Kingdom-wide comparison reveals conserved diurnal gene expression in Archaeplastida

Ferrari, Camilla; Proost, Sebastian; Janowski, Marcin; Becker, Jörg; Nikoloski, Zoran; Bhattacharya, Debashish; Price, Dana C.; Tohge, Takayuki; Bar‐Even, Arren; Fernie, Alisdair R.; Stitt, Mark; Mutwil, Marek

doi:10.1101/387316

Cited by 4 publications

(3 citation statements)

References 79 publications

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“…Each RNA-seq data deposited in this database contains specific references to the study in which the data were generated and the type of materials, treatments, and data analyses that were used. Specifically, for gene expression data mining, we have retrieved gene expression data for the following species: Selaginella moellendorffii [37][38][39], Zea mays [40,41], O. sativa [42,43], M. truncatula [44,45], Glycine max [46,47], Solanum lycopersicum [48], and Solanum tuberosum [49]. The accessions of the TDP1α and TDP1β genes for the species taken into consideration are provided in Table S3.…”

Section: Gene Expression Data Miningmentioning

confidence: 99%

“…The gene expression data, recovered from BAR, refers to experiments carried out to study the diurnal cycle [37], root meristems [38], and shoot meristems [39]. The generated heatmap (Figure 4) evidences the expression patterns for the SmTDP1α (Smo170833) and SmTDP1β (Smo415650) genes in the considered samples/conditions.…”

Section: Expression Profiles Of Tdp1α and Tdp1β In The Archaic Vasculmentioning

confidence: 99%

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Plant TDP1 (Tyrosyl-DNA Phosphodiesterase 1): A Phylogenetic Perspective and Gene Expression Data Mining

Mutti

Raveane

Pagano

et al. 2020

Genes

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The TDP1 (tyrosyl-DNA phosphodiesterase 1) enzyme removes the non-specific covalent intermediates between topoisomerase I and DNA, thus playing a crucial role in preventing DNA damage. While mammals possess only one TDP1 gene, in plants two genes (TDP1α and TDP1β) are present constituting a small gene subfamily. These display a different domain structure and appear to perform non-overlapping functions in the maintenance of genome integrity. Namely, the HIRAN domain identified in TDP1β is involved in the interaction with DNA during the recognition of stalled replication forks. The availability of transcriptomic databases in a growing variety of experimental systems provides new opportunities to fill the current gaps of knowledge concerning the evolutionary origin and the specialized roles of TDP1 genes in plants. Whereas a phylogenetic approach has been used to track the evolution of plant TDP1 protein, transcriptomic data from a selection of representative lycophyte, eudicots, and monocots have been implemented to explore the transcriptomic dynamics in different tissues and a variety of biotic and abiotic stress conditions. While the phylogenetic analysis indicates that TDP1α is of non-plant origin and TDP1β is plant-specific originating in ancient vascular plants, the gene expression data mining comparative analysis pinpoints for tissue- and stress-specific responses.

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Section: Gene Expression Data Miningmentioning

confidence: 99%

Section: Expression Profiles Of Tdp1α and Tdp1β In The Archaic Vasculmentioning

confidence: 99%

Plant TDP1 (Tyrosyl-DNA Phosphodiesterase 1): A Phylogenetic Perspective and Gene Expression Data Mining

Mutti

Raveane

Pagano

et al. 2020

Genes

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“…Thus, the nanosieve device also has potential for quantitative studies of cell mechanics by controlling the PDMS deformation [35–37]. This configuration can also be applied to study the metabolic and physiological responses of the trapped microalgae cells to external chemical/mechanical triggering [38, 39].…”

Section: Discussionmentioning

confidence: 99%

Single Chlamydomonas reinhardtii cell separation from bacterial cells and auto‐fluorescence tracking with a nanosieve device

et al. 2020

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A planar, transparent, and adaptable nanosieve device is developed for efficient microalgae/bacteria separation. In the proposed method, a sacrificial layer is applied with dual photolithography patterning to achieve a 1D channel with a very low aspect ratio (1:10 000). A microalgae/bacteria mixture is then introduced into the deformable PDMS nanochannel. The hydrodynamic deformation of the nanochannel is regulated to allow the bacteria cells to pass through while leaving the microalgae cells trapped in the device. At a flow rate of 4 μL/min, the supernatant collected from the device is indistinguishable from a control solution, indicating that nearly all the microalgae cells are trapped in the device. Additionally, this device is capable of single cell auto-fluorescence tracking. These microalgae cells demonstrate minimal photobleaching over 250 s laser exposure and could be used to monitor hazardous compounds in the sample with a continuous flow. This method will be valuable to purify microalgae samples containing contaminations and study single-cell heterogeneity.

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

Tan

Ferrari

et al. 2019

Preprint

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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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Kingdom-wide comparison reveals conserved diurnal gene expression in Archaeplastida

Cited by 4 publications

References 79 publications

Plant TDP1 (Tyrosyl-DNA Phosphodiesterase 1): A Phylogenetic Perspective and Gene Expression Data Mining

Plant TDP1 (Tyrosyl-DNA Phosphodiesterase 1): A Phylogenetic Perspective and Gene Expression Data Mining

Single Chlamydomonas reinhardtii cell separation from bacterial cells and auto‐fluorescence tracking with a nanosieve device

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

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