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De novo characterization of foliar transcriptome in Chenopodium amaranticolor and analysis of the differentially expressed genes during the stage of hypersensative response induced by distinct plant viruses

ABSTRACT: 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.

ORGANISM(S): Chenopodium amaranticolor

PROVIDER: GSE38451 | GEO | 2013/02/20

SECONDARY ACCESSION(S): PRJNA167927

REPOSITORIES: GEO

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Project description:Wheat streak mosaic virus (WSMV) and Triticum mosaic virus (TriMV) are type members of Tritimovirus and Poacevirus genera, respectively, in the family Potyviridae, and are transmitted by wheat curl mites. Co-infection of these two viruses causes synergistic interaction with increased virus accumulation and disease severity in wheat. In this study, we examined the effects of synergistic interaction between WSMV and TriMV on endogenous small (s) RNAs and virus-specific small interfering RNAs (vsiRNAs) in susceptible (Arapahoe) and temperature-sensitive resistant (Mace) wheat cultivars at 27C and 18C. Single- and double-infections in wheat caused a shift in the profile of endogenous sRNAs from 24 nt being the most predominant in healthy plants to 21 nt in infected wheat. Additionally, we report high-resolution vsiRNA maps of WSMV and TriMV in singly- and doubly-infected wheat cultivars Arapahoe and Mace at 18C and 27C. Massive amounts of 21 and 22 nt vsiRNA reads were accumulated in Arapahoe at both temperatures and in Mace at 27C but not at 18C. The plus- and minus-sense vsiRNAs were distributed throughout the genomic RNAs in Arapahoe at both temperature regimens and in Mace at 27C, although some regions of genomic RNAs serve as hot-spots with an excessive number of vsiRNAs. The positions of vsiRNA peaks were conserved among wheat cultivars Arapahoe and Mace, suggesting that Dicer-like enzymes of susceptible and resistant wheat cultivars are similarly accessed the genomic RNAs of WSMV and TriMV. Additionally, several cold-spot regions were found in the genomes of TriMV and WSMV with no or a few vsiRNAs, indicating that certain regions of WSMV and TriMV genomes are not accessible to Dicer-like enzymes. The high-resolution map of endogenous and vsiRNAs from wheat cultivars synergistically infected with WSMV and TriMV at two temperature regimens form a foundation for understanding the virus-host interactions, effect of synergistic interactions on host defense mechanisms, and virus resistance mechanisms in wheat. Small RNA was sequenced from two wheat cultivars (Mace and Araphahoe), at two temperatures 18C and 27C, for healthy (control/uninfected), infected with wheat streak mosaic virus (WSMV), infected with Triticum mosaic virus (TriMV), and a double-infecttion of WSMV and TriMV.

Project description:We established an Arabidopsis thaliana Columbia (Col-0) and Cucumber mosaic virus strain HYY [CMV(HYY)] patho-system and identified a necrotic cell death. The global gene expression analysis of the necrotic cell death and HR cell death developed in cucumber mosaic virus-inoculated leaves of A. thaliana was performed by RNA-seq, respectively. The samples for RNA-seq were collected from the cell death leaves showing HR cell death at 3dpi and showing necrotic cell death at 5dpi, respectively. The sequence data was first preprocessed by FASTQ in basespace of illumine.The sequence reads were processed with Trimmomatic (version 0.38) for adaptor trimming and quality trimming. The processed reads were mapped to the genome sequences of A.thaliana ecotype Col-0, CMV(Y) and CMV(Ho) with STAR (version 2.7) with its default settings. Read counts per each A.thaliana gene were retrieved by the quantification option of STAR. The obtained read counts were normalized and statistically tested using DESeq2 R package 3.7. Adjusted p-values were calculated with Benjamini-Hochberg procedure, and the threshold for adjusted p-value was set to 0.05 in the present study. The independent filtering in DESeq2 was performed to filter out the genes with low mean normalized counts, with an automatically optimized threshold; 5,906 genes which passed the independent filtering in both of the two comparisons (i.e, necrotic cell death vs mock and HR cell death vs control) were further analyzed for differential expression. Genes with adjusted p-value of <0.05 and a fold change of >4 or <0.25 were considered as DEGs. Of the 5,906 genes analyzed, 202 genes showed >4-fold up-regulation upon either HR cell death or necrotic cell death induction (adjusted p < 0.05). Thirty-five of them were common in HR cell death or necrotic cell death induction, while 149 and 18 were unique to HR cell death or necrotic cell death induction, respectively. Sixty-two genes showed <0.25-fold down-regulation upon either HR or necrosis induction (adjusted p < 0.05). Seven of them were common , while 43 and 12 were specific for HR cell death or necrotic cell death induction, respectively. Collectively, the necrotic cell death displayed a distinct gene expression pattern compare to HR cell death.

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De novo characterization of foliar transcriptome in Chenopodium amaranticolor and analysis of the differentially expressed genes during the stage of hypersensative response induced by distinct plant viruses

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