FIG. 5.

SS-RNA is not detected in RTBV-infected rice plants. (A) The RTBV pgRNA is represented twice, by solid and dashed curved lines, with the SS-RNA as a straight line colinear with the 3′ end of the pgRNA. The antisense probes transcribed from RTPA-L or RTPA-2 are represented above the upper and lower diagrams, respectively, and thick lines indicate the position and expected sizes (in nucleotides) of protected RNA fragments corresponding to the 5′ and 3′ ends of the pgRNA and the SS-RNA. The diagram is not to scale, and the nos sequences on the probes are not indicated. (B) RNase protection analysis of total RNA (5-μg aliquots) from RTBV-infected rice plants using probes covering the terminal redundancy (RTPA-L), the 3′ end of the terminal redundancy (RTPA-2), or a 135-nt fragment of the RTBV pgRNA spanning the end of ORF III and the beginning of ORF IV (IV-CAT [10] protects a 135-nt internal fragment on the pgRNA). Fragments obtained with probe RTPA-L corresponding to the 5′ (RT) and 3′ ends of the RTBV pgRNA are indicated on the left, as well as the expected position of SS-RNA. A longer fragment (RT2) is also indicated (see text for possible explanations). Fragments protected by the RTPA-2 and IV-CAT probes are labeled on the right. Note that the RTPA-2 probe does not distinguish between SS-RNA and the 3′ end of pgRNA.