RNA-sequencing reveals early, dynamic transcriptome changes in the corollas of pollinated petunias

Abstract

BackgroundPollination reduces flower longevity in many angiosperms by accelerating corolla senescence. This response requires hormone signaling between the floral organs and results in the degradation of macromolecules and organelles within the petals to allow for nutrient remobilization to developing seeds. To investigate early pollination-induced changes in petal gene expression, we utilized high-throughput sequencing to identify transcripts that were differentially expressed between corollas of pollinated Petunia × hybrida flowers and their unpollinated controls at 12, 18, and 24 hours after opening.ResultsIn total, close to 0.5 billion Illumina 101 bp reads were generated, de novo assembled, and annotated, resulting in an EST library of approximately 33 K genes. Over 4,700 unique, differentially expressed genes were identified using comparisons between the pollinated and unpollinated libraries followed by pairwise comparisons of pollinated libraries to unpollinated libraries from the same time point (i.e. 12-P/U, 18-P/U, and 24-P/U) in the Bioconductor R package DESeq2. Over 500 gene ontology terms were enriched. The response to auxin stimulus and response to 1-aminocyclopropane-1-carboxylic acid terms were enriched by 12 hours after pollination (hap). Using weighted gene correlation network analysis (WGCNA), three pollination-specific modules were identified. Module I had increased expression across pollinated corollas at 12, 18, and 24 h, and modules II and III had a peak of expression in pollinated corollas at 18 h. A total of 15 enriched KEGG pathways were identified. Many of the genes from these pathways were involved in metabolic processes or signaling. More than 300 differentially expressed transcription factors were identified.ConclusionsGene expression changes in corollas were detected within 12 hap, well before fertilization and corolla wilting or ethylene evolution. Significant changes in gene expression occurred at 18 hap, including the up-regulation of autophagy and down-regulation of ribosomal genes and genes involved in carbon fixation. This transcriptomic database will greatly expand the genetic resources available in petunia. Additionally, it will guide future research aimed at identifying the best targets for increasing flower longevity by delaying corolla senescence.Electronic supplementary materialThe online version of this article (doi:10.1186/s12870-014-0307-2) contains supplementary material, which is available to authorized users.

Senescence and Abiotic Stress Induce Expression of Autophagy-related Genes in Petunia

“…Flower senescence is genetically determined, and it can be accelerated by pollination. Several petunia ATG genes have been identified and reported to be regulated during pollinationinduced flower senescence (Broderick et al, 2014;Shibuya et al, 2013). We found that PhATG4, PhATG5, PhATG6, PhATG7, PhATG8a, and PhATG13 were also upregulated during the age-induced senescence of unpollinated flowers (Fig.…”

“…x Primers were designed for this manuscript using cDNA sequences identified by Broderick et al (2014). with 0.5°C increments every 5 s).…”

“…Primer sequences and their sources are listed in Table 2. Petunia ATG genes were identified in an RNAseq experiment from pollinated corollas (Broderick et al, 2014), and six genes were selected for further gene expression characterization in this study (Table 2). RNA-seq data are available in the Sequence Read Archive database at National Center for Biotechnology Information [NCBI BioProject ID:PRJNA259884 (National Center for Biotechnology Information Resource Coordinators, 2017)].…”

“…Accelerated leaf senescence has been observed in a number of atg mutants (Doelling et al, 2002;Yoshimoto et al, 2004). An RNA-seq experiment in petunia has also identified eight ATG genes that were upregulated during the pollination-induced senescence of corollas (Broderick et al, 2014). These genes mapped throughout the autophagy Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway, including autophagy induction, vesicle nucleation, and vesicle expansion and completion.…”

“…Flower and leaf longevity is genetically determined, but it can be reduced by environmental stress (Lim et al, 2007;van Doorn and Woltering, 2008). Flower senescence can also be accelerated by pollination (Broderick et al, 2014;van Doorn and Woltering, 2008). The premature senescence of flowers and foliage caused by abiotic stresses reduces visual quality of finished plants, which translates into economic losses for growers and retailers (Cassaniti et al, 2013;Fisher et al, 2016;Villarino and Mattson, 2011;Wu et al, 2017).…”