GTax: improving de novo transcriptome assembly by removing foreign RNA contamination

Area of Science:

• Bioinformatics
• Genomics
• Transcriptomics

Background:

• Complete reference genomes are unavailable for many organisms due to cost and complexity.
• De novo reference transcriptomes offer a cost-effective alternative but are prone to RNA contamination.
• Foreign RNA contamination can lead to inaccurate downstream analyses, including chimeric transcript formation.

Purpose of the Study:

• To introduce GTax, a novel taxonomy-structured database for identifying and removing foreign contamination in RNA sequencing data.
• To demonstrate the utility of GTax in improving the quality of de novo transcriptome assemblies.
• To validate the effectiveness of contamination removal in reducing chimeric transcripts.

Main Methods:

• Development of GTax, a database organizing genomic sequences by taxonomic structure.
• Utilizing BLAST for sequence alignment to detect foreign contaminants within RNA sequencing samples.
• Performing de novo transcriptome assembly on Solanum lycopersicum (tomato) samples before and after contamination removal.

Main Results:

• GTax effectively identifies foreign sequences in RNA-Seq data.
• Removal of identified contaminants prior to assembly significantly reduces the incidence of chimeric transcripts.
• The de novo transcriptome assembly of tomato showed a marked decrease in chimeric transcripts after employing GTax for contamination control.

Conclusions:

• GTax provides a valuable tool for ensuring the accuracy of de novo transcriptome assemblies by addressing RNA contamination.
• Implementing GTax can improve the reliability of genomic data, especially for organisms lacking a reference genome.
• This approach enhances the quality of transcriptomic data, facilitating more robust biological insights.