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A novel plant virus with a double-stranded (ds) RNA genome was detected in Lilium spp. in China by high-throughput sequencing, tentatively named “Lily amalgavirus 2” (LAV2). The genomic RNA of LAV2 is 3432 nucleotides (nt) and encodes a large fusion protein with 1053 amino acids (aa). It encodes two open reading frames (ORFs). The two ORFs putative...
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Context 1
... Domain Database (CDD) of the NCBI database. A multiple sequence alignment was made using CLUSTAL X [17], and domain motifs were identied using GeneDoc software [18]. A multiple alignment of the RdRp encoded by LAV2 and those of ten members of the genus Amalgavirus showed that the LAV2 RdRp contains all seven conserved motifs (I to VII) ( Fig. 2A), these results were consistent with LAV1 ...
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... likelihood phylogenies were inferred under the model automatically selected by IQ-TREE for 1000 ultrafast bootstraps [19,20]. Phylogenetic analysis based on the RdRp aa sequence showed that LAV2 clustered into a group with members of the genus Amalgavirus, and LAV2 formed a separate branch in the genus Amalgavirus of the family Amlgaviridae (Fig. 2B). Amino acids sequence comparison showed that the ORF1 and ORF '1+2' sequences of LAV2 had the highest identity (22.56% and 44.78%, respectively) to that of LAV1, and ORF1 had 16.97%-21.88% identity, ORF '1+2' had 33.46%-44.15% identity to the other members of the genus Amalgavirus. Complete nucleotide sequence comparison showed that ...
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