Evolution of photoperiod sensing in plants and algae

Serrano-Bueno, Gloria; Romero–Campero, Francisco J.; Lucas-Reina, Eva; Romero, Javier; Valverde, Federico

doi:10.1016/j.pbi.2017.03.007

Cited by 45 publications

(48 citation statements)

References 63 publications

(92 reference statements)

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“…5C-J). As previously shown (Serrano-Bueno et al , 2017), only CCA1 / LHY / RVE and LUX families are present in most of the species, indicating that the three major loops are not complete in the early-diverging algae Cyanophora and Porphyridium, because PRR genes (morning loop), TOC1 (central loop), ELF3 / ELF4 / GI / ZTL (evening loop) are absent in these two algae (Fig. 5A, C-J).…”

Section: Resultssupporting

confidence: 67%

“…Photosynthetic organisms are capable of perceiving day length and the alternation of light and dark through two primary systems: light-dark detection and the circadian clock (Serrano-Bueno et al , 2017). In addition, light acts as the energy source that drives photosynthesis.…”

Section: Introductionmentioning

confidence: 99%

“…Studies in Drosophila melanogaster show that in addition to gene expression, splicing, RNA editing and non-coding RNA expression are highly affected by diurnal regulation (Hughes et al , 2012), whereas studies in mammals highlight the importance of diurnal regulation when applied to pharmaceutical applications (Zhang et al , 2014; Archer et al , 2014; Mure et al , 2018). Furthermore, recent studies on plants have shown a moderate level of conservation of diurnal responses among distantly related species, along with occasional divergent evolution of specific mechanisms (de los Reyes et al , 2017; Serrano-Bueno et al , 2017).…”

Section: Introductionmentioning

confidence: 99%

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Kingdom-wide comparison reveals conserved diurnal gene expression in Archaeplastida

Ferrari

Proost

Janowski

et al. 2018

Preprint

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Plants have adapted to the diurnal light-dark cycle by establishing elaborate transcriptional programs that coordinate innumerable metabolic, physiological, and developmental responses to the external environment. These transcriptional programs have been studied in only a few species, and their function and conservation across algae and plants is currently unknown. We performed a comparative transcriptome analysis of the diurnal cycle of nine members of Archaeplastida, and we observed that, despite large phylogenetic distances and dramatic differences in morphology and lifestyle, diurnal transcriptional programs of these organisms are similar. However, the establishment of multicellularity coincided with the uncoupling of cell division from the diurnal cycle and decreased diurnal control of the expression of the biological pathways. Hence, our study provides evidence for the universality of diurnal gene expression and elucidates its evolutionary history among different photosynthetic eukaryotes.Introduction:

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Section: Resultssupporting

confidence: 67%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Kingdom-wide comparison reveals conserved diurnal gene expression in Archaeplastida

Ferrari

Proost

Janowski

et al. 2018

Preprint

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“…Taking Arabidopsis as model, a much simpler clock has been described in Chlamydomonas and Ostreococcus , where only some genes of the higher plant circadian clock have been identified so far (Mittag et al, 2005; Corellou et al, 2009). In this way, most evolutionary studies have focused on phylogenetic analyses of the key genes regulating the circadian clock (Serrano-Bueno et al, 2017) whereas the analysis of global rhythmic patterns conservation and evolution among different photosynthetic species still remains to be explored.…”

Section: Introductionmentioning

confidence: 99%

Evolution of Daily Gene Co-expression Patterns from Algae to Plants

et al. 2017

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Daily rhythms play a key role in transcriptome regulation in plants and microalgae orchestrating responses that, among other processes, anticipate light transitions that are essential for their metabolism and development. The recent accumulation of genome-wide transcriptomic data generated under alternating light:dark periods from plants and microalgae has made possible integrative and comparative analysis that could contribute to shed light on the evolution of daily rhythms in the green lineage. In this work, RNA-seq and microarray data generated over 24 h periods in different light regimes from the eudicot Arabidopsis thaliana and the microalgae Chlamydomonas reinhardtii and Ostreococcus tauri have been integrated and analyzed using gene co-expression networks. This analysis revealed a reduction in the size of the daily rhythmic transcriptome from around 90% in Ostreococcus, being heavily influenced by light transitions, to around 40% in Arabidopsis, where a certain independence from light transitions can be observed. A novel Multiple Bidirectional Best Hit (MBBH) algorithm was applied to associate single genes with a family of potential orthologues from evolutionary distant species. Gene duplication, amplification and divergence of rhythmic expression profiles seems to have played a central role in the evolution of gene families in the green lineage such as Pseudo Response Regulators (PRRs), CONSTANS-Likes (COLs), and DNA-binding with One Finger (DOFs). Gene clustering and functional enrichment have been used to identify groups of genes with similar rhythmic gene expression patterns. The comparison of gene clusters between species based on potential orthologous relationships has unveiled a low to moderate level of conservation of daily rhythmic expression patterns. However, a strikingly high conservation was found for the gene clusters exhibiting their highest and/or lowest expression value during the light transitions.

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“…Photosynthetic organisms use two primary systems, photoreceptors and the circadian clock to detect light and measure time (and thus the photoperiod) respectively (Serrano-Bueno et al, 2017). Light quality and quantity is detected by photoreceptors, which have evolved across different photosynthetic organisms.…”

Section: Introductionmentioning

confidence: 99%

Diurnal.plant.tools: comparative transcriptomic and co-expression analyses of diurnal gene expression of the Archaeplastida kingdom

Tan

Ferrari

et al. 2019

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Almost all organisms coordinate some aspects of their biology through the diurnal cycle. Photosynthetic organisms, and plants especially, have established complex programs that coordinate physiological, metabolic and developmental processes with the changing light. The diurnal regulation of the underlying transcriptional processes is observed when groups of functionally related genes (gene modules) are expressed at a specific time of the day. However, studying the diurnal regulation of these gene modules in the plant kingdom was hampered by the large amount of data required for the analyses. To meet this need, we used gene expression data from 17 diurnal studies spanning the whole Archaeplastida kingdom (Plantae kingdom in the broad sense) to make an online diurnal database. We have equipped the database with tools that allow user-friendly cross-species comparisons of gene expression profiles, entire co-expression networks, co-expressed clusters (involved in specific biological processes), time-specific gene expression, and others. We exemplify how these tools can be used by studying three important biological questions: (i) the evolution of cell division, (ii) the diurnal control of gene modules in algae and (iii) the conservation of diurnally-controlled modules across species. The database is freely available at http://diurnal.plant.tools/.

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Evolution of photoperiod sensing in plants and algae

Cited by 45 publications

References 63 publications

Kingdom-wide comparison reveals conserved diurnal gene expression in Archaeplastida

Kingdom-wide comparison reveals conserved diurnal gene expression in Archaeplastida

Evolution of Daily Gene Co-expression Patterns from Algae to Plants

Diurnal.plant.tools: comparative transcriptomic and co-expression analyses of diurnal gene expression of the Archaeplastida kingdom

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