High-resolution expression profiling of selected gene sets during plant immune activation

Pingtao Ding, Bruno Pok Man Ngou, Oliver J. Furzer, Toshiyuki Sakai, Ram Krishna Shrestha, Dan MacLean, Jonathan D. G. Jones

Research output: Contribution to journalArticlepeer-review

10 Citations (Scopus)
15 Downloads (Pure)

Abstract

The plant immune system involves detection of pathogens via both cell-surface and intracellular receptors. Both receptor classes can induce transcriptional reprogramming that elevates disease resistance. To assess differential gene expression during plant immunity, we developed and deployed quantitative sequence capture (CAP-I). We designed and synthesized biotinylated single-strand RNA bait libraries targeted to a subset of defense genes, and generated sequence capture data from 99 RNA-seq libraries. We built a data processing pipeline to quantify the RNA-CAP-I-seq data, and visualize differential gene expression. Sequence capture in combination with quantitative RNA-seq enabled cost-effective assessment of the expression profile of a specified subset of genes. Quantitative sequence capture is not limited to RNA-seq or any specific organism and can potentially be incorporated into automated platforms for high-throughput sequencing.

Original languageEnglish
Pages (from-to)1610-1619
Number of pages10
JournalPlant Biotechnology Journal
Volume18
Issue number7
Early online date8 Jan 2020
DOIs
Publication statusPublished - Jul 2020

Keywords

  • ARABIDOPSIS
  • BIOSYNTHESIS
  • DEFENSE RESPONSES
  • DISEASE RESISTANCE
  • ESSENTIAL COMPONENT
  • ISOCHORISMATE
  • NLR
  • READ ALIGNMENT
  • REPRESSION
  • SALICYLIC-ACID
  • SYSTEMIC ACQUIRED-RESISTANCE
  • data visualization
  • high-resolution expression profiling
  • plant immunity
  • quantitative RNA-seq
  • sequence capture
  • transcriptional regulation

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