Figure 1. Genome organization.

(a) SeMV is a single stranded RNA virus with genome size of 4147 nt. The 5′ end of the genome is covalently linked to VPg and the 3′ end lacks polyA tail. ORF 1 encodes movement protein and ORF 3 encodes the coat protein which is expressed through a subgenomic RNA (sgRNA). The ORF 2 codes for two polyproteins 2a and 2ab. The numbers indicate the position of start and stop codons in each of the ORFs. The polyprotein 2a contains N-terminal membrane anchor (MA)-protease-VPg-p10-p8 domains. The polyprotein 2ab contains N-terminal membrane anchor (MA)-protease-VPg-RdRp. The RdRp is expressed through a −1 ribosomal frame shifting mechanism. The numbers in the polyproteins 2a and 2ab indicate the cleavage site positions. (b) Features of infectious clone: The infectious construct was initially made in pBluescript SK+ vector and later subcloned into pRD400 vector. The infectious construct consists 2×35S Promoter-SeMV cDNA-sTobRV RZ (Ribozyme)-Nos terminator. It has additional 4 nt at the 5′ end (5′ CCTC 3′) and 21 nt at the 3′end. The 3′ terminal two nucleotides present in the wild type viral RNA are absent in this clone (5′ AAA T 3′ instead of 5′ AAA TGT 3′). The ribozyme self cleavage site is shown by a curved arrow.