Integrated single-base resolution maps of transcriptome, sRNAome and methylome of Tomato yellow leaf curl virus (TYLCV) in tomato

Abstract

Geminiviruses are plant ssDNA viruses that replicate through dsDNA intermediates and form minichromosomes which carry the same epigenetic marks as the host chromatin. During the infection, geminiviruses are targets of the post-transcriptional and transcriptional gene silencing machinery. To obtain insights into the connection between virus-derived small RNAs (vsRNAs), viral genome methylation and gene expression, we obtained the transcriptome, sRNAome and methylome from the geminivirus Tomato yellow leaf curl virus -infected tomato plants. The results showed accumulation of transcripts just at the viral ORFs, while vsRNAs spanned the entire genome, showing a prevalent accumulation at regions where the viral ORFs overlapped. The viral genome was not homogenously methylated showing two highly methylated regions located in the C1 ORF and around the intergenic region (IR). The compilation of those results showed a partial correlation between vsRNA accumulation, gene expression and DNA methylation. We could distinguish different epigenetic scenarios along the viral genome, suggesting that in addition to its function as a plant defence mechanism, DNA methylation could have a role in viral gene regulation. To our knowledge, this is the first report that shows integrative single-nucleotide maps of DNA methylation, vsRNA accumulation and gene expression from a plant virus.

A virus-encoded protein suppresses methylation of the viral genome through its interaction with AGO4 in the Cajal body

“…In light of the role of AGO4 in RdDM and to directly assess the impact of V2 and AGO4 on the methyl-state of the viral DNA, we used bisulfite sequencing (BS-seq) to measure DNA methylation of the intergenic region (IR) of the viral genome, which presents the highest methylation levels during the infection ( Piedra-Aguilera et al, 2019 ). As shown in Figure 4A , cytosine methylation in this region in all contexts (CG, CHG, and CHH) was almost undetectable in the wild-type viral genome in local infections at 3 or 9 days post-inoculation (dpi), while it reached ~60% and~80%, respectively, in the V2 null mutant ( Figure 4A ; Figure 4—figure supplement 1A ; Supplementary file 1 ).…”

DNA Methylation Analysis of the Citrullus lanatus Response to Cucumber Green Mottle Mosaic Virus Infection by Whole-Genome Bisulfite Sequencing

“…For instance, reduced representation bisulfite sequencing (RRBS) of cucumber mosaic virus (CMV)-infected Nicotiana tabacum revealed that DMRs are enriched within CHH sequence contexts and are mainly located on the gene body [34]. Deep sequencing of bisulfite-treated DNA (BS-Seq) on TYLCV-infected tomato identify different epigenetic scenarios in the viral genome, suggesting that DNA methylation plays roles in plant defense and viral gene regulation [43]. Currently, whole-genome bisulfite sequencing (WGBS) has emerged as a powerful approach for studying DNA methylation by providing genome-wide methylation profiles at single-base resolution [44].…”

Towards Exploitation of Adaptive Traits for Climate-Resilient Smart Pulses

“…However, technological advancements have made it feasible to identify methylomes at a single-base resolution using BS-seq in soybean [248]. Methylome profiles studied among diverse accessions in key crop species including chickpea and soybean showed thousands of differentially methylated regions (DMRs) [248,249,250]. Genome-wide cytosine methylation analysis has been done on soybean for roots, stems, leaves, and cotyledons of developing seeds at single-base resolution.…”