title: Revealing impaired pathways in the an11 mutant by high-throughput characterization of Petunia axillaris and Petunia inflata transcriptomes.
abstract: 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 de novo read assembly, a large catalogue of transcripts for Petunia axillaris and Petunia inflata. 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 Petunia axillaris and Petunia inflata and to explore the molecular basis of the seed coat defects in a Petunia hybrida mutant, anthocyanin 11 (an11), lacking a WD40-repeat (WDR) transcription regulator. Among the transcripts differentially expressed in an11 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 P. axillaris, P. inflata and P. hybrida.
authors.affiliation: Department of Biotechnology, University of Verona, Strada Le Grazie 15, 37134 Verona, Italy.
authors.forename: Sara
authors.initials: S
authors.lastname: Zenoni
authors.forename: Nunzio
authors.initials: N
authors.lastname: D'Agostino
authors.forename: Giovanni B
authors.initials: GB
authors.lastname: Tornielli
authors.forename: Francesca
authors.initials: F
authors.lastname: Quattrocchio
authors.forename: Maria L
authors.initials: ML
authors.lastname: Chiusano
authors.forename: Ronald
authors.initials: R
authors.lastname: Koes
authors.forename: Jan
authors.initials: J
authors.lastname: Zethof
authors.forename: Flavia
authors.initials: F
authors.lastname: Guzzo
authors.forename: Massimo
authors.initials: M
authors.lastname: Delledonne
authors.forename: Luigi
authors.initials: L
authors.lastname: Frusciante
authors.forename: Tom
authors.initials: T
authors.lastname: Gerats
authors.forename: Mario
authors.initials: M
authors.lastname: Pezzotti
mesh_terms: D001483:Base Sequence; D016384:Consensus Sequence; D015536:Down-Regulation / Q000235:genetics; D035264:Flowers / Q000166:cytology / Q000235:genetics / Q000502:physiology; D020869:Gene Expression Profiling; D018506:Gene Expression Regulation, Plant / Q000235:genetics; D018745:Genome, Plant / Q000235:genetics; D059014:High-Throughput Nucleotide Sequencing; D058977:Molecular Sequence Annotation; D009154:Mutation; D020411:Oligonucleotide Array Sequence Analysis; D032306:Petunia / Q000737:chemistry / Q000166:cytology / Q000235:genetics* / Q000502:physiology; D010936:Plant Extracts / Q000737:chemistry; D010940:Plant Proteins / Q000235:genetics* / Q000378:metabolism; D044945:Proanthocyanidins / Q000032:analysis / Q000096:biosynthesis*; D018749:RNA, Plant / Q000235:genetics; D036226:Seedlings / Q000166:cytology / Q000235:genetics / Q000502:physiology; D012639:Seeds / Q000737:chemistry / Q000166:cytology / Q000235:genetics / Q000502:physiology; D017422:Sequence Analysis, DNA; D014157:Transcription Factors / Q000235:genetics / Q000378:metabolism; D059467:Transcriptome; D015854:Up-Regulation / Q000235:genetics
chemical_list: D010936:Plant Extracts; D010940:Plant Proteins; D044945:Proanthocyanidins; D018749:RNA, Plant; D014157:Transcription Factors; C013221:proanthocyanidin