RNA-seq of Petunia floral buds

This experiment was carried out to analyse the expression differences of genes involved in anthocyanin and flavonol production between Petunia species. RNA was sequenced from mature buds (sepals and reproductive organs removed) of P. axillaris ssp. axillaris N, P. exserta, and the three genotypes segregating from an introgression line between the two species: IL2-1 (region of chromosome II segregating in P. exserta genetic background). Three biological replicates were sequenced per P. a. ssp. axillaris N and P. exserta sample; four biological replicates were sequenced for each of the introgression line genotypes. For each biological replicate, three buds were homogenized in liquid nitrogen and RNA extracted using Trizol (Life Technologies) according to the manufacturer''s description. RNA was sent to the Lausanne Genomic Technologies Facility (Lausanne, Switzerland) for sequencing. Cluster generation was performed with the sequencing libraries using the Illumina TruSeq PE Cluster Kit (v.3). Samples were paired-end sequenced for 50 bp. The resulting sequences were used to construct a de novo transcriptome assembly for P. exserta, and for differential expression analysis.