Rhythms of Transcription in Field-Grown Sugarcane Are Highly Organ Specific

Abstract

Circadian clocks improve plant fitness in a rhythmic environment. As each cell has its own circadian clock, we hypothesized that sets of cells with different functions would have distinct rhythmic behaviour. To test this, we investigated whether different organs in field-grown sugarcane follow the same rhythms in transcription. We assayed the transcriptomes of three organs during a day: leaf, a source organ; internodes 1 and 2, sink organs focused on cell division and elongation; and internode 5, a sink organ focused on sucrose storage. The leaf had twice as many rhythmic transcripts (>68%) as internodes, and the rhythmic transcriptomes of the internodes were more like each other than to those of the leaves. Among the transcripts expressed in all organs, only 7.4% showed the same rhythmic pattern. Surprisingly, the central oscillators of these organs -the networks that generate circadian rhythms -had similar dynamics, albeit with different amplitudes. The differences in rhythmic transcriptomes probably arise from amplitude differences in tissue-specific circadian clocks and different sensitivities to environmental cues, highlighted by the sampling under field conditions. The vast differences suggest that we must study tissue-specific circadian clocks in order to understand how the circadian clock increases the fitness of the whole plant.

Circadian rhythms driving a fast‐paced root clock implicate species‐specific regulation in Medicago truncatula

“…Tissue-specific oscillatory mechanism dominates rhythmic transcriptome in M. truncatula roots We found 30.66% oscillating transcriptomes in the shoots of M. truncatula under LL conditions, which is consistent with previous studies in A. thaliana, barley (Müller et al, 2020), sugarcane (Dantas et al, 2020), rice, and poplar (Filichkin et al, 2011). However, only 2.76% (726) oscillating transcripts were detected in the roots of M. truncatula, which is much less than the 30% oscillating leaf transcripts.…”

“…The liver-specific oscillation could lead to larger cells and higher protein levels after feeding, promoting more effective detoxification and digestion (Sinturel et al, 2017). A previous study suggested that at least two pathways, one mediating organ specificity and the other conferring rhythmicity, could contribute to the generation of tissue-specific rhythms (Dantas et al, 2020). These two pathways are tightly coupled to modulate tissuespecific circadian rhythms, which might be necessary for the adaptation of different organs to their microenvironments.…”

Antisense Transcription in Plants: A Systematic Review and an Update on cis-NATs of Sugarcane

“…Almost 12% of the interrogated genes presented antisense expression and in most cases, the SS/AS pairs presented co-expression [ 44 ]. The same oligo array was used to study sugarcane gene expression in several conditions [ 79 , 80 , 81 , 82 , 83 , 84 , 154 , 155 ] but the data on antisense expression was not always addressed. The antisense expression was observed in eight experimental data publications ( Table 1 ), which are briefly presented here.…”

“…In order to update the antisense expression scenario in sugarcane, we explored transcriptomic data from multiple published experiments. Eight published experiments ( Table 1 ) used the same oligo array [ 44 ] to study the gene expression of different sugarcane genotypes under greenhouse [ 44 , 79 , 80 , 81 ] or field conditions [ 33 , 82 , 83 , 84 ] and treatments such as drought and ethylene pulverization. This customized oligo array (CaneRegNet—Agilent Technologies) includes 21,901 probes in duplicate, which represent 14,522 different sugarcane-assembled sequences (SAS) from the SUCEST database (Sugarcane Expressed Sequence Tag project) [ 85 ].…”

Layers of crosstalk between circadian regulation and environmental signalling in plants

“…The diel regulation of the transcriptome under naturally fluctuating conditions has been investigated in crops such as rice (Oryza sativa), sugarcane (Saccharum sp. ), pineapple (Ananas comosus), and Arabidopsis species [150][151][152][153][154][155][156][157][158][159] . Investigation of 24 h changes in the transcriptome of field-grown rice found that temperature and high light intensity were major regulators of 24 h fluctuations of transcript abundance in the leaves 151 .…”