Changes in maize transcriptome in response to maize Iranian mosaic virus infection

Abstract

BackgroundMaize Iranian mosaic virus (MIMV, genus Nucleorhabdovirus, family Rhabdoviridae) causes an economically important disease in maize and other gramineous crops in Iran. MIMV negative-sense RNA genome sequence of 12,426 nucleotides has recently been completed. Maize Genetics and Genomics database shows that 39,498 coding genes and 4,976 non-coding genes of maize have been determined, but still some transcripts could not be annotated. The molecular host cell responses of maize to MIMV infection including differential gene expression have so far not been elucidated.Methodology/Principal findingsComplementary DNA libraries were prepared from total RNA of MIMV-infected and mock-inoculated maize leaves and sequenced using Illumina HiSeq 2500. Cleaned raw transcript reads from MIMV-infected maize were mapped to reads from uninfected maize and to a maize reference genome. Differentially expressed transcripts were characterized by gene ontology and biochemical pathway analyses. Transcriptome data for selected genes were validated by real-time quantitative PCR.Conclusion/SignificanceApproximately 42 million clean reads for each treatment were obtained. In MIMV-infected maize compared to uninfected plants, 1689 transcripts were up-regulated and 213 transcripts were down-regulated. In response to MIMV infection, several pathways were activated in maize including immune receptor signaling, metabolic pathways, RNA silencing, hormone-mediated pathways, protein degradation, protein kinase and ATP binding activity, and fatty acid metabolism. Also, several transcripts including those encoding hydrophobic protein RCI2B, adenosylmethionine decarboxylase NAC transcription factor and nucleic acid binding, leucine-rich repeat, heat shock protein, 26S proteasome, oxidoreductases and endonuclease activity protein were up-regulated. These data will contribute to the identification of genes and pathways involved in plant-virus interactions that may serve as future targets for improved disease control.

Transcriptomics of plant–virus interactions: a review

“…Another group of genes, which expression were altered, in viral infection was the photosynthesis genes as: phytochrome B, calmodulin binding and ferredoxin-NADP root (fnr1). This is because the induction of these genes may be related to yellow stripe and chlorosis symptoms on the leaves (Ghorbani et al 2018a). Here again we can verify the importance of studies using transcriptomic tools for the understanding of different mechanisms of the virus-plant interaction.…”

“…Analyses about the viral-host interaction were also perfomed. Maize plants infected and not infected by MIMV displayed different metabolic profiles modulated by MIMV infection, including biosynthesis of secondary metabolites, proteasome, protein processing in endoplasmic reticulum, photosynthesis and two pathways with significant roles in pathogen defense: fatty acid (FA) metabolism and degradation (Ghorbani et al 2018a). These pathways are important because have been showed that FA are able to modulate the basal effector-triggered and systemic immunity in plants, besides to be biosynthetic precursors for cuticular components or the phytohormone jasmonic acid (Kachroo and Kachroo 2009).…”

Detection and profiling of circular RNAs in uninfected and maize Iranian mosaic virus-infected maize

“…Contaminating genomic DNA was removed during mRNA purification. Whole transcriptome RNA was enriched by Macrogen by depleting ribosomal RNA, and six independent cDNA libraries were prepared using poly(A) enrichment from 3 plants each of MIMV-infected and non-infected maize [27].…”

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

“…RNA-Seq has been used to find insights in several plant-virus interactions, including model plants such as Arabidopsis thaliana (Sun et al, 2016;Wu et al, 2016), plants of agronomical importance such as Oryza sativa (Blazquez et al, 2013;Wong et al, 2015), Zea mays (Chakrabarty et al, 2018), Manihot esculenta (Fang et al, 2014;Amuge et al, 2017;Anjanappa et al, 2018), Solanum tuberosum (Goyer et al, 2015;Stare et al, 2017) and tropical fruits such as C. papaya (Madroñero et al, 2018). However, to date (04-10-2019), a Google Scholar search, the NCBI PMC database, and the Web of Science using the queries "plant", "virus", "interaction", "transcriptome", "RNA-Seq", and "Colombia" with different combinations did not yield any results for plant-virus interactions research developed in Colombia.…”