Research Article: Genome-wide profiling of piRNAs in the whitefly Bemisia tabaci reveals cluster distribution and association with begomovirus transmission

Date Published: March 12, 2019

Publisher: Public Library of Science

Author(s): Md Shamimuzzaman, Daniel K. Hasegawa, Wenbo Chen, Alvin M. Simmons, Zhangjun Fei, Kai-Shu Ling, Youjun Zhang.

http://doi.org/10.1371/journal.pone.0213149

Abstract

The whitefly Bemisia tabaci MEAM1 is a notorious vector capable of transmitting many plant viruses, resulting in serious crop loss and food shortage around the world. To investigate potential sRNA-mediated regulatory mechanisms in whiteflies that are affected by virus acquisition and transmission, we conducted small RNA (sRNA) deep sequencing and performed genome-wide profiling of piwi-interacting RNAs (piRNAs) in whiteflies that were fed on tomato yellow leaf curl virus (TYLCV)-infected or non-infected tomato plants for 24, 48, and 72 h. In the present study, piRNA reads ranging from 564,395 to 1,715,652 per library were identified and shown to distribute unevenly in clusters (57 to 96 per library) on the whitefly (B. tabaci MEAM1) genome. Among them, 53 piRNA clusters were common for all treatments. Comparative analysis between libraries generated from viruliferous and non-viruliferous whiteflies identified five TYLCV-induced and 24 TYLCV-suppressed piRNA clusters. Approximately 62% of piRNAs were derived from non-coding sequences including intergenic regions, introns, and untranslated regions (UTRs). The remaining 38% were derived from coding sequences (CDS) or repeat elements. Interestingly, six protein coding genes were targeted by the TYLCV-induced piRNAs. We identified a large number of piRNAs that were distributed in clusters across the whitefly genome, with 60% being derived from non-coding regions. Comparative analysis revealed that feeding on a virus-infected host caused induction and suppression of only a small number of piRNA clusters in whiteflies. Although piRNAs primarily regulate the activity of transposable elements, our results suggest that they may have additional functions in regulating protein coding genes and in insect-virus interactions.

Partial Text

Small RNAs (sRNAs) are 19–31 nucleotide (nt) non-coding regulatory elements commonly found in plants, animals, including insects [1–4]. They play important roles in regulating gene expression, transposable elements (TE), or parasite immunity [2,5–7]. Major classes of sRNAs include small interfering RNAs (siRNAs) and microRNAs (miRNAs), which are primarily involved in silencing gene expression [1,2]. Another class of sRNAs known as PIWI-interacting RNAs (piRNAs) has been identified in vertebrate and invertebrate animals [4,5,8,9]. These piRNAs ranging from 26 to 31 nt are considered to regulate the activity of transposable elements as well as to silence the expression of protein coding genes [9–11].

piRNAs are widely known to be involved in silencing the activity of transposable elements. Numerous studies on the piRNA pathway have broadened our understanding of the role of piRNA-mediated regulation of TEs in genetic, biological and developmental processes [40–42]. Additionally, piRNAs also regulate the activity of protein coding genes reported for a number of insect species. More recently different groups have reported that piRNAs target the non-coding sequences as well [8,13]. We found that the highest percentage of piRNAs in whitefly is derived from non-coding sequences (Fig 1B), which makes it challenging to infer their potential functions. However, transposable elements and protein coding genes are also targeted by piRNAs.

 

Source:

http://doi.org/10.1371/journal.pone.0213149

 

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