Altered Expression of MicroRNAs and Target mRNAs in Tomato Root and Stem Tissues upon Different Viral Infection

Abstract

MicroRNAs (miRNAs) are post‐transcriptional regulators that are involved in numerous biological processes in both plants and animals. In plants, root and stem tissues play essential roles in their anchorage to soil as well as in nutrient and water uptake and transfer. We have quantified the expression alterations of eleven miRNAs and their target mRNAs in tomato root and stem tissues after infection with Cucumber mosaic virus (CMV)‐Fny, CMV‐FnyΔ2b (a CMV‐Fny 2b‐deletion mutant), CMV‐Fny‐satT1 (CMV‐Fny plus an aggressive satellite (sat) RNA variant satT1) and Tomato aspermy virus (TAV)‐Bj. From 21 days postinoculation onwards, we found the stem tissues were ‘hollow’ in CMV‐Fny‐satT1 infected tomatoes, and a ‘fibrosis’ phenotype was observed in stems of TAV‐Bj infected plants. In addition, this phenotype was associated with the decreasing of tomato lateral root numbers upon the two infections. Consistence with these phenotypic alterations, tomato miRNA/mRNA levels upon different viral infections were changed by different degrees. Based on our results, the interference of different viral infections with tomato miRNA pathways were analysed and the correlations between miRNAs/mRNAs expression alterations and tomato symptoms were discussed.

The advance of tomato disease-related microRNAs

“…On the one hand, TFs regulate miRNAs by binding to the upstream cis-acting elements of MIRNA genes. In tomato, the conserved miR169 was identified in response to CMV, TAV, ToLCV, B. cinerea Plant Cell Rep and P. infestans (Feng et al 2013b;Jin et al 2012;Naqvi et al 2010;Sun et al 2014). Gene promoter analysis indicated that Box-W1 (one kind of pathogen-induced ciselements in plants) is located in the MIR169 promoter region .…”

“…In 21 days post-inoculation (dpi) of cucumber mosaic virus (CMV)-and tomato aspermy virus (TAV)-infected tomato stems, miR156 noticeably accumulated, which correlated to the hollow and fibrosis phenotype (Feng et al 2013b). MiR156 has been a pivotal regulator in shoot maturation (Wu and Poethig 2006) and trichome distribution (Yu et al 2010) through targeting Squamosa promoter binding protein-like (SPL) transcription factor (TF).…”

“…et al (2010),Feng et al (2013b),Jin and Wu (2015),Lang et al et al (2010),Feng et al (2011),Jin and Wu (2015),Luan et al (2015),Naqvi et al et al (2012), (2013a), Jin et al (2012), Naqvi et al (2010), Tsushima et al (2015) miR162 B. cinerea, CMV, PSTVd, TAV, ToLCV DCL1 Cillo et al (2009), Diermann et al (2010), Feng et al (2011), Jin and Wu (2015), Naqvi et al et al (2009), Feng et al (2009), Jin and Wu (2015), Luan et al (2015), Naqvi et al et al (2009), Feng et al (2013b), Jin and Wu (2015), Lang et al (2011), Tsushima et al al. (2010), Feng et al (2012), Lang et al (2011), Naqvi et al et al (2009), Feng et al (2013a), Jin and Wu (2015), Lang et al (2011), Naqvi et al et al (2013b), Jin et al (2012), Naqvi et al (2010), Sun et al (2014) miR171 B. cinerea, CMV, PSTVd, TAV, ToLCV SCL Feng et al (2013a), Jin et al (2012), Lang et al (2011), Naqvi et al (2008), Tsushima et al et al (2010), Feng et al (2013a), Jin and Wu (2015), Naqvi et al et al (2009), Diermann et al (2010), Feng et al (2013b), Jin and Wu (2015), Lang et al et al (2010), Jin and Wu (2015), Lang et al (2011), Luan et al (2015), Naqvi et al PSTVd, P. syringae NBS-LRR Jin and Wu (2015), Luan et al (2015), Shivaprasad et al (2012), Sun et al -LRR Luan et al (2015), Sun et al (2014), Tsushima et al (2015) SPL squamosa promoter-binding protein-like, MYB myeloblastosis, ARF auxin response factor, DCL dicer-like, HD-ZIP homeodomain leucine zipper, NAC NAM/ATAF/CUC, AGO argonaute, NF-YA nuclear transcription factor Y subunit alpha, SCL scarecrow-like, AP2 apetala 2, TCP TEOSINTE BRANCHED/CYCLOIDEA/PCF GRF growth regulating factor, CSD copper/zinc binding superoxide dismutase, UBE ubiquitin conjugating enzyme, NBS-LRR nucleotide binding site-leucine-…”

A dynamic degradome landscape on miRNAs and their predicted targets in sugarcane caused by Sporisorium scitamineum stress

“…During the late stage of wheat stripe rust infection, wheat miR408 was downregulated, and the expression of target gene chemocyanin-like protein ( CLP1 ) was induced, which in turn inhibited the growth of mycelia in leaf [ 22 ]. After inoculation of tomato stalks with cucumber mosaic virus (CMV) and tomato aspermy virus (TAV), miR156 was accumulated, resulting in hollow and fibrotic stalks [ 23 ]. In addition, tomato plants overexpressing miR156 showed phenotypic symptoms that are similar to that of pathogen infections, indicating that miR156 regulates the interaction of tomato with pathogens [ 24 ].…”

Detection of disease in Cucurbita maxima Duch. ex Lam. caused by a mixed infection of Zucchini yellow mosaic virus, Watermelon mosaic virus, and Cucumber mosaic virus in Southeast China using a novel small RNA sequencing method

“…In total, 9 C. maxima (cultivar: Miben) plants were planted in a greenhouse with a temperature range of 23 °C to 28 °C, 60% humidity, and natural light. Each single strain of ZYMV, WMV, and CMV was reconstituted from infectious clones as described previously (Feng et al, 2013), and maintained on Nicotiana tabacum . Inoculation was carried out by mechanical inoculation (abrade sap mix with SiC particles) on the first true leaves of 14-day-old C. maxima seedlings, with sap prepared from leaf tissues of diseased samples from the experimental field of Jihua National Agricultural Technology Garden homogenized in 20 volumes of 100-mM sodium phosphate buffer, pH 7.2.…”