Changes in relative expression levels of viroid-specific small RNAs and microRNAs in tomato plants infected with severe and mild symptom-inducing isolates of Potato spindle tuber viroid

Abstract

The dahlia isolate of Potato spindle tuber viroid (PSTVd-D) shares 97 % sequence homology with PSTVd-intermediate (PSTVd-I), but differs at eight positions in the nucleotide sequence from PSTVd-I: five substitutions at positions 42, 43, 127, 202, and 311, two insertions at 63/64 and 312/313, and one deletion at 119. PSTVd-D accumulates slowly and induces very mild symptoms in tomato (cv. Rutgers) plants. In contrast, PSTVd-I propagates faster and induces severe symptoms. Here we used deep-sequencing analysis of PSTVd-specific small RNAs (PSTVd-sRNA) that accumulate in PSTVd-I- and PSTVd-D-infected tomato plants to reveal that the number of PSTVd-sRNA reads extensively decreased in PSTVd-D-infected leaf and stem tissues, especially those derived from the regions containing the nucleotides 119, 127, and 202, in which the nucleotide sequence differed between the severe and mild symptom-inducing isolates. In comparison with healthy controls, relative expression levels (i.e., number of reads by deep sequencing) of various host microRNAs changed after infection with PSTVd-I and PSTVd-D. The relative abundance of miR159 and miR162 in PSTVd-I- and PSTVd-D-infected leaf and stem tissues decreased to nearly 50 % of that in healthy tissues. In PSTVd-I- and PSTVd-D-infected stem tissues, miR319, which is approximately five times more abundant in stem tissues than in leaves, also decreased to 33–63 % of that in healthy controls.