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Gene expression was based on alignment to a reference genome using Tophat2 + Cufflinks approach.
Initially, high quality reads from all control and innoculated citrus samples were mapped to reference genome. Using the reference transcriptome annotation of Citrus sinensis reference genome, new transcript and isoform discovery pipeline was performed. All genes (annotated and new ones) are available at 'Download' section. Then, differential analysis was performed, to calculate expression variation between pairs of libraries, including the following information: FPKM expression, Log2(Fold-change), p-value and adjusted (p-value).
Results from DGE analysis for each citrus cultivar can be reach by the following links:
