The landscape of abiotic and biotic stress-responsive splice variants with deep RNA-seq datasets in hot pepper

Abstract

Alternative splicing (AS) is a widely observed phenomenon in eukaryotes that plays a critical role in development and stress responses. In plants, the large number of RNA-seq datasets in response to different environmental stressors can provide clues for identification of condition-specific and/or common AS variants for preferred agronomic traits. We report RNA-seq datasets (350.7 Gb) from Capsicum annuum inoculated with one of three bacteria, one virus, or one oomycete and obtained additional existing transcriptome datasets. In this study, we investigated the landscape of AS in response to environmental stressors, signaling molecules, and tissues from 425 total samples comprising 841.49 Gb. In addition, we identified genes that undergo AS under specific and shared stress conditions to obtain potential genes that may be involved in enhancing tolerance to stressors. We uncovered 1,642,007 AS events and identified 4,354 differential alternative splicing genes related to environmental stressors, tissues, and signaling molecules. This information and approach provide useful data for basic-research focused on enhancing tolerance to environmental stressors in hot pepper or establishing breeding programs.

Beyond NGS data sharing for plant ecological resilience and improvement of agronomic traits

“…This method has identified genes, NLR genes and transcription factors that respond to biotic and abiotic stresses, revealing potential stress-related genes for complex environmental conditions. Transcriptome research is vital for understanding how plants respond to stresses by identifying active genes in various conditions 23 , 24 . The innovative integrated network analysis strategy utilized in this study offers a valuable approach for comprehending gene regulation and can be used to enhance crop resilience against environmental stressors in various plant species.…”

An improved bacterial mRNA enrichment strategy in dual RNA sequencing to unveil the dynamics of plant-bacterial interactions

“…These include an unlimited dynamic range, reduced bias, independence from annotations, and the absence of issues related to probe design or cross-hybridization [ 9 , 10 ]. RNA-seq can distinguish between different mRNA isoforms and non-coding RNAs (ncRNAs), as well as detect splice junctions and precisely locate transcript boundaries [ 11 – 14 ]. In spite of these advantages, RNA-seq for the transcriptional analysis of plant-microbe interactions remains technically challenging, particularly with the microbial transcriptomics.…”