Genome organization of representative members of the family
Secoviridae. Each RNA is shown with ORFs represented
with boxes. Circles depict VPg molecules covalently attached at the
5′-end of the RNAs. Black circles represent VPg confirmed
experimentally and open circles represent putative VPgs. Poly(A) tails are
represented at the 3′-end of the RNAs when present (An). Red and blue arrows above the sequences represent regions of
extensive sequence identity between RNAs 1 and 2. In the latter, for
torradoviruses, this identity is also characterized by conserved indels.
Protein domains with conserved motifs for the putative NTP-binding protein
(NTB, shown in orange), VPg (purple), proteinase (Pro, yellow),
RNA-dependent RNA polymerase (Pol, red), movement protein (MP, green) and
coat protein(s) (CP, blue) are shown. The star represents a conserved motif
found in the protease cofactor (Co-Pro) protein of comoviruses and in the
equivalent protein of other viruses. Proteinase cleavage sites identified
experimentally or deduced by sequence comparisons are indicated by solid or
dotted vertical lines, respectively. Possible ORFs in the genome of
waikaviruses are shown with dotted rectangles and putative subgenomic RNAs
are shown by dotted arrows below the waikavirus genome. Representatives of
each nepovirus subgroup (Sg A, B, C) are also depicted.