Genome-wide miRNA and piRNA profiles of the vector whitefly, Bemisia tabaci during feeding on Tomato yellow leaf curl virus-infected tomato

The whitefly, Bemisia tabaci MEAM1 is a devastating vector capable of transmitting hundreds of plant viruses, including Tomato yellow leaf curl virus (TYLCV), to important food and fiber crops. Here we performed genome-wide profiling of micro RNAs (miRNAs) and piwi-interacting RNAs (piRNAs) in whiteflies after feeding on TYLCV-infected tomato or uninfected tomato for 24, 48 and 72 h. Overall, 160 miRNAs were discovered, 68 of which were conserved and 92 were B. tabaci-specific miRNAs. Majority of the genes that were predicted to be targeted by miRNAs had gene ontologies related to metabolic processes. We identified two miRNAs that were differentially expressed in whiteflies when fed on TYLCV-infected tomato compared to whiteflies that fed on uninfected tomato. The identified piRNAs were expressed as clusters throughout the whitefly genome. A total of 53 piRNA clusters were expressed across all time points and treatments, while 5 piRNA clusters were exclusively expressed in whiteflies that fed on TYLCV-infected tomato, and 24 clusters were exclusively expressed in whiteflies that fed on uninfected tomato. Approximately 62% of all identified piRNAs were derived from non-coding sequences that included intergenic regions, introns, and UTRs with unknown functions. The remaining 38% of piRNAs were derived from coding sequences (CDS) and repeat elements. Transposable elements targeted by piRNA clusters included both class I retrotransposons such as Gypsy, Copia, and LINEs and class II DNA transposons such as MITE, hAT, and TcMar. Lastly, six protein coding genes were targeted in whiteflies that fed on TYLCV-infected tomato. Information on how TYLCV influences miRNA and piRNA expression in whiteflies provides a greater understanding of regulatory pathways involved in mediating whitefly-virus interactions, and will facilitate the identification of novel targets for RNAi control. Overall design: Deep sequencing of small RNAs was isolated from total RNA from whiteflies fed on either TYLCV-infected tomato or uninfected tomato for 24, 48, and 72 h. Three biological replicates were performed for each time point.

白粉虱（Bemisia tabaci MEAM1）作为一种破坏力极强的媒介生物，能够传播包括番茄黄化卷叶病毒（TYLCV）在内的数百种植物病毒，对重要的粮食和纤维作物构成严重威胁。本研究对白粉虱在食用感染TYLCV的番茄或未感染番茄后24小时、48小时和72小时内的miRNA（小干扰RNA）和piRNA（piwi相互作用RNA）的全基因组进行了分析。总计发现了160个miRNA，其中68个为保守型，92个为白粉虱特异性miRNA。预测为miRNA靶向的基因中，大部分与代谢过程相关的基因本体学。在白粉虱食用感染TYLCV的番茄与食用未感染番茄的对比中，我们鉴定出两种在表达上有差异的miRNA。所识别的piRNA以簇状形式表达于白粉虱的基因组中。在所有时间点和处理中，共表达53个piRNA簇，其中5个簇仅在食用感染TYLCV的番茄的白粉虱中表达，而24个簇仅在食用未感染番茄的白粉虱中表达。大约62%的piRNA来自非编码序列，包括基因间区、内含子和未知功能的UTR。剩余的38%piRNA来自编码序列（CDS）和重复元件。piRNA簇靶向的转座子包括I类反转录转座子，如Gypsy、Copia和LINEs，以及II类DNA转座子，如MITE、hAT和TcMar。最后，在食用感染TYLCV的番茄的白粉虱中，有六个蛋白质编码基因被靶向。关于TYLCV如何影响白粉虱中miRNA和piRNA表达的资料，有助于深入理解介导白粉虱与病毒相互作用的调节通路，并将促进RNAi控制新靶点的发现。总体设计：对食用感染TYLCV的番茄或未感染番茄的白粉虱在24小时、48小时和72小时后提取的总RNA中的小RNA进行了深度测序。每个时间点进行了三个生物重复。