Overview
The client sought bioinformatics support to test a hypothesis regarding plant-insect interactions. The study involved analyzing small RNA and mRNA sequencing data from multiple plant genotypes treated with various insect species and mock treatments. The goal was to identify plant genes potentially targeted by insect-derived small RNAs, providing insights into plant defense mechanisms.
Our client
An academic research institute in Germany specializing in agricultural research. The organization sought our bioinformatics solutions to integrate and analyze complex, multi-dimensional plant genomics data.
Client’s challenge
The client’s challenge involved handling diverse and high-dimensional data generated from small RNA sequencing and mRNA sequencing experiments. With multiple plant genotypes and various insect treatment conditions, extracting meaningful insights from this dataset required a tailored, scalable, and reproducible genome analysis approach.
Client’s goals
The main objective was to decode complex plant-insect interactions by identifying plant genes potentially targeted by insect-derived small RNAs. The research intended to lay the groundwork for pest-resistance strategies using modern bioinformatics solutions.
Our approach
To address the client’s needs, we designed a multi-step bioinformatics workflow to analyze small RNA and mRNA sequencing data systematically. Our approach involved:
Data processing and normalization
We collected small RNA sequencing and mRNA sequencing data from various plant genotypes exposed to insect treatments, and conducted quality control to assess base quality, GC content, and adapter contamination.
Target gene prediction
Using computational algorithms, we identified insect-derived small RNAs that may target plant genes. Further, we screened for putative target genes by evaluating their complementarity and binding affinity to the insect-derived small RNAs.
Functional annotation of candidate genes
Performed functional annotation of candidate genes to identify their biological roles in plant defense mechanisms and mapped candidate genes to known plant genomics defense-related pathways or gene families involved in insect resistance.
Literature validation and reporting
We conducted an extensive literature review to verify the biological relevance of identified genes, linking them to known insect-resistance pathways or stress tolerance in plants. We also prepared a detailed report on the candidate genes, including their functions, importance, and association to the insect-resistance pathways.
Our solution
- Created a robust analysis pipeline to screen for plant target genes putatively affected by insect small RNAs.
- Conducted foundational literature research to validate and support the identified candidate genes.
Conclusion
The bioinformatics solution identified high-confidence candidate genes linked to insect resistance, with 70% supported by literature. This provided a strong foundation for targeted research and breeding, enabling the client to decode complex plant-insect interactions and advance pest resistance strategies through data curation and advanced computational biology services.
