Circadian Oscillation of the Lettuce Transcriptome under Constant Light and Light–Dark Conditions

Abstract

Although, the circadian clock is a universal biological system in plants and it orchestrates important role of plant production such as photosynthesis, floral induction and growth, there are few such studies on cultivated species. Lettuce is one major cultivated species for both open culture and plant factories and there is little information concerning its circadian clock system. In addition, most of the relevant genes have not been identified. In this study, we detected circadian oscillation in the lettuce transcriptome using time-course RNA sequencing (RNA-Seq) data. Constant light (LL) and light–dark (LD) conditions were used to detect circadian oscillation because the circadian clock has some basic properties: one is self-sustaining oscillation under constant light and another is entrainment to environmental cycles such as light and temperature. In the results, 215 contigs were detected as common oscillating contigs under both LL and LD conditions. The 215 common oscillating contigs included clock gene-like contigs CCA1 (CIRCADIAN CLOCK ASSOCIATED 1)-like, TOC1 (TIMING OF CAB EXPRESSION 1)-like and LHY (LATE ELONGATED HYPOCOTYL)-like, and their expression patterns were similar to those of Arabidopsis. Functional enrichment analysis by GO (gene ontology) Slim and GO Fat showed that the GO terms of response to light stimulus, response to stress, photosynthesis and circadian rhythms were enriched in the 215 common oscillating contigs and these terms were actually regulated by circadian clocks in plants. The 215 common oscillating contigs can be used to evaluate whether the gene expression pattern related to photosynthesis and optical response performs normally in lettuce.

The circadian clock shapes the Arabidopsis transcriptome by regulating alternative splicing and alternative polyadenylation

“…So, our results suggest that there are two subgroups of circadian genes: one group with oscillation behavior both at light-dark condition and continuous light are only regulated by core clock mechanism, while the other group with continuous light-specific oscillation are regulated by core clock mechanism and also by another pathway that is effective at light-dark condition. Our result is consistent with the conclusion of a previous study in which they adopted a different approach for rhythmicity analysis (35) and also with the finding of a recent study showing continuous-dark specific oscillation in the liver of mice (44) We also observed the same phenomenon with the oscillating AS and APA events: some events became rhythmic only under constant light, and the oscillation profiles of AS and APA events dramatically altered with the change of light regimen. All these suggest that plants organize genome-wide transcriptional and posttranscriptional oscillation according to the timing and duration of light and dark periods.…”

“…1A, Supplemental Fig. S1A), similar to the observation in lettuce (35). Our RT-qPCR analyses of LHCA6 and RBCS2B genes verified that these genes oscillate under continuous light, but not at light-dark condition.…”

Changes in ambient temperature are the prevailing cue in determining Brachypodium distachyon diurnal gene regulation

“…Most estimates of daily gene expression patterns have been determined for protein-coding genes using gene or genome tiling microarrays (Edwards et al, 2006;Covington et al, 2008;Michael et al, 2008b;Hazen et al, 2009;Khan et al, 2010;Filichkin et al, 2011). More recently, RNAseq was applied to measure diurnal or circadian-associated transcript expression in sugarcane (Saccharum officinarum), S. viridis, Sedum album, lettuce, Douglas fir, Physcomitrella patens, and several algal species (Hotta et al, 2013;Zones et al, 2015;Higashi et al, 2016;Cronn et al, 2017;Huang et al, 2017;Ferrari et al, 2019;Wai et al, 2019). Estimates for the proportion of protein-coding genes that are controlled by the circadian clock generally range between 6% and 15%.…”

Complex interactions between day length and diurnal patterns of gene expression drive photoperiodic responses in a perennial C4 grass

“…Given the nature of circadian rhythm, time-series experiments coupled with transcriptome studies represent key steps towards understanding the complex sensing and signalling process of photoperiod changes (Doherty & Kay, 2010). Although many RNA-seq studies have provided a global perspective that describes the contribution of circadian rhythmic to gene regulation networks in plants (Higashi, Aoki, Nagano, Honjo, & Fukuda, 2016;Khan, Rowe, & Harmon, 2010;Michael et al, 2008;Xu et al, 2011), most studies focus on day-night cycles under certain day-length conditions or circadian rhythms under constant light conditions. Few studies to date have globally examined the impact of day length on the diurnal rhythmic patterns of the transcriptome (but see Dalchau et al, 2010;Michael et al, 2008).…”