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.

Keywords: circadian clocks; enrichment; lettuce; oscillations; plant factories; transcriptome.

FIGURE 1

Scheme of oscillating analysis and the number of detected contigs. (A) Numbers in colored boxes indicate the detected number of contigs. (B) Venn diagram showing unique and shared contigs under LL and LD conditions.

FIGURE 2

Global analysis of 215 oscillating contigs using the molecular timetable method under LL (A) and LD (B) conditions. (A) The time at the top right of the plot area indicates sampling time. CT0 (Circadian Time 0) is the time at the first sampling point. The range from blue to pink represents subjective night-time. Each plot indicates individual contig expression. (B) ZT0 (Zeitgeber Time 0) is the time at the first sampling point. The range from blue to pink represents night-time. Each plot indicates individual contig expression.

FIGURE 3

Expression pattern of clock gene-like contigs under LL (A) and LD (B) conditions. The red and blue lines indicate the expression patterns in lettuce and Arabidopsis, respectively. Clock gene expression data of Arabidopsis thaliana were obtained from the Diurnal database. Gray area in (B) represents the dark period.

FIGURE 4

Functional categorization of 215 oscillating contigs. Biological process (A), cellular component (B) and molecular function (C).

FIGURE 5

Functional enrichment analysis of 215 oscillating contigs. Response to stimulus (A), biological regulation (B), metabolic process (C) and other function (D). The size of the circles represents the gene numbers. The color of each circle represents the enrichment P-value. The positions of nodes were changed manually.