The hypersensitive response (HR) system of Chenopodium spp. confers broad-spectrum virus resistance. However, scant knowledge exists at the genomic level for Chenopodium, thus impeding the advanced molecular research of this attractive feature. Hence we took advantage of RNA-seq to survey the foliar transcriptome of C. amaranticolor, one Chenopodium species being widely used as laboratory indicator for pathogenic viruses, in order to facilitate the characterization of the HR-type of virus resistance. In a single run, we obtained 39,868,984 reads with 3,588,208,560 bp, which were assembled into 112,453 unigenes (3,848 clusters and 108,605 singletons). BlastX search against the NCBI NR database identified 62,482 sequences with a cut-off E-value above 10-5. Assembled sequences were annotated with gene descriptions, GO, COG and KEGG terms. A dataset containing 738 resistance gene analogs and sequences represent 6 key signaling proteins within the R proteins-directed signaling pathway was generated. Additionally, using RNA-Seq digital gene expression analysis, we investigated the gene expression profiles over the stage of HR induced by Tobacco mosaic virus and Cucumber mosaic virus in C. amaranticolor leaves, and identified numerous candidate genes specifically or commonly regulated by these two distinct viruses at early and late stages of the HR. Specifically, the dynamic changes of the differently expressed genes enriched in the pathway of plant-pathogen interaction were analyzed. To our knowledge, this is the first study to elucidate the genetic makeup of Chenopodium spp., providing a starting-point for future functional genomics studies on Chenopodium.
Overall design: Analysis of the differentially expressed genes over the stage of hypersensative response induced by viruses in C. amaranticolor
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