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.
Highlights
Geminiviruses constitute a large family of plant viruses with circular single-stranded DNA genomes packaged within geminate particles[1,2]
The fact that elements of the RdDM canonical pathway seem to be involved in geminiviral genome methylation[37,47,50], suggests that virus-derived small RNAs (vsRNAs) could be directing viral DNA methylation
The low representation of vsRNAs that we have found at the intergenic region (IR) of Tomato yellow leaf curl virus (TYLCV) is in accordance with the results previously obtained by high resolution RNA blots[59,60] or deep sequencing[30,31,33,34] for other geminiviruses
Summary
Geminiviruses constitute a large family of plant viruses with circular single-stranded DNA (ssDNA) genomes packaged within geminate particles[1,2]. In the Geminiviridae family, Begomovirus is the largest genus and comprises most of the viral species infecting dicotyledonous plants Geminiviruses amplify their single-stranded genomes in the nuclei of infected cells by three replication strategies: complementary strand replication (CSR), rolling circle replication (RCR) and recombination-dependent replication (RDR)[3,4]. The IR encompasses the origin of replication, which includes a stem-loop structure containing a conserved nonanucleotide sequence required for the cleavage and joining of the viral DNA during replication[11] and the regulatory DNA replication elements needed for Rep binding (iterons)[12,13]. There are two reports on TYLCV vsRNAs generated during the infection in tomato which provide limited information, since the data came from a reduced number of reads (1212 reads)[29] or belonged to field-collected tomato samples infected in most cases, with other tomato viruses[32]
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