This consideration is in line with a similar prediction by Machida et al. [37], who identified relatively abundant PSTVd-sRNAs in tomato leaves by low-scale sequencing.
In any case, the massive data generated by deep sequencing should allow to a more exhaustive retrieval than the limited datasets obtained by low-scale sequencing.
On the other hand, Machida et al. [37] identified similar levels of and PSTVd-sRNAs by low-scale sequencing in tomato infected by this viroid.
Previous efforts of characterizing vd-sRNAs by low-scale sequencing revealed that vd-sRNAs of PSTVd [40] and CEVd [38] are the most abundant in tomato plants infected by these viroids.
In line with this considerations, it is important that a peak corresponding to 24-nt vd-sRNAs has not been identified in the size distribution profiles of vd-sRNAs from the chloroplast-replicating Peach latent mosaic viroid sequenced by low-scale [62] and deep sequencing [63].
The relative abundance of 24-nt vd-sRNAs is again in contrast with previous results obtained by low-scale sequencing of vd-sRNAs from PSTVd and CEVd infecting tomato, in which two prominent peaks of 21- and 22-nt RNAs and negligeble [38], [40] or very low levels [37] of the 24-nt vd-sRNAs were detected.
However, it is surprising the low frecuency of 24-nt vd-sRNAs detected by low-scale sequencing in tissues infected by PSTVd and CEVd [23] [25], which having a nuclear accumulation site appear as good candidates for being also targeted by DCL3.
From Supplementary Figure S2, it can be seen that co-expression interactions are best predicted by low-scale STMs and depend only weakly on the mixture level of the PP/PD networks.
As suggested from previous small-scale experiments [ 38], we indeed observed that in naked DNA, the enzyme preferentially cuts tetramers with a central d A-T) step, but without the requirement of flanking d A-T dG bastepsuggested butlowithout experimenthe
The virus-host interactome, i.e. the whole set of protein interactions occurring within virus-infected cells, has been investigated in the last decades by the mean of low scale experiments focusing on single viral proteins.
