Time-Course Microarray Analysis Reveals Differences between Transcriptional Changes in Tomato Leaves Triggered by Mild and Severe Variants of Potato Spindle Tuber Viroid

Abstract

Viroids are small non-capsidated non-coding RNA replicons that utilize host factors for efficient propagation and spread through the entire plant. They can incite specific disease symptoms in susceptible plants. To better understand viroid-plant interactions, we employed microarray analysis to observe the changes of gene expression in “Rutgers” tomato leaves in response to the mild (M) and severe (S23) variants of potato spindle tuber viroid (PSTVd). The changes were analyzed over a time course of viroid infection development: (i) the pre-symptomatic stage; (ii) early symptoms; (iii) full spectrum of symptoms and (iv) the so-called ‘recovery’ stage, when stem regrowth was observed in severely affected plants. Gene expression profiles differed depending on stage of infection and variant. In S23-infected plants, the expression of over 3000 genes was affected, while M-infected plants showed 3-fold fewer differentially expressed genes, only 20% of which were specific to the M variant. The differentially expressed genes included many genes related to stress; defense; hormone metabolism and signaling; photosynthesis and chloroplasts; cell wall; RNA regulation, processing and binding; protein metabolism and modification and others. The expression levels of several genes were confirmed by nCounter analysis.

Genome-Wide Transcriptomic Analysis Reveals Insights into the Response to Citrus bark cracking viroid (CBCVd) in Hop (Humulus lupulus L.)

“…The comprehensive analysis of gene expression patterns in viroid-infected plant is crucial to understanding the cellular and molecular mechanisms for viroid pathogenesis and further development of disease management strategies. Previously published studies have used different methods, such as differential display reverse transcriptase PCR (DDRT-PCR) [ 19 ] and microarray analysis [ 20 , 21 ], to gain an overview of altered gene expression in host plant upon viroid infection. Recently, next-generation sequencing (NGS) technologies, such as Solexa/Illumina RNA-Seq and digital gene expression (DGE), have provided a novel and powerful platform for global profiling of transcriptome and have several advantages over microarray analysis in terms of sensitivity of range of detection, higher reproducibility, and cost efficiency [ 22 ].…”

Identification and Molecular Mechanisms of Key Nucleotides Causing Attenuation in Pathogenicity of Dahlia Isolate of Potato Spindle Tuber Viroid

“…Changes in host transcriptome caused by viroid infection have been analyzed in various viroid–host combinations [ 53 , 54 , 55 , 56 , 57 , 58 , 59 , 60 ]. Infected plants are characterized by the fluctuations in several observables such as expressions of genes involved in plant innate immunity, defense responses, signal transduction and hormone metabolism.…”

“…The fluctuations lead to the development of disease symptoms. The pathogenicity-related protein 1B1 ( PR1b1 ), TCHS2 and expansin ( slEXPA ) genes [ 32 , 53 , 59 , 64 , 65 , 66 ], among others, can be clearly associated with viroid disease symptoms. Samples collected from PSTVd mutants infected plants were analyzed to determine the correlation between the expression of three previously identified genes and the severity of disease symptoms.…”

“…Chalcone synthase is a key enzyme in flavonoid biosynthesis pathways and catalyzes the synthesis of various secondary metabolites [ 73 ]. Previously, the tomato cultivars ‘Rutgers’ and ‘Heinz 1706’ infected with PSTVd-I, PSTVd-S23 (GenBank: X76846), or PSTVd-M (GenBank: X76844), exhibited stunted growth and leaf malformation as well as a significant reduction in the levels of expression of TCHS2 gene [ 53 , 59 ]. Interestingly, PSTVd-I, PSTVd-S23, and PSTVd-M are all PSTVd isolates with a C at nucleotide position 42 and a deletion of U at position 64.…”

“…Furthermore, it was shown in various viroid–host combinations that genes involved in plant innate immunity, mainly calcium-dependent protein kinase and mitogen-activated protein kinase cascade or genes involved in hypersensitive response, cell wall enhancement, and hormone signaling were activated by viroid infection. These observations also suggested that the expression of a large number of genes, such as those involved in defense responses, hormone metabolisms, signal transduction, photosynthesis, chloroplast, cell wall, and regulation of RNA expression are affected by viroid infection, leading to the development of disease symptoms [ 53 , 54 , 55 , 56 , 57 , 58 , 59 , 60 ].…”