Identification of RNAi-Related Genes and Transcriptome Assembly of Loblolly Pine (Pinus taeda, L.) Seedlings Exposed to Insect-Specific dsRNA

Abstract

Considerable research has focused on gene silencing in tree-feeding insects, but how trees recognize and process double-stranded RNA (dsRNA) engineered to target plant pests is unknown. We performed transcriptomic assembly, preliminary differential expression analysis, and in silico annotation on loblolly pine (Pinus taeda, L.) seedlings exposed to southern pine beetle-specific dsRNA. This pilot study sought to elucidate the baseline response of seedlings challenged with insect-specific dsRNA. Treated and untreated seedlings were sequenced and following transcriptome assembly 20 RNAi-related proteins (RRPs) were annotated. Differential gene expression analysis conducted using DESeq2 followed by pathway enrichment revealed 7131 differentially expressed transcripts, of which 33% were upregulated and 67% were downregulated. Only two RRPs selected for analysis were upregulated in treated seedlings, showing a lack of detectable RNAi response with our methodology. Beyond RNAi-related proteins, pathway enrichment mapped to immune response systems and genetic and cellular processing. Upregulated transcripts included autophagy, amino sugar and nucleotide sugar metabolism, and plant hormone signal transduction. Downregulated transcripts included RNA degradation and fatty acid metabolism pathways. Multiple DICER-LIKE and ARGONAUTE proteins were also annotated in five other North American pines, revealing diversity among these crucial proteins. Understanding host plant response to RNAi-mediated pest control is essential to further develop this technology against tree pests.