De novo transcriptome assembly and the effect of foreign RNA contamination

Multiple next-generation-sequencing (NGS)-based studies are enabled by the availability of a reference genome of the target organism. Unfortunately, several organisms remain unannotated due to the cost and complexity of generating a complete (or close to complete) reference genome. These unannotated organisms, however, can also be studied if a de novo reference transcriptome is assembled from whole transcriptome sequencing experiments. This technology is cost effective and widely used but is susceptible to off-target RNA contamination. In this manuscript, we present GTax, a taxonomy structured database of genomic sequences that can be used with BLAST to detect and remove foreign contamination in RNA sequencing samples before assembly. In addition, we investigate the effect of foreign RNA contamination on a de novo transcriptome assembly of Solanum lycopersicum (tomato). Our study demonstrates that removing foreign contamination in sequencing samples reduces the number of assembled chimeric transcripts.