Insect-specific virus discovery platform for biological control of western flower thrips

Overview

Western flower thrips (Frankliniella occidentalis) is one of the most destructive crop pests worldwide and a super-vector of plant viruses that cause major economic losses across vegetables, ornamentals, and field crops. This program applies metagenomic virome discovery to identify insect-specific viruses (ISVs) that naturally replicate only in thrips and are transmitted to their progeny. These ISVs represent a promising, targeted approach to biologically control WFT populations and reduce their ability to transmit crop diseases, offering an alternative or complement to chemical insecticides.

The value proposition for partners is access to a curated pipeline of novel ISV candidates sourced from geographically and host-diverse WFT populations, along with the genomic and phylogenetic characterization needed to prioritize candidates for downstream genetic engineering aimed at suppressing thrips fitness and/or vector competence.

Technical specifications

Discovery approach:

• Deep transcriptome sequencing of WFT populations collected from diverse crops and surrounding weed reservoirs across North Carolina and California field sites
• Ribosomal RNA depletion prior to cDNA library preparation to capture both poly(A) and non-poly(A) viral transcripts, enabling exhaustive discovery of DNA and RNA viruses
• Paired-end multiplex sequencing on an Illumina NovaSeq 600 SP platform
• Removal of host-derived reads by mapping against the WFT reference genome, followed by de novo assembly of unmapped reads
• BLAST-based virus identification and phylogenetic analysis performed by a specialist in virus evolution

Sample scope:

• Pooled insect samples spanning developmental stages and tissues
• Field populations supplied through Extension cooperators across multiple crops and reservoir habitats
• Existing poly(A)-enriched RNAseq libraries leveraged to expand candidate discovery

Deliverables:

• Catalog of ISV genome sequences with phylogenetic placement
• Prioritized list of candidates suitable for genetic modification targeting WFT fitness and/or vector competence

Technology readiness level

This is an early-stage discovery and validation program (TRL 3–4). The team has generated foundational RNAseq resources from WFT developmental stages and tissues and is now expanding into comprehensive rRNA-depleted sequencing to capture the full viral diversity, including non-poly(A) genomes. Field sampling during the 2021 season across North Carolina and California populations will provide the ecological breadth needed to identify broadly distributed and novel ISV candidates. Downstream genetic modification of selected ISVs for biocontrol applications represents the next phase of development and would benefit from partners with expertise in insect transformation, regulatory science, and biocontrol product development.