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Title: Global Analyses of Small Interfering RNAs from Sour Orange seedlings Infected with Different Citrus tristeza virus Genotypes

item SAPONARI, MARIA - Institute De Virologia
item GIAMPETRUZZI, ANNALISA - University Of Bari
item DODDAPANENI, HARSHA - University Of Iowa
item LOCONSOLE, GIULIANA - University Of Bari
item XIONG, ZHONGGUO - University Of Arizona
item SALDARELLI, PASQUALE - Institute De Virologia
item Yokomi, Raymond - Ray

Submitted to: International Organization of Citrus Virologists Proceedings
Publication Type: Abstract Only
Publication Acceptance Date: 10/22/2010
Publication Date: 11/7/2010
Citation: Saponari, M., Giampetruzzi, A., Doddapaneni, H., Loconsole, G., Xiong, Z., Saldarelli, P., Yokomi, R.K. 2010. Global Analyses of Small Interfering RNAs from Sour Orange seedlings Infected with Different Citrus tristeza virus Genotypes[abstract]. International Organization of Citrus Virologists Proceedings. 31:s64.

Interpretive Summary:

Technical Abstract: RNA silencing is a sequence-specific regulatory mechanism in development and maintenance of genome integrity and functions in plant antiviral defense mechanisms. Small interfering RNAs (siRNAs) are key mediators of RNA silencing. To study CTV-host interactions and disease expression, profiles of viral (v) siRNAs associated with Citrus tristeza virus (CTV) infections were assessed from large-scale siRNA sequencing from sour orange (SO) seedlings infected with single or mixed infections of a T3-, VT-, or a non-standard CTV genotype showing different symptom phenotypes. Short reads (ca. 8-10 million obtained with Illumina Genome Analyzer II) were processed: 21 and 24 nucleotide size classes were predominant from CTV-infected SO; whereas 24nt size class was dominate in healthy SO. The distribution and frequencies of CTV-derived reads from 18 to 26bp in length were aligned on the CTV genome. The most abundant CTV siRNAs were within the 3’ end encompassing the genes encoding for P18, P13, P20, P23 and 3’UTR. Approximately 60% of the CTV-siRNAs were sense vs. 40% antisense and predominantly in the 21 and 22nt size classes. These patterns were similar for all three genotypes tested and generally equal in abundance. As in other plants, this suggests the Dicer-like proteins (DCL)-2 and DCL-4 are playing the main role in biogenesis of CTV-derived siRNAs in citrus. When vsiRNAs were grouped based on the 5’ terminal nucleotide, all genotypes including positive and negative strands, showed a preference for U at the 5’-end. This is known to stabilize vsiRNAs through its association with the RNA-silencing-related protein Argonaute 1 (AGO1). This is a first report of vsiRNAs derived from different CTV genotypes infecting SO and has resulted in a strategy for accurate read assignment for different CTV genotypes and comparative analysis of vsiRNAs profiles in association with symptom expression. This data will help determine the mechanism of cross protection and should lead to development of stable cross protection strategies that prevent economic damage of virulent CTV strains.