Thellungiella salsuginea)

Project description:Salt stress responses of Arabidopsis thaliana and Eutrema salsugineum (Thellungiella salsuginea)

| PRJNA290732 | ENA

Insights into salt tolerance from the genome of Thellungiella salsuginea.

Project description:Thellungiella salsuginea, a close relative of Arabidopsis, represents an extremophile model for abiotic stress tolerance studies. We present the draft sequence of the T. salsuginea genome, assembled based on ~134-fold coverage to seven chromosomes with a coding capacity of at least 28,457 genes. This genome provides resources and evidence about the nature of defense mechanisms constituting the genetic basis underlying plant abiotic stress tolerance. Comparative genomics and experimental analyses identified genes related to cation transport, abscisic acid signaling, and wax production prominent in T. salsuginea as possible contributors to its success in stressful environments.

| S-EPMC3409768 | biostudies-literature

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