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Genome-wide piRNA profiles of the virus transmitting whitefly, Bemisia tabaci during feeding on TYLCV-infected tomato

Kai-shu Ling: USDA-ARS

<div>Piwi-interacting RNAs (piRNAs) are 26-31 nucleotide (nt) non-coding small RNAs (sRNAs) commonly found in animals. The whitefly, <em>Bemisia tabaci </em>MEAM1 is a devastating vector capable of transmitting many plant viruses, including <em>Tomato yellow leaf curl virus </em>(TYLCV), to important crop plants. To investigate potential sRNA mediated regulatory mechanisms in whiteflies that are affected by virus acquisition and transmission, we performed genome-wide profiling of piRNAs in whiteflies feeding on tomato plants with or without infection by TYLCV for 24, 48 and 72 h. Results revealed that piRNAs were expressed as clusters throughout the whitefly genome. piRNAs ranging from 564,395 to 1,715,652 were identified in sRNA libraries prepared at three time points and aggregated in between 57 and 96 clusters. Comparative analysis across all time points identified 53 commonly expressed piRNA clusters. We also identified five TYLCV-induced and 24 TYLCV-suppressed piRNA clusters. Approximately 62% of all identified piRNAs are derived from non-coding sequences that include intergenic regions, introns, and UTRs with unknown functions. The remaining 38% of piRNAs are derived from coding sequences (CDS) and repeat elements. Six protein coding genes were targeted by the TYLCV-induced piRNAs, but their function in anti-viral defense or virus transmission is not obvious. TEs targeted by piRNA clusters include both class I retrotransposons such as Gypsy, Copia, and LINEs and class II DNA transposons such as MITE, hAT, and TcMar. Our enhanced understanding of whitefly piRNA pathway might facilitate the identification of novel targets for RNAi control.</div>