Validation of differential gene expression of transcriptome assembly via nanostring® technologies analysis platform

Abstract

Ganoderma boninense is a white rot fungus that causes basal stem rot (BSR) disease that contributes to profit loss in the oil palm industry. Transcriptome profiling using RNA-sequencing (RNA-seq) approach had been conducted to discover the differential express transcripts which relate to BSR disease that might potentially be utilised as biomarker for selection of Ganoderma tolerant oil palm. To validate the expression of transcripts in medium throughput manner after large scale transcriptome profile, new approaches are available such as reverse transcription quantitative PCR (RT-qPCR) of Fluidigm's BioMark HD system that runs on microfluidic chips, and NanoString's nCounter system that gives absolute counts of the mRNA itself without involving cDNA synthesis and PCR amplification. In this study, differential express transcripts were identified from the comparative transcriptomic of the transcriptome of near-rot section of basal stem tissue of oil palm infected with G. boninense against healthy non-infected palms. Then, whether the transcript abundances measured using RNA-seq method was correlated with the nCounter system for the selected transcripts was assessed. Based on the selected 24 transcripts, transcript abundances measured was significantly correlated between RNA-seq and nCounter system (p < 0.001). Out of 24 assessed transcripts, three transcripts were highly similar in the measured expression profiles using both platforms. From the three transcripts, only two showed potential as biomarkers for detecting G. boninense tolerant trait in oil palm.