AI Article Synopsis
- High-throughput deep sequencing revealed that Rice stripe virus (RSV) variations consisted mainly of single nucleotide polymorphisms (SNPs) and insertion-deletions (InDels), with SNPs being more uniformly distributed across the genome.
- The InDels were primarily located in intergenic regions and noncoding areas, showing no clear insertion patterns, but all inserted sequences originated from the virus itself.
- Notably, the RSV genome derived from N. benthamiana plants exhibited significantly more SNPs and InDels compared to strains from O. sativa plants, indicating that different host plants exert distinct selection pressures on the virus.
Article Abstract
High-throughput deep sequencing and variant detection showed that variations of Rice stripe virus (RSV) populations obtained from small brown planthopper-transmitted rice plants and sap-inoculated N. benthamiana plants were single nucleotide polymorphisms (SNPs) and insertion-deletions (InDels). The SNPs were more uniform across RSV genome, but InDels occurred mainly in the intergenic regions (IRs) and in the 5' or 3' noncoding regions. There were no clear patterns of InDels, although the inserted sequences were all from virus itself. Six, one, and one non-synonymous substitutions were respectively observed in the RdRP ORF, IR and the movement protein ORF. These non-synonymous substitutions were found to be stable, resulting in new consensus sequences in the NBL11 RSV population. Furthermore, the numbers of SNPs and InDels in RSV genome from N. benthamiana plants were much higher than that from O. sativa plants. These differences are likely caused by selection pressures generated by different host plants.
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| http://dx.doi.org/10.1016/j.virol.2018.08.005 | DOI Listing |
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