Abstract
Sequence accessions attributable to novel plant amalgaviruses have been found in the Transcriptome Shotgun Assembly database. Sixteen accessions, derived from 12 different plant species, appear to encompass the complete protein-coding regions of the proposed amalgaviruses, which would substantially expand the size of genus Amalgavirus from 4 current species. Other findings include evidence for UUU_CGN as a +1 ribosomal frameshifting motif prevalent among plant amalgaviruses; for a variant version of this motif found thus far in only two amalgaviruses from solanaceous plants; for a region of α-helical coiled coil propensity conserved in a central region of the ORF1 translation product of plant amalgaviruses; and for conserved sequences in a C-terminal region of the ORF2 translation product (RNA-dependent RNA polymerase) of plant amalgaviruses, seemingly beyond the region of conserved polymerase motifs. These results additionally illustrate the value of mining the TSA database and others for novel viral sequences for comparative analyses.
Highlights
Amalgaviridae is a recently recognized taxon that currently comprises four species of plant viruses (Blueberry latent virus, Rhododendron virus A, Southern tomato virus, and Vicia cryptic virus M) in one genus (Amalgavirus) (Adams et al, 2014; Liu and Chen, 2009; Martin et al, 2011; Sabanadzovic et al, 2009, 2010)
One question that arises is whether the Transcriptome Shotgun Assembly (TSA)-derived sequences characterized here represent transcripts of chromosomal or extrachromosomal, host or viral, origin
This is notably unlike the case for the TSA-derived sequences listed in Table 1, which approximate the lengths of complete plant amalgavirus genomes and have the expected long open reading frames (ORFs) for expressing ORF1p and ORF1 þ2p
Summary
Amalgaviridae is a recently recognized taxon that currently comprises four species of plant viruses (Blueberry latent virus, Rhododendron virus A, Southern tomato virus, and Vicia cryptic virus M) in one genus (Amalgavirus) (Adams et al, 2014; Liu and Chen, 2009; Martin et al, 2011; Sabanadzovic et al, 2009, 2010). These plant amalgaviruses have small dsRNA genomes (3427– 3437 bp) and have not yet been shown to form bona fide virions. The ORF2-encoded portion of this fusion protein is indicated by conserved sequence motifs to be the viral RNA-dependent RNA polymerase (RdRp)
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