Transcriptomics of plant–virus interactions: a review

Abstract

Posing as one of the major threats for a wide range of plant species, viruses are responsible for huge losses in crop production around the world. The design of new efficient molecular strategies aiming plant resistance requires a holistic view of the complex mechanisms underlying the plant-virus interactions, as well as the discovery of all virus-associated functional components involved in disease. Most of plant viruses present RNA genomes, which aspects of structural diversity and function are frequently difficult to be described using classical molecular biology approaches. As a promising alternative, the advancing field of transcriptomics has shaded light on the understanding of a plethora of plant-virus interactions, in model and crop plants. The advent of RNA sequencing (RNA-seq) and its several variants, such as sRNA-seq and Degradome-seq, has brought the study of plant-virus interactions in a new age. Previously unknown players acting during virus infections are now structurally and functionally described. In this review, we focus on the advances of plant-virus interactions study promoted by the expanding field of transcriptomics. We present an overview of state-ofart of the plant-virus interactions study, regarding important aspects of plant physiology and virology, following by a succinct description of the main transcriptomic approaches used in this field. A detailed description of the use of transcriptomic approaches for some of main plant virus genres during host-interactions is also presented. Finally, we bring concluding remarks discussing the importance of transcriptomics in the study of plant viral diseases, and the future prospects of new approaches in transcriptomics with potential of use in plant-virus interaction studies. Keywords Functional genomics Á Plant physiology Á Plant virology Á Gene expression Á RNA-seq Larissa Goulart Zanardo and Gilza Barcelos de Souza have contributed equally to this manuscript.

Transcriptome Analysis Shows Activation of Stress and Defense Responses by Silencing of Chlorophyll Biosynthetic Enzyme CHLI in Transgenic Tobacco

“…The CPRGs downregulation has been extensively reported as a characteristic feature during the plant-virus interactions [ 3 , 24 , 25 , 26 ]. Because CPRGs downregulation is quite usual in the chlorotic tissues, our current and previous studies [ 18 , 19 , 20 , 27 , 28 ] have consistently supported that the reduced expression of CPRGs preceding visible chlorosis is the primary pathway for chlorosis development.…”

Impaired expression of chloroplast HSP90C chaperone activates plant defense responses leading to a disease symptom-like phenotype

“…Among the transcriptome changes above, downregulation of chloroplast and photosynthesis-related genes (CPRGs) or group 1 genes has been widely reported in symptomatic tissues of different combinations of host plants and viruses (Satoh et al ., 2010; Postnikova and Nemchinov, 2012; Mochizuki et al ., 2014; Zanardo et al ., 2019). Although it is natural that the expression of CPRGs is downregulated in chlorotic tissue, the present study, together with our previous results (Waliullah et al ., 2014, 2015; Bhor et al ., 2017 a , b ) strongly suggest that the CPRGs downregulation preceding visible chlorosis is the primary pathway of chlorosis development.…”

Next generation sequencing and proteomics in plant virology: how is Colombia doing?

“…When the virus overcomes the plant responses, the plant became susceptible, and disease symptoms are triggered. Therefore, in plant-virus interactions, a high transcriptome reprogramming is given, and several sets of genes are modulated in response to the viral infection (Hanley-Bowdoin et al, 2004;Bengyella et al, 2015;Zanardo et al, 2019). The study of the molecular bases of plant-virus interaction is essential for finding genes or pathways involved in plant defense or critical components for virus infection, replication, or movement.…”

“…The study of the molecular bases of plant-virus interaction is essential for finding genes or pathways involved in plant defense or critical components for virus infection, replication, or movement. Taken together, this knowledge is pivotal for crop improvement programs directed at plant resistance to viral diseases (Hillung et al, 2016;Zanardo et al, 2019). Among approaches for transcriptome study, currently, whole transcriptome sequencing commonly called RNA-Seq is one of the most widely applied.…”