Open AccessHigh‐resolution expression profiling of selected gene sets during plant immune activation
Author(s) -
Ding Pingtao,
Ngou Bruno Pok Man,
Furzer Oliver J.,
Sakai Toshiyuki,
Shrestha Ram Krishna,
MacLean Dan,
Jones Jonathan D. G.
Publication year - 2020
Publication title -
plant biotechnology journal
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 3.525
H-Index - 115
eISSN - 1467-7652
pISSN - 1467-7644
DOI - 10.1111/pbi.13327
Subject(s) - biology , gene , rna seq , rna , computational biology , gene expression , gene expression profiling , transcriptome , biotinylation , sequence analysis , genetics , microbiology and biotechnology
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.