GSE157752
NGS of small RNA reads in sampled potato plants from the highlands of Colombia
Potato yellow vein virus (PYVV) was detected by RT-PCR in potatoes grown in the Central Colombian highlands, north of Bogotá (~3000 mt height).  At this altitude viral whitefly vectors are largely absent, but infection persists because of the use of uncertified tubers.  Plants with typical PYVV-induced yellowing symptoms, as well as with atypical yellowing or non-symptomatic were sampled at three separate geographical locations.  And five of them were subjected to Next Generation Sequencing (NGS) of their small RNA (sRNA) populations.  Contigs to any virus were assembled, and complete or almost complete sequences of four PYVV isolates were thus re-constructed, all from symptomatic plants.  Three viral isolates infected plants singly, while the fourth one co-infected the plant together with a potyvirus (potato virus Y, PVY).  Relative proportions of sRNAs to each of the three viral genomic RNAs were assessed and found to remain comparable between the four infections.  Genomic regions were identified as hotspots to sRNA formation, or as regions that induced poorly sRNAs.  Furthermore, PYVV titers in the mixed vs. the single infections were found to be remained comparable, indicating absence of synergistic/antagonistic effect of the potyvirus on the accumulation of PYVV. Overall design: 5 different potato plant samples analysed by NGS of their small RNA (sRNA) populations