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

Takanobu Higashi,Hirokazu Fukuda,Mie N Honjo,Koh Aoki,Atsushi J Nagano

doi:10.3389/fpls.2016.01114

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.

Highlights

The circadian clock is a universal biological system in plants that has been well-studied in Arabidopsis (Harmer et al, 2000; Haydon et al, 2011; Farré and Weise, 2012)
972 and 144 contigs were detected as unique contigs that oscillated only under LL or LD conditions, respectively; and 279 contigs were detected as shared contigs that oscillated under both LL and LD conditions (Figure 1B)
This is not surprising, given that the periodicity of gene expression depends on light conditions and there was a clear difference between LL and LD conditions

Summary

Introduction

The circadian clock is a universal biological system in plants that has been well-studied in Arabidopsis (Harmer et al, 2000; Haydon et al, 2011; Farré and Weise, 2012). Controlling circadian clocks has potential to enhance productivity of cultivated species such as broccoli, petunia and lettuce by effects on growth, floral induction and pest resistance (Goodspeed et al, 2013; Fenske et al, 2015; Higashi et al, 2015; Tanigaki et al, 2015; Thiruvengadam et al, 2015; Zhai et al, 2015). These results show that controlling circadian clocks has potential to achieve high efficiency in plant production. Because circadian clocks are readily controlled by external stimuli, especially light and temperature, one target among plant production systems is closed-type plant factories as environmental parameters are readily tightly controlled (Rensing and Ruoff, 2002; Fukuda et al, 2013)

Methods

Results

Conclusion