Genes differentially transcribed in any area. Clustering analysis was performed on the 416 transcripts showing a significant differential expression in any area compared to the reference strain Ifakara (P ≤ 0.001 and FC ≥ 3). Clustering of transcripts and conditions were based on differences between mean Log2 ratios in each area versus reference using Euclidean distance and complete linkage algorithm. Colour scale (green to red) indicates fold change versus reference strain. The number of transcripts represented in each cluster is shown within bracket. Gene Ontology (GO) term enrichment analyses were performed for each main cluster with all terms belonging to the category ‘molecular function’. GO terms showing an adjusted P value ≤ 0.05 were considered significantly enriched compared to all detected transcripts (hypergeometric test followed by Benjamini and Hockberg multiple testing correction). Colour scale (white to orange) indicates enrichment significance. Few non-significant GO terms are displayed for clarity.