Optimized method for differential gene expression analysis in non-model species: Case of Cedrela odorata L

The following protocol introduces a targeted methodological approach of differential gene expression analysis, which is particularly beneficial in the context of non-model species. While we acknowledge that biological complexity often involves the interplay of multiple genes in any given biological response our method provides a strategy to streamline this complexity, enabling researchers to focus on a more manageable subset of genes of interest. In this context, red cedar transcriptome (Cedrela odorata L.) and known or hypothetical genes related to the response to herbivory were used as reference. The protocol key points are:•Implementation of a transcriptome thinning process to eliminate redundant and non-coding sequences, optimizing the analysis and reducing processing time.•Use of a custom gene database to identify and retain coding sequences with high precision.•Focus on specific genes of interest, allowing a more targeted analysis for specific experimental conditions. This approach holds particular value for pilot studies, research with limited resources, or when rapid identification and validation of candidate genes are needed in species without a reference genome.