Transcriptome profiling of the cold response and signaling pathways in Lilium lancifolium

Abstract

BackgroundLilium lancifolium, a very important cold-resistant wild flower for lily cold resistance breeding, is widely distributed in southwestern and northeastern China. To gain a better understanding of the cold signaling pathway and the molecular metabolic reactions involved in the cold response, we performed a genome-wide transcriptional analysis using RNA-Seq.ResultsApproximately 104,703 million clean 90- bp paired-end reads were obtained from three libraries (CK 0 h, Cold-treated 2 h and 16 h at 4°C); 18,736 unigenes showed similarity to known proteins in the Swiss-Prot protein database, and 15,898, 13,705 and 1849 unigenes aligned to existing sequences in the KEGG and COG databases (comprising 25 COG categories) and formed 12 SOM clusters, respectively. Based on qRT-PCR results, we studied three signal regulation pathways —the Ca2+ and ABA independent/dependent pathways —that conduct cold signals to signal transduction genes such as LlICE and LlCDPK and transcription factor genes such as LlDREB1/CBF, LlAP2/EREBP, LlNAC1, LlR2R3-MYB and LlBZIP, which were expressed highly in bulb. LlFAD3, Llβ-amylase, LlP5CS and LlCLS responded to cold and enhanced adaptation processes that involve changes in the expression of transcripts related to cellular osmoprotectants and carbohydrate metabolism during cold stress.ConclusionsOur study of differentially expressed genes involved in cold-related metabolic pathways and transcription factors facilitated the discovery of cold-resistance genes and the cold signal transcriptional networks, and identified potential key components in the regulation of the cold response in L lancifolium, which will be most beneficial for further research and in-depth exploration of cold-resistance breeding candidate genes in lily.Electronic supplementary materialThe online version of this article (doi:10.1186/1471-2164-15-203) contains supplementary material, which is available to authorized users.

De novo assembly and characterization of stress transcriptome and regulatory networks under temperature, salt and hormone stresses in Lilium lancifolium

“…And also, several studies have revealed its better capacity for resisting high and low temperature, and changing drought than other lilies. While, the in-depth plant protection and the research of the gene expression profile under various abiotic stresses is imperative facing the critical reduction of L. lancifolium, which could contribute to improve other plants' stress resistance quality by using molecular techniques [12].…”

Virus-induced gene silencing (VIGS) in <i>Lilium leichtlinii</i> using the <i>Cucumber mosaic virus</i> vector

“…An abundance of Lilium gene sequences have been identified via NGS in an effort to characterize agriculturally important traits Villacorta-Martin et al 2015;Wang et al 2014), and as a result, the establishment of reversegenetics tools is an urgent issue for the functional characterization of the identified sequences. Because VIGS is able to alter plant phenotypes in relatively short periods of time and allows researchers to characterize phenotypes that might be lethal in stable transgenic plants, the technique should be valuable for the functional screening of expressed sequences.…”

“…Several genes involved in anthocyanin and carotenoid biosyntheses have been studied in lilies (Jeknić et al 2012;Lai et al 2012;Nakatsuka et al 2003Nakatsuka et al , 2009Yamagishi et al 2010aYamagishi et al , 2010b. Recently, the transcriptomes of several lily organs have been sequenced using next-generation sequencing (NGS), and a variety of potentially important novel genes have been identified Villacorta-Martin et al 2015;Wang et al 2014), although their specific functions remain to be determined.…”

Mechanisms of vegetative propagation in bulbs : a molecular approach

“…focused on sequencing the transcriptome of leaves (Wang et al 2014), bulblets (Li et al 2014b) and meristem-enriched tissue (Villacorta- Martin et al 2015) of different Lilium cultivars, using the Illumina HiSeq sequencing platform. These studies resulted in the identification of 37,843 unigenes for leaves (Wang et al 2014), 52,901 unigenes in bulblets (Li et al 2014b) and 42,430 genes for the meristem-enriched lily tissues (Villacorta- Martin et al 2015).…”