Abstract
A novel potyvirus was discovered in pecan (Carya illinoensis) showing leaf mosaic symptom through the use of deep sequencing of small RNAs. The complete genome of this virus was determined to comprise of 9,310 nucleotides (nt), and shared 24.0% to 58.9% nucleotide similarities with that of other Potyviridae viruses. The genome was deduced to encode a single open reading frame (polyprotein) on the plus strand. Phylogenetic analysis based on the whole genome sequence and coat protein amino acid sequence showed that this virus is most closely related to Lettuce mosaic virus. Using electron microscopy, the typical Potyvirus filamentous particles were identified in infected pecan leaves with mosaic symptoms. Our results clearly show that this virus is a new member of the genus Potyvirus in the family Potyviridae. The virus is tentatively named Pecan mosaic-associated virus (PMaV). Additionally, profiling of the PMaV-derived small RNA (PMaV-sRNA) showed that the most abundant PMaV-sRNAs were 21-nt in length. There are several hotspots for small RNA production along the PMaV genome; two 21-nt PMaV-sRNAs starting at 811 nt and 610 nt of the minus-strand genome were highly repeated.
Highlights
RNA silencing is an antiviral immunity and fundamental cellular mechanism that regulates gene expression through the production of small RNAs
It contains a single long open reading frame (ORF), which encodes a large polyprotein that is cleaved into 11 mature proteins including P3N-PIPO (P3 N-terminus-pretty interesting potyvirus ORF)[8], which is produced by ribosomal frameshift during translation or transcriptional slippage during RNA synthesis in the P3 cistron[9]
After searching against the GenBank database, we found 35 contigs which shared some similarities with the genome sequences of other potyviruses, such as turnip mosaic virus (TuMV), lettuce mosaic virus (LMV), sweet potato feathery mottle virus (SPFMV) and plum pox virus (PPV), suggesting that one or more potyviruses were present in our sample
Summary
RNA silencing is an antiviral immunity and fundamental cellular mechanism that regulates gene expression through the production of small RNAs (sRNAs). The typical genomic RNA is a linear positive sense single-strand RNA ranging in size from 9,000 ~ 12,000 nucleotides It contains a single long ORF, which encodes a large polyprotein that is cleaved into 11 mature proteins including P3N-PIPO (P3 N-terminus-pretty interesting potyvirus ORF)[8], which is produced by ribosomal frameshift during translation or transcriptional slippage during RNA synthesis in the P3 cistron[9]. Pecan (Carya illinoensis) is native to central and southern North America It is an excellent multipurpose tree, providing a source of nutritious edible nuts, furniture-grade wood, and aesthetic value for the landscape. Small RNA profiles of this virus suggest that the RNA silencing-mediated antiviral immunity mechanism is applicable to pecan To our knowledge, this the first viral disease found in pecan
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