Revealing impaired pathways in the <i>an11</i> mutant by high‐throughput characterization of <i>Petunia axillaris</i> and <i>Petunia inflata</i> transcriptomes

<jats:title>Summary</jats:title><jats:p>Petunia is an excellent model system, especially for genetic, physiological and molecular studies. Thus far, however, genome‐wide expression analysis has been applied rarely because of the lack of sequence information. We applied next‐generation sequencing to generate, through <jats:italic>de novo</jats:italic> read assembly, a large catalogue of transcripts for <jats:italic>Petunia axillaris</jats:italic> and <jats:italic>Petunia inflata.</jats:italic> On the basis of both transcriptomes, comprehensive microarray chips for gene expression analysis were established and used for the analysis of global‐ and organ‐specific gene expression in <jats:italic>Petunia axillaris</jats:italic> and <jats:italic>Petunia inflata</jats:italic> and to explore the molecular basis of the seed coat defects in a <jats:italic>Petunia hybrida</jats:italic> mutant, <jats:italic>anthocyanin 11</jats:italic> (<jats:italic>an11</jats:italic>), lacking a WD40‐repeat (WDR) transcription regulator. Among the transcripts differentially expressed in <jats:italic>an11</jats:italic> seeds compared with wild type, many expected targets of AN11 were found but also several interesting new candidates that might play a role in morphogenesis of the seed coat. Our results validate the combination of next‐generation sequencing with microarray analyses strategies to identify the transcriptome of two petunia species without previous knowledge of their genome, and to develop comprehensive chips as useful tools for the analysis of gene expression in <jats:italic>P. axillaris</jats:italic>, <jats:italic>P. inflata and P. hybrida.</jats:italic></jats:p>