Abstract
SummaryThe 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.
Highlights
Sequence capture followed by next-generation sequencing has broad applications in cost-effective exploration of biological processes at high resolution (Jupe et al, 2013; Mercer et al, 2014)
To assess differential gene expression during plant immunity, we developed and deployed quantitative sequence capture (CAP-I)
Sequence capture in combination with quantitative RNA sequencing (RNA-seq) enabled cost-effective assessment of the expression profile of a specified subset of genes
Summary
Sequence capture followed by next-generation sequencing has broad applications in cost-effective exploration of biological processes at high resolution (Jupe et al, 2013; Mercer et al, 2014). Sequence capture can help generate high-resolution quantitative data sets to assess changes in abundance of selected genes. 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 (Jones and Dangl, 2006). To assess differential gene expression during plant immunity, we developed and deployed quantitative sequence capture (CAP-I). 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
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