A planarian nidovirus expands the limits of RNA genome size

Amir Saberi; Anastasia A. Gulyaeva; John L. Brubacher; Phillip A. Newmark; Alexander E. Gorbalenya

We obtained several lines of evidence for upregulated transcription of the 3'ORFs-like region (Fig. 4B-D; SI Text). The PSCNV genome contains a pair of 59 and 57-nt imperfect repeats with 86% identity starting at positions 3 and 28,389, respectively (Fig. 4B) ; their positioning immediately upstream of ORF1a-like and at the border between ORF1b-and 3'ORFs-like regions resembles that of leader and body transcription-regulating sequences (l-and bTRSs) in other nidoviruses (49) . Accordingly, we found a sharp (~3-fold) change in RNA-seq read coverage at the bTRS. We identified an RNA species (by 5'-RACE), whose first two and following 57 nucleotides matched the genomic 5'-terminal AU followed by the bTRS (Fig. 4B) , suggesting the presence of a subgenomic mRNA produced by discontinuous transcription. Furthermore, the bTRS potentially forms strong complementary interactions with its upstream and downstream sequences (Fig. 4C ). When unwound, the upstream sequence can form a duplex with the lTRS, bringing together the two spatially separated genomic regions, consistent with a model of discontinuous subgenomic RNA synthesis (Fig. 4D) resembling that of other nidoviruses (50) .