In depth investigation of gene regulation mechanisms for virus defense in Cassava

The time of "junk DNA" is long over but we are still not clear what all this non coding DNA is for. In the last years we learned a lot about the small and long non-coding RNA and entered in a world with several new dimensions of gene regulation. On one side smallRNAs directly interact with the mature transcripts and inhibit translation or even break the transcript down. On the other side smallRNAs regulate DNA methylation which directly or via transposable elements regulate gene expression. Further, smallRNA are a crucial element in plants to defend themselves against virus and probably other pathogen infestations by "down regulating" viral transcripts. In the last 3 years we developed a plant model in cassava to investigate the resistance mechanism of cassava against the cassava mosaic disease (CMD) to study exactly these three mechanisms of gene regulation. Two genetically very similar cassava genotypes developed differently their resistance against CMD; one is highly resistance while the other develop severe symptoms and never recover from the infection. We sequenced extensively the transcriptome, the smallRNAs and the DNA methylation profile of both genotypes unchallenged and under viral stress. We developed proof-of-concept scripts to integrate the data and to demonstrate how the viral impact changes the different parameter to regulate genes. Whether all regulated genes are part of the resistance mechanism is still to proof.