Two-dimensional analysis provides molecular insight into flower scent of Lilium ‘Siberia’

Abstract

Lily is a popular flower around the world not only because of its elegant appearance, but also due to its appealing scent. Little is known about the regulation of the volatile compound biosynthesis in lily flower scent. Here, we conducted an approach combining two-dimensional analysis and weighted gene co-expression network analysis (WGCNA) to explore candidate genes regulating flower scent production. In the approach, changes of flower volatile emissions and corresponding gene expression profiles at four flower developmental stages and four circadian times were both captured by GC-MS and RNA-seq methods. By overlapping differentially-expressed genes (DEGs) that responded to flower scent changes in flower development and circadian rhythm, 3,426 DEGs were initially identified to be candidates for flower scent production, of which 1,270 were predicted as transcriptional factors (TFs). The DEGs were further correlated to individual flower volatiles by WGCNA. Finally, 37, 41 and 90 genes were identified as candidate TFs likely regulating terpenoids, phenylpropanoids and fatty acid derivatives productions, respectively. Moreover, by WGCNA several genes related to auxin, gibberellins and ABC transporter were revealed to be responsible for flower scent production. Thus, this strategy provides an important foundation for future studies on the molecular mechanisms involved in floral scent production.

SMRT and Illumina RNA Sequencing and Characterization of a Key NAC Gene LoNAC29 during the Flower Senescence in Lilium oriental ‘Siberia’

“…The room temperature ranged from 15 to 25 • C. The air humidity was kept at 60-70%. The development stages of the lily flower were defined according to Shi et al [17], with minor modification: stage 1, flower bud grows to the largest size, color of tepals does not turn white; stage 2, early opening, the upper one third of the tepals were opened with an angle of 30 degrees; stage 3, full opening, the tepals extend to the maximum extent; stage 4, flowers are senescent, the tepals are wilting (Figure 1). Flowers of different stages were sampled at the same time, with three biological replicates for each stage.…”

“…Cogent analysis was carried out with default parameters, according to the method described in [27]. The k-mer profiles of non-redundant transcripts from our SMRT sequencing (group B) and three published transcriptomes based on Illumina sequencing in lilies [16][17][18] (group A) were created, pairwise distances of transcripts were calculated, and similar transcripts were clustered into families based on their k-mer values. For each family, similar transcripts were reconstructed into one new transcript by using a De Bruijn graph method.…”

“…Through Illumina sequencing, several transcription factors, such as Ethylene Responsive Factor (ERF), Auxin Responsive Factor (ARF), basic Helix-Loop-Helix (bHLH), HD-Zip, and MADS-box, were found to be related to flower senescence in petunia (Petunia hybrida), and their function was verified by virus-induced gene silencing (VIGS) [15]. In lilies, Illumina sequencing is also widely used to screen key genes involved in flower aroma synthesis [16,17], vernalization of bulbs [18], and flower color formation [19]. Illumina sequencing is efficient for obtaining gene expression patterns and for screening for important differentially expressed genes.…”

“…spp.) is a perennial bulb flower of the Lilium genus, and one of the top four cut flowers in the world [17]. The vase life of lily cut flowers is relatively short, because senescence seriously affects its ornamental quality, leading to great economic loss.…”

Transcriptomic profiling of the flower scent biosynthesis pathway of Cymbidium faberi Rolfe and functional characterization of its jasmonic acid carboxyl methyltransferase gene

“…With the rapid development of “omics” approaches, high-throughput studies have been applied to obtain enormous amounts of data for elucidating the metabolic pathways of different organisms as well as their underlying molecular mechanisms. Because RNA-seq enables the analysis of the transcripts of large numbers of active genes and complex metabolite networks in species without a clear genomic background, it has become a preferred method to guide the direction for extensive performance improvement [20, 24–27]. Since the main component of flower fragrance in Cymbidium faberi is MeJA, the blooming flowers and withered flowers were compared to screen out differentially expressed genes (DEGs) and related metabolic pathways by comparative transcriptome sequencing, focusing especially on flower scent biosynthesis.…”