Comparison of whole transcriptome and targeted RNA sequencing for ecological high-throughput transcriptomics

In 2019, the US EPA organized a federal government challenge aimed at identifying and evaluating low cost, high-throughput, RNA sequencing technologies that could support the aims of a new program in ecological high-throughput transcriptomics. Innovators worldwide were invited to demonstrate their solutions in an open competition. Each responding Solver was provided a set of nine pooled RNA samples from each of four species of aquatic organisms (n = 36 samples total). Five Solutions submitted by three Solver teams were evaluated according to a pre-defined scoring rubric that considered accuracy, precision, transcriptome coverage for each species, cost per sample, and throughput. A targeted approach (TempO-Seq) that employed sentinel gene sets representing 5–11 % of the whole transcriptome was ranked as the top solution. However, all were viable approaches and had specific strengths and weaknesses. In a follow up investigation, transcriptomic points of departure based on a sentinel gene set were generally found to fall within a factor of 10 or less of those based on whole transcriptome sequencing. Results support the conclusion that a wide range of sequencing technologies and approaches are suitable for the work. Detailed and transparent reporting of the approaches used will help support uptake in science-based decision-making.