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Kingdom-wide comparison reveals conserved diurnal gene expression in Archaeplastida

Published on Aug 15, 2018in bioRxiv
· DOI :10.1101/387316
Camilla Ferrari2
Estimated H-index: 2
(MPG: Max Planck Society),
Sebastian Proost17
Estimated H-index: 17
(MPG: Max Planck Society)
+ 9 AuthorsMarek Mutwil17
Estimated H-index: 17
(MPG: Max Planck Society)
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Abstract
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.
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Published on Dec 1, 2018in Scientific Reports 4.01
Hokuto Nakayama4
Estimated H-index: 4
(UC Davis: University of California, Davis),
Tomoaki Sakamoto9
Estimated H-index: 9
(Nara Institute of Science and Technology)
+ 8 AuthorsNeelima Sinha40
Estimated H-index: 40
(UC Davis: University of California, Davis)
Because natural variation in wild species is likely the result of local adaptation, it provides a valuable resource for understanding plant-environmental interactions. Rorippa aquatica (Brassicaceae) is a semi-aquatic North American plant with morphological differences between several accessions, but little information available on any physiological differences. Here, we surveyed the transcriptomes of two R. aquatica accessions and identified cryptic physiological differences between them. We fi...
3 Citations Source Cite
Published on Mar 16, 2018in Science 41.04
Ludovic S. Mure6
Estimated H-index: 6
(Salk Institute for Biological Studies),
Hiep D. Le10
Estimated H-index: 10
(Salk Institute for Biological Studies)
+ 8 AuthorsOuria Dkhissi-Benyahya2
Estimated H-index: 2
(UCBL: Claude Bernard University Lyon 1)
INTRODUCTION The interaction among cell-autonomous circadian oscillators—daily cycles of activity–rest and feeding–fasting—produces diurnal rhythms in gene expression in almost all animal tissues. These rhythms control the timing of a wide range of functions across different organs and brain regions, affording optimal fitness. Chronic disruption of these rhythms predisposes to and are hallmarks of numerous diseases and affective disorders. RATIONALE Time-series gene expression studies in a limit...
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Published on Dec 1, 2017in BMC Bioinformatics 2.51
Sebastian Proost17
Estimated H-index: 17
(MPG: Max Planck Society),
Agnieszka Krawczyk1
Estimated H-index: 1
(MPG: Max Planck Society),
Marek Mutwil17
Estimated H-index: 17
(MPG: Max Planck Society)
Background Since experimental elucidation of gene function is often laborious, various in silico methods have been developed to predict gene function of uncharacterized genes. Since functionally related genes are often expressed in the same tissues, conditions and developmental stages (co-expressed), functional annotation of characterized genes can be transferred to co-expressed genes lacking annotation. With genome-wide expression data available, the construction of co-expression networks, wher...
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Published on Oct 1, 2017in New Phytologist 7.30
Anna Malin Linde1
Estimated H-index: 1
(Uppsala University),
D. Magnus Eklund13
Estimated H-index: 13
(Uppsala University)
+ 9 AuthorsTokitaka Oyama22
Estimated H-index: 22
(Kyoto University)
While angiosperm clocks can be described as an intricate network of interlocked transcriptional feedback loops, clocks of green algae have been modelled as a loop of only two genes. To investigate the transition from a simple clock in algae to a complex one in angiosperms, we performed an inventory of circadian clock genes in bryophytes and charophytes. Additionally, we performed functional characterization of putative core clock genes in the liverwort Marchantia polymorpha and the hornwort Anth...
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Published on Jul 13, 2017in Frontiers in Plant Science 4.11
Pedro Reyes2
Estimated H-index: 2
(University of Seville),
Francisco José Romero Campero19
Estimated H-index: 19
(University of Seville)
+ 2 AuthorsFederico Valverde19
Estimated H-index: 19
(University of Seville)
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...
2 Citations Source Cite
Published on Jun 1, 2017in Current Opinion in Plant Biology 7.51
Gloria Serrano-Bueno1
Estimated H-index: 1
(University of Seville),
Francisco José Romero Campero19
Estimated H-index: 19
(University of Seville)
+ 2 AuthorsFederico Valverde19
Estimated H-index: 19
(University of Seville)
Measuring day length confers a strong fitness improvement to photosynthetic organisms as it allows them to anticipate light phases and take the best decisions preceding diurnal transitions. In close association with signals from the circadian clock and the photoreceptors, photoperiodic sensing constitutes also a precise way to determine the passing of the seasons and to take annual decisions such as the best time to flower or the beginning of dormancy. Photoperiodic sensing in photosynthetic org...
7 Citations Source Cite
Published on May 1, 2017in Plant Journal 5.73
Colin Ruprecht9
Estimated H-index: 9
(MPG: Max Planck Society),
Sebastian Proost17
Estimated H-index: 17
(MPG: Max Planck Society)
+ 6 AuthorsMarek Mutwil17
Estimated H-index: 17
(MPG: Max Planck Society)
Summary Molecular evolutionary studies correlate genomic and phylogenetic information with the emergence of new traits of organisms. These traits are, however, the consequence of dynamic gene networks composed of functional modules, which might not be captured by genomic analyses. Here, we established a method, which combines large-scale genomic and phylogenetic data with gene co-expression networks, to extensively study the evolutionary make-up of modules in the moss Physcomitrella patens and i...
27 Citations Source Cite
Published on Mar 1, 2017in Bioresource Technology 6.67
Lin Zhou2
Estimated H-index: 2
(CAS: Chinese Academy of Sciences),
Dujia Cheng3
Estimated H-index: 3
(CAS: Chinese Academy of Sciences)
+ 4 AuthorsYuhan Sun55
Estimated H-index: 55
(CAS: Chinese Academy of Sciences)
Abstract The growth of microalgae is inhibited by high concentration phenol due to reactive oxygen species. An evolved strain tolerated to 500 mg/L phenol, Chlorella sp. L5, was obtained in previous study. In this study, comparative transcriptomic analysis was performed for Chlorella sp. L5 and its original strain ( Chlorella sp. L3). The tolerance mechanism of Chlorella sp. L5 for high concentration phenol was explored on genome scale. It was identified that the up-regulations of the related ge...
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Published on Jan 1, 2017in New Phytologist 7.30
Rajesh K. Singh9
Estimated H-index: 9
(Umeå University),
Tetiana Svystun1
Estimated H-index: 1
(Lund University)
+ 2 AuthorsRishikesh P. Bhalerao8
Estimated H-index: 8
(KSU: King Saud University)
(Table presented.). Summary: Trees growing in boreal and temperate regions synchronize their growth with seasonal climatic changes in adaptive responses that are essential for their survival. These trees cease growth before the winter and establish a dormant state during which growth cessation is maintained by repression of responses to growth-promotive signals. Reactivation of growth in the spring follows the release from dormancy promoted by prolonged exposure to low temperature during the win...
47 Citations Source Cite
Published on Dec 1, 2016in Nature Structural & Molecular Biology 12.11
Maria A. Nohales2
Estimated H-index: 2
,
Steve A. Kay98
Estimated H-index: 98
This Review examines the molecular mechanisms underlying the plant circadian clock, highlighting the functions of transcriptional circuits and post-translational regulation in timing and describing how clock components integrate and respond to environmental signals.
53 Citations Source Cite