Small RNA and methylation responses in susceptible and tolerant landraces of cassava infected with South African cassava mosaic virus

• Published in: Virus research 2016-10, Vol.225, p.10-22
• Main Authors: Rogans, Sarah Jane, Allie, Farhahna, Tirant, Jason Edward, Rey, Marie Emma Chrissie
• Format: Article
• Language: English
• Subjects: Argonaute Proteins - metabolism; Begomovirus - physiology; Cassava; Disease Susceptibility; Geminiviridae; Geminivirus; Gene Expression Profiling; Host-Pathogen Interactions - genetics; Manihot - physiology; Manihot - virology; Manihot esculenta; Methylation; Phenotype; Plant Diseases - genetics; Plant Diseases - virology; Recovery; RNA, Plant; RNA, Viral; Tolerance; Virus-derived small RNA
• ISSN: 0168-1702; 1872-7492
• DOI: 10.1016/j.virusres.2016.08.011

•Tolerance to South African cassava mosaic virus in TME3 is associated with sequestration of siRNAs, efficient PTGS and lower viral load.•In susceptible T200, high numbers of vsRNAs correlated with high DNA A titres and severe symptoms.•Lack of viral genome methylation was observed in both landraces.•AC1, AV1 and the ORF overlapping regions are potential hotspots for DNA A.•Both BC1 and BV1 on DNA B were evenly targeted by vsRNAs. Endogenous small RNAs (sRNAs) associated with gene regulatory mechanisms respond to virus infection, and virus-derived small RNAs (vsRNAs) have been implicated in recovery or symptom remission in some geminivirus-host interactions. Transcriptional gene silencing (TGS) (24 nt vsRNAs) and post transcriptional gene silencing (PTGS) (21–23 nt vsRNAs) have been associated with geminivirus intergenic (IR) and coding regions, respectively. In this Illumina deep sequencing study, we compared for the first time, the small RNA response to South African cassava mosaic virus (SACMV) of cassava landrace TME3 which shows a recovery and tolerant phenotype, and T200, a highly susceptible landrace. Interestingly, different patterns in the percentage of SACMV-induced normalized total endogenous sRNA reads were observed between T200 and TME3. Notably in virus-infected T200 there was an increase in 21 nt sRNAs during the early pre-symptomatic response (12dpi) compared to mock, while in TME3, the 22 nt sRNA size class was predominant at 32days post infection with SACMV. While vsRNAs of 21–24 nt size classes mapped to the entire SACMV DNA-A and DNA-B genome components in T200 and TME3, vsRNA population counts were lower at 32 (symptomatic stage) and 67 dpi (recovery stage) in tolerant TME3 compared with T200 (non-recovery). It is suggested that the high accumulation of primary vsRNAs, which correlated with high virus titers and severe symptoms in susceptible T200, may be due to failure to target SACMV-derived mRNA. Likewise, in contrast, in TME3 low vsRNA counts may represent efficient PTGS of viral mRNA, leading to a depletion/sequestration of vsRNA populations, supporting a role for PTGS in tolerance/recovery in TME3. Notably, in TME3 at recovery (67 dpi) the percentage (expressed as a percentage of total vsRNA counts) of redundant and non-redundant (unique) 24 nt vsRNAs increased dramatically. Since methylation of the SACMV genome was not detected by bisulfite sequencing, and vsRNA counts targeting the intergenic region (where the promoters reside)