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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:Cruciferous 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.The 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.In 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.

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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.

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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.

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