Figure 1

Schematic representation of the design and analysis pipeline. Three Ae. aegypti strains, LVP, CTM and RexD, were used to generate one RNA-seq library each starting from total RNA of 90 mosquitoes (45 blood-fed and 45 sugar-fed). Approximately 100 nucleotides were sequenced at both ends of each cDNA using Illumina technology. RNA-seq libraries were analyzed using the TopHat/Cufflinks suite with the AaegL1.2 genome annotation. The AaegL1.2 genome annotation was used as guide for gene annotation in Cufflinks, which was run to allow the identification of novel transcriptional units (NTUs). NTUs were annotated by Blast2GO and SNPs identified by Freebayes. SNPs in annotated genes were identified by Freebayes. The effect of the SNPs on the predicted coding sequence was identified by snpEff using the AaegL1.2 genome annotation as a strict reference for gene annotation.