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

Area of Science:

• Environmental science
• Genomics
• Molecular biology

Background:

• The US Environmental Protection Agency (EPA) initiated a challenge to find cost-effective, high-throughput RNA sequencing technologies.
• This initiative supports a new program in ecological high-throughput transcriptomics.

Purpose of the Study:

• To identify and evaluate innovative RNA sequencing technologies for ecological applications.
• To assess the performance of different sequencing approaches based on predefined criteria.

Main Methods:

• A federal government challenge invited global innovators to submit RNA sequencing solutions.
• Five solutions from three teams were tested using nine pooled RNA samples from four aquatic species (36 samples total).
• Evaluation criteria included accuracy, precision, transcriptome coverage, cost per sample, and throughput.

Main Results:

• The targeted TempO-Seq approach, using sentinel gene sets, was ranked highest.
• All submitted solutions demonstrated viability with varying strengths and weaknesses.
• Transcriptomic points of departure using sentinel genes were comparable to whole transcriptome sequencing.

Conclusions:

• A variety of RNA sequencing technologies and approaches are suitable for ecological high-throughput transcriptomics.
• Transparent reporting of methods is crucial for integrating these technologies into science-based decision-making.
• Sentinel gene set approaches offer a viable alternative to whole transcriptome sequencing for certain applications.