Global alteration of microRNAs and transposon-derived small RNAs in cotton (Gossypium hirsutum) during Cotton leafroll dwarf polerovirus (CLRDV) infection

Abstract

Small RNAs (sRNAs) are a class of non-coding RNAs ranging from 20- to 40-nucleotides (nts) that are present in most eukaryotic organisms. In plants, sRNAs are involved in the regulation of development, the maintenance of genome stability and the antiviral response. Viruses, however, can interfere with and exploit the silencing-based regulatory networks, causing the deregulation of sRNAs, including small interfering RNAs (siRNAs) and microRNAs (miRNAs). To understand the impact of viral infection on the plant sRNA pathway, we deep sequenced the sRNAs in cotton leaves infected with Cotton leafroll dwarf virus (CLRDV), which is a member of the economically important virus family Luteoviridae. A total of 60 putative conserved cotton miRNAs were identified, including 19 new miRNA families that had not been previously described in cotton. Some of these miRNAs were clearly misregulated during viral infection, and their possible role in symptom development and disease progression is discussed. Furthermore, we found that the 24-nt heterochromatin-associated siRNAs were quantitatively and qualitatively altered in the infected plant, leading to the reactivation of at least one cotton transposable element. This is the first study to explore the global alterations of sRNAs in virus-infected cotton plants. Our results indicate that some CLRDV-induced symptoms may be correlated with the deregulation of miRNA and/or epigenetic networks.

High-throughput sequencing reveals small RNAs involved in ASGV infection

“…These virus-derived siRNAs (vsiRNAs) subsequently regulate viral RNA expression through a process known as RNA silencing. In addition to vsiRNA production, plants’ endogenous small RNA (sRNA) pathways are also affected by viral infection [6–8]. …”

microRNAs as reference genes for quantitative PCR in cotton

“…Cotton ( Gossypium hirsutum ) plants of the cultivar FM966 (Fibermax966), susceptible to Cotton blue disease, were grown in green house conditions (26 +/-2°C) and at 30 days pos germination were infected with CLRDV using viruliferous aphids ( Aphis gossypii Glover) as described previously [37]. Leaves of non-infected plants were used as non-infected control.…”

“…All of them show uniform and stable expression levels in leaves and during infection caused by CLRDV [37]. Four protein-coding reference genes already described for cotton were selected: actin 4 ( GhACT ), elongation factor 1-alfa 5 ( GhEF1 ), protein phosphatase 2A ( GhPP2A1 ) and ubiquitin 14 ( GhUBQ14 ) [35, 36].…”

“…For that, the putative myo-inositol oxygenase GhMIOX (EST number 193219349 ortholog of At4g26260 ) [46] and miR164 [47] relative expression levels were assayed in flowers versus leaves. Relative expression of cotton GhDCL2 and 4 [39], and of miR159, 164, 2118, 2910 and 3476 [37] were assayed in virus infected versus uninfected plants. All the primers used are described S1 Table.…”

The MicroRNA156 system: A tool in plant biotechnology

“…In fact, many miRNAs were also shown to be involved in tolerance to cold and heat in model plants (Sunkar and Zhu, 2004;Liu et al, 2008;Lv et al, 2010) and sugarcane (Thiebaut et al, 2012), oxidation in Arabidopsis (Sunkar et al, 2006), iron and sulfur deprivation in Arabidopsis (Kong and Yang, 2010;Kawashima et al, 2011), and heavy metal toxicity response in plants such as Besides abiotic stress, a number of distinct miRNAs respond to biotic stress agents, including viruses, bacteria, fungi, and nematodes, with evidence provided in Arabidopsis (Katiyar-Agarwal et al, 2006;Navarro et al, 2006;Hewezi et al, 2008;Ruiz-Ferrer and Voinnet, 2009), tobacco (Bazzini et al, 2007), Brassica (He et al, 2008), soybean , and cotton (Romanel et al, 2012). According to Padmanabhan et al (2013), SPL6 is a novel positive regulator in Nucleotide Binding-Leucine Rich Repeat (NB-LRR) receptormediated plant innate immunity in Arabidopsis.…”