RNA-seq and microarray complement each other in transcriptome profiling.

Area of Science:

• Microbiology
• Genomics
• Molecular Biology

Background:

• RNA sequencing (RNA-seq) and microarray are common for genome-wide transcriptome profiling.
• Existing studies show good correlation between RNA-seq and microarray data.
• The complementary nature of these methods, considering their strengths and limitations, remains unexplored.

Purpose of the Study:

• To investigate whether RNA-seq and microarray complement each other in transcriptome profiling.
• To assess the performance of both methods in detecting known target genes of the HrpX transcription factor.

Main Methods:

• Transcriptome profiling of wild-type and hrpX mutant strains of *Xanthomonas citri subsp. citri* using RNA-seq and microarray.
• Comparative analysis of gene expression levels quantified by both methods.
• Validation of differentially expressed genes (DEGs) using quantitative reverse transcription PCR (qRT-PCR).

Main Results:

• Gene expression levels from RNA-seq and microarray showed strong correlation (Spearman's rho > 0.76) at absolute and relative levels.
• Expression data from both methods correlated well with qRT-PCR results for DEGs (Spearman's rho = 0.58 to 0.94).
• While 72% of known HrpX target genes were detected by both methods, 28% were uniquely identified by either RNA-seq or microarray, alongside 55 newly identified DEGs.

Conclusions:

• RNA-seq and microarray analyses are complementary for comprehensive transcriptome profiling.
• Together, these methods provide a more complete understanding of the HrpX regulome.
• The combined approach enhances the identification of novel differentially expressed genes.