Biology subjects

Ramos-Gonzalez, M.

Publications and source records attributed to Ramos-Gonzalez, M..

4 recordsLinked to original sources

bioRxiv2026

Photoperiodic Plasticity of Transcriptomic and Photosynthetic Rhythms in the Liverwort Marchantia polymorpha

Earth's translation around the Sun and tilted rotational axis drive periodic seasonal changes in day length, or photoperiod, in temperate zones. In photosynthetic organisms, light acts not only as an environmental cue but also as the primary energy source. Therefore, characterizing the plasticity of oscillating molecular systems during photoperiod acclimation is essential for understanding the temporal orchestration of physiological processes in these organisms. Although photoperiodic plasticity has been extensively studied in angiosperms and microalgae, its impact on the molecular rhythms in non-vascular plants (bryophytes) remains poorly understood. In this study, we performed an integrative temporal analysis combining transcriptomic and photosynthetic approaches in the non-vascular model plant Marchantia polymorpha. Plants were grown under long (summer) and short (winter) photoperiods and subsequently transferred to constant light or darkness to unravel the light/dark-responsive and circadian components of their rhythmic transcriptome profiles. Plants under short photoperiod exhibited a higher number of rhythmic genes and an advance in their expression pattern, affecting several pathways including photosynthesis. However, only ~25% of these genes remained oscillating under constant conditions. We further identified dusk responsiveness and dawn anticipation as key features of the rhythmic patterns in Marchantia polymorpha. These patterns were associated with specific transcription factors, highlighting a potential role for MpHY5 in circadian regulation in this liverwort. Consistent with the transcriptomic results, analyses of photosynthetic physiology and chloroplast photorelocation revealed a general anticipation under short photoperiods and mechanisms mitigating photooxidative stress at dawn in both photoperiods.

plant biology↗

bioRxiv2026

Unveiling the Epigenomic Control of Temperature Acclimation in Marine Phytoplankton through Multiomics Integration

Temperature plays a central role in marine phytoplankton biogeographical dynamics, physiology and gene expression. Nonetheless, the transcriptional regulatory mechanisms controlling temperature acclimation in marine phytoplankton are yet to be characterized. Ostreococcus tauri was chosen as a model species for green marine phytoplankton due to its cellular and genomic simplicity, as well as its evolutionary position within the green lineage. In this study, epigenomic and transcriptomic data were integrated to characterize changes induced by temperature in the trimethylation of histone 3 at lysines 27 and 4 (H3K27me3 and H3K4me3) epigenetic marks established by the Polycomb (PcG) and Trithorax group (TrxG) complexes, respectively. H3K27me3 was found to be a repressive mark responding to temperature, showing predominantly significant increased levels at high temperatures. While H3K4me3 was associated with active transcription, presenting less evident variations in cultures acclimated to different temperatures. H3K27me3 was found only marginally associated with transposable elements, being mostly involved in the repression of specific biological processes, such as gene expression control by transcription factors, meiosis, motors proteins and cytoskeletal structures. No significant conservation was found between the H3K27me3 gene targets in the model plant Arabidopsis thaliana and Ostreococcus tauri. Nonetheless, transcriptions factors belonging to the MADS-box, WRKY and AP2 families were consistently repressed by H3K27me3 in both species, unveiling that, although the specific downstream targets of this epigenetic mark have diversified during evolution, its role in modulating higher order regulatory nodes remains evolutionary conserved.

plant biology↗

bioRxiv2026

Transcriptomic Insights into Drought Tolerance Enhancement in Bread Wheat Induced by a Microalgae-based Biostimulant

Bread wheat (Triticum aestivum) is a staple food crucial for global caloric intake and food security. The current climate emergency demands the development of sustainable agricultural practices, particularly in the context of drought-induced yield reductions in bread wheat. Microalgae-based biostimulants have emerged as promising tools to enhance crop tolerance to drought stress while concurrently mitigating atmospheric CO2 accumulation. This study characterizes the transcriptomic responses to the foliar application of the microalgae-based biostimulant LRMTM in drought-stressed and fully irrigated wheat plants unveiling its mode of action. Drought stress at the tillering stage significantly altered gene expression activating key pathways related to phosphate starvation response (PSR), inositol phosphate signaling, and tocopherol biosynthesis. The application of the microalgae-based biostimulant LRMTM in drought-stressed plants further enhanced the expression of drought-responsive genes, particularly those involved in PSR and carbon fixation. Specific responses to LRMTM treatment in drought-stressed plants were also found related to abscisic acid (ABA) signaling activating genes involved in stomata closure, which plays a critical role in drought tolerance. In fully irrigated plants, LRMTM treatment was also beneficial modulating circadian rhythms, shade avoidance and attenuating stress responses. Phenotypic analysis showed that LRMTM-treated plants exhibited enhanced drought tolerance, increased height and spike length even under fully irrigated conditions. These results indicate that the microalgae-based biostimulant LRMTM not only enhances wheat response to drought but also promotes growth and productivity in both stressed and non-stressed conditions which could contribute to the development of sustainable agriculture in the face of the current climate challenges.

plant biology↗

bioRxiv2023

PharaohFUN: PHylogenomic Analysis foR plAnt prOtein History and FUNction elucidation

Since DNA sequencing has become commonplace, the development of efficient methods and tools to explore gene sequences has become indispensable. In particular, despite photosynthetic eukaryotes constituting the largest percentage of terrestrial biomass, computational functional characterization of gene sequences in these organisms still predominantly relies on comparisons with Arabidopsis thaliana and other angiosperms. This paper introduces PharaohFUN, a web application designed for the evolutionary and functional analysis of protein sequences in photosynthetic eukaryotes, leveraging orthology relationships between them. PharaohFUN incorporates a homogeneous representative sampling of key species in this group, bridging clades that have traditionally been studied separately, thus establishing a comprehensive evolutionary framework to draw conclusions about sequence evolution and function. For this purpose, it incorporates modules for exploring gene tree evolutionary history, expansion and contraction events, ancestral states, domain identification, multiple sequence alignments, and diverse functional annotation. It also incorporates different search modes to facilitate its use and increase its reach within the community. Tests were performed on the whole transcription factor toolbox of Arabidopsis thaliana and on CCA1 protein to assess its utility for both large-scale and fine-grained phylogenetic studies. These exemplify how PharaohFUN accurately traces the corresponding evolutionary histories of these proteins by unifying results for land plants, streptophyte and chlorophyte microalgae. Thus, PharaohFUN democratizes access to these kind of analyses in photosynthetic organisms for every user, independently of their prior training in bioinformatics.

evolutionary biology↗