Profile of small interfering RNAs from cotton plants infected with the polerovirus Cotton leafroll dwarf virus

Abstract

BackgroundIn response to infection, viral genomes are processed by Dicer-like (DCL) ribonuclease proteins into viral small RNAs (vsRNAs) of discrete sizes. vsRNAs are then used as guides for silencing the viral genome. The profile of vsRNAs produced during the infection process has been extensively studied for some groups of viruses. However, nothing is known about the vsRNAs produced during infections of members of the economically important family Luteoviridae, a group of phloem-restricted viruses. Here, we report the characterization of a population of vsRNAs from cotton plants infected with Cotton leafroll dwarf virus (CLRDV), a member of the genus Polerovirus, family Luteoviridae.ResultsDeep sequencing of small RNAs (sRNAs) from leaves of CLRDV-infected cotton plants revealed that the vsRNAs were 21- to 24-nucleotides (nt) long and that their sequences matched the viral genome, with higher frequencies of matches in the 3- region. There were equivalent amounts of sense and antisense vsRNAs, and the 22-nt class of small RNAs was predominant. During infection, cotton Dcl transcripts appeared to be up-regulated, while Dcl2 appeared to be down-regulated.ConclusionsThis is the first report on the profile of sRNAs in a plant infected with a virus from the family Luteoviridae. Our sequence data strongly suggest that virus-derived double-stranded RNA functions as one of the main precursors of vsRNAs. Judging by the profiled size classes, all cotton DCLs might be working to silence the virus. The possible causes for the unexpectedly high accumulation of 22-nt vsRNAs are discussed. CLRDV is the causal agent of Cotton blue disease, which occurs worldwide. Our results are an important contribution for understanding the molecular mechanisms involved in this and related diseases.

Comparative analysis of virus-specific small RNA profiles of three biologically distinct strains of Potato virus Y in infected potato (Solanum tuberosum) cv. Russet Burbank

“…The findings were also similar to the findings of Kreuze et al (2009) where they reported the prevalence of positive sense vsiRNAs over negative sense in virus-infected sweet potato plants. Another study conducted by Silva et al (2011) on cotton leafroll dwarf virus (CLDV) reported equal population of sense versus antisense derived vsiRNAs in virus-infected cotton plants. The ratio of sense versus antisense vsiRNAs was in the range of 1.1:1 to 1.25:1 in all the sRNA libraries generated from PVY-infected potato plants.…”

Comparison of small RNA profiles in Nicotiana benthamiana and Solanum lycopersicum infected by polygonum ringspot tospovirus reveals host-specific responses to viral infection

“…Although 22 nt cucumber mosaic virus-vsRNAs produced by AtDCL2 were poor effectors of antiviral defense in Arabidopsis , predominant accumulation of 22-nt vsRNAs has been shown in previous studies on plant virus infections, such as cotton leafroll dwarf virus in cotton (Silva et al, 2011), cymbidium ring spot virus in N. benthamiana (Donaire et al, 2009), and turnip crinkle virus infections in Arabidopsis (Deleris et al, 2006). In these latter interactions, activity of the silencing-suppressor proteins P19 and P38, which, respectively, sequesters 21 nt duplex siRNAs (Vargason et al, 2003), and blocks AtDCL4 activity (Azevedo et al, 2010), could determine the observed high accumulation of 22 nt vsRNAs.…”

Literature review of baseline information to support the risk assessment of RNAi‐based GM plants

“…The "basal" plant state found in Arabidopsis (or, for example, cotton (Silva et al, 2011)) is four Dicers, which presumably evolved through duplications of an ancestral Dicer (Margis et al, 2006) (Figure 48). Some plants (such as monocots) have higher counts of Dicer homologsthere are five in poplar and eight in rice; the additional Dicers evolved through duplications of one of the four "basic" plant Dicers (Margis et al, 2006;Kapoor et al, 2008;.…”