The relationships of genome organization among elongated (rod-shaped and filamentous) plant viruses have been analyzed. Sequences in coding and noncoding regions of barley stripe mosaic virus (BSMV) RNAs 1, 2, and 3 were compared with those of the monopartite RNA genomes of potato virus X (PVX), white clover mosaic virus (WClMV), and tobacco mosaic virus, the bipartite genome of tobacco rattle virus (TRV), the quadripartite genome of beet necrotic yellow vein virus (BNYVV), and icosahedral tricornaviruses. These plant viruses belong to a supergroup having 5'-capped genomic RNAs. The results suggest that the genomic elements in each BSMV RNA are phylogenetically related to those of different plant RNA viruses. RNA 1 resembles the corresponding RNA 1 of tricornaviruses. The putative proteins encoded in BSMV RNA 2 are related to the products of BNYVV RNA 2, PVX RNA, and WClMV RNA. Amino acid sequence comparisons suggest that BSMV RNA 3 resembles TRV RNA 1. Also, it can be proposed that in the case of monopartite genomes, as a rule, every gene or block of genes retains phylogenetic relationships that are independent of adjacent genomic elements of the same RNA. Such differential evolution of individual elements of one and the same viral genome implies a prominent role for gene reassortment in the formation of viral genetic systems.

Nucleotide sequences of the genomic RNA beta components of hordeiviruses poa semilatent virus (PSLV) and lychnis ringspot virus (LRSV) were determined. PSLV and LRSV closely resemble barley stripe mosaic virus (BSMV), type hordeivirus, in the gene arrangement of their RNAs beta, comprising 5'-proximal beta a (coat protein) gene and downstream triple gene block (TGB) coding for the beta b, beta c, and beta d putative transport proteins. The beta a, beta b, beta c, and beta d proteins of the three hordeiviruses showed significant sequence similarity, with the respective proteins of PSLV and BSMV being closer to each other than to their counterparts of LSRV. Comparisons of the TGB-encoded proteins of hordeiviruses, potexviruses, carlaviruses, and furoviruses indicate that the first and second TGB genes belong to the monophyletic groups, whereas the third gene may have multiple ancestry. LRSV, PSLV, and BSMV showed remarkable variation in the 3'-untranslated regions of their genomic RNAs. Among the three hordeiviruses, LRSV has the shortest 3'-noncoding region that lacks tentative pseudoknot-forming elements conserved upstream of the 3'-tRNA-like structure in the BSMV and PSLV genomes. On the other hand, LRSV RNA beta, like that of BSMV, contained the internal poly(A) sequence that is absent from PSLV RNA.

Genomic RNA sequence of a tobamovirus infecting cruciferae plants (cr-TMV) was determined. The RNA is composed of 6312 nucleotides and contains four ORFs encoding the proteins of 122K (ORFI), 178K (ORF2), 29K (ORF3) and 18K (capsid protein, 0RF4). ORF4 overlaps 0RF3 by 74 nucleotides and the overlapping region can be folded into a stable hairpin structure. The 3'-terminal region of the cr-TMV RNA preceding the tRNA-like structure was shown to form six potentially stable pseudoknots.

Six species of 3′‐coterminal poly(A) ‐containing RNAs of subgenomic (sg) size have been found in plants infected with potato virus X (PVX): two major (0.9 kb — the coat protein mRNA, and 2.1 kb) and four minor (1.4, 1.8, 3.0 and 3.6 kb). The 5′‐end of the shortest sgRNA is located 26 nucleotides upstream of the initiating codon of the coat protein gene (812 nucleotides from the 3′‐terminal poly(A) tract of the PVX genomic RNA). Double‐stranded analogues have been found for most sgRNAs. The genomic‐size double‐stranded RNA (the replicative form) is shown to carry a poly(A)‐poly(U) hybrid of a predominant length of 150–250 bp on one end, and an unpaired G residue on the other (the 3′‐end of the negative chain). In contrast to this(—) the chains of double‐stranded 0.9 and 2.1 kbp sgRNAs lack the unpaired G and both end in C.

The cloned cDNA copies corresponding to 1300 nucleotides adjacent to the 3'-terminal poly(A) tract of the potato virus X (PVX) genome have been sequenced. The amino acid sequences of three open reading frames were deduced from the nucleotide sequence. Two putative small nonstructura1 polypeptides corresponding to the open reading frames adjacent to the coat protein cistron possess some properties of membrane-associated proteins. Direct sequence homology and common structural peculiarities exist between the PVX small proteins and the putative small nonstructural proteins encoded by RNA 2 of hordeiviruses and furoviruses cDNA; Cloning; Amino acid sequence; Sequence homology; Membrane-bound protein; (Plant virus)