Small RNA-based interactions between rice and the viruses which cause the tungro disease

Abstract

Rice tungro disease is caused by a complex of two viruses, Rice tungro bacilliform virus (RTBV) and Rice tungro spherical virus (RTSV). To examine the RNAi-based defence response in rice during tungro disease, we characterized the virus-derived small RNAs and miRNAs by Deep Sequencing. We found that, while 21 nt/22 nt (nucleotide) siRNAs are predominantly produced in a continuous, overlapping and asymmetrical manner from RTBV, siRNA accumulation from RTSV were negligible. Additionally, 54 previously known miRNAs from rice, predicted to be regulating genes involved in plant defence, hormone signaling and developmental pathways were differentially expressed in the infected samples, compared to the healthy ones. This is the first study of sRNA profile of tungro virus complex from infected rice plants. The biased response of the host antiviral machinery against the two viruses and the differentially-expressed miRNAs are novel observations, which entail further studies.

Small RNA-Omics for Plant Virus Identification, Virome Reconstruction, and Antiviral Defense Characterization

“…In a few reported cases, virus-derived small RNAs were below detection by small RNA sequencing, although the corresponding virus could be identified by other methods. For instance, in a co-infected rice plant, PCR-positive for rice tungro spherical virus (RTSV, Waikavirus, Secoviridae ) and rice tungro bacilliform virus (RTBV, Tungrovirus, Caulimoviridae ), only RTBV-derived siRNAs could be readily identified by deep sequencing, while RTSV-specific reads were negligible and comparable to those in a control “virus-free” plant ( Zarreen et al, 2018 ). Since another waikavirus and viral species from other genera of Secoviridae are readily identified by small RNA sequencing (see Supplementary Table S1 and references therein) and because rice plants can generate siRNAs from many types of RNA and DNA viruses ( Yan et al, 2010 ; Jiang et al, 2012 ; Xu et al, 2012 ; Kreuze, 2014 ; Rajeswaran et al, 2014a ; Hong et al, 2015 ; Wu J. et al, 2015 ; Xu and Zhou, 2017 ; Yang et al, 2017 ; Jimenez et al, 2018 ; Lan et al, 2018 ; see Supplementary Table S1 and Supplementary List S1 ), the failure to identify RTSV-specific siRNAs can be explained by low titer of the virus.…”

Characteristic Dissection of Xanthomonas oryzae pv. oryzae Responsive MicroRNAs in Rice

“…Likewise, comprehensive analysis of miRNAs roles in rice sheath blight has also been investigated to uncover the pathogenic mechanisms of Rhizoctonia solani (R. solani) [21], and only one paper, to date, reported that osa-miR164a promoted the rice susceptibility to R. solani by targeting the OsNAC60 [16]. Several independent studies have monitored the expression alterations of miRNAs in virally-infected rice plants by small RNA profiling and/or degradome sequencing [22,23]. Experimentally, the manipulation of four miRNAs, osa-miR528 [24], osa-miR171b [25], osa-miR444 [26] and osa-miR319 [27], were involved in rice antiviral defense.…”

Metagenomic Analysis of Marigold: Mixed Infection Including Two New Viruses

“…Since its first description demonstrating that the viral siRNAs could be used for viral genome assembly and virus discovery, sRNA deep sequencing has been widely used in virus identification and a large number of new viruses were recorded [ 45 , 46 ]. But the small size and discontinuity of the siRNA reads and the low number of reads may complicate the genome assembling process, even for accurate virus detection [ 47 , 48 ]. Recently studies reported that deep sequencing of the ribo-depleted total RNA outperformed the sRNA data in terms of the percentage of coverage that could be obtained particularly with the de novo assembled contigs [ 49 ].…”