High‐resolution expression profiling of selected gene sets during plant immune activation. Issue 7 (27th January 2020)

• Record Type: Journal Article
• Authors: Ding, Pingtao; Ngou, Bruno Pok Man; Furzer, Oliver J.; Sakai, Toshiyuki; Shrestha, Ram Krishna; MacLean, Dan; Jones, Jonathan D. G.
• Is Part Of: Plant biotechnology journal. Volume 18:Issue 7(2020)
• Page Start: 1610
• Page End: 1619
• Publication Date: 2020-01-27
• Subjects: sequence capture -- high‐resolution expression profiling -- quantitative RNA‐seq -- data visualization -- transcriptional regulation -- plant immunity -- NLR; Plant biotechnology -- Periodicals; Plant genetic engineering -- Periodicals; 630.272
• DOI: 10.1111/pbi.13327
• Languages: English
• ISSNs: 1467-7644

Abstract

Summary: 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.