Ontology highlight
ABSTRACT:
PROVIDER: PRJNA814727 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR18293242.fastq.gz | Fastqsanger.gz | |||
| SRR18293243.fastq.gz | Fastqsanger.gz | |||
| SRR18293244.fastq.gz | Fastqsanger.gz | |||
| SRR18293245.fastq.gz | Fastqsanger.gz |
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Project description:Transcriptomic Response to High Light in the Charophyte Klebsormidium nitens
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Project description:During the evolution of life on Earth, the conquest of land by plants played a pivotal role producing a boost in land biomass, a substantial drop in atmospheric CO2, an increase in oxygen and the emergence of new terrestrial habitats facilitating land colonization by animals. Therefore, the characterization of the molecular mechanisms that allowed plant terrestralization is a cornerstone in evolutionary studies. Viridiplantae or the green lineage is divided into two clades Chlorophyta or green microalgae and Streptophyta that in turn splits into Embryophyta or land plants and Charophyta. The latest are mainly considered aquatic algae although some facultative terrestrial species has been identified. Charophyta are generally accepted as the extant algal species most closely related to current land plants and, therefore, they are used in evolutionary studies on plant terrestralization. High light irradiance was one of the major stressors that ancestral charophytic algae needed to overcome during the transition from aquatic to terrestrial environments. In this study, we have chosen the facultative terrestrial early charophytic alga Klebsormidium nitens to perform an integrative transcriptomic and metabolomic analysis under high light in order to unveil key mechanisms involved in the early steps of plants terrestralization. We found a fast chloroplast retrograde signaling possibly mediated by reactive oxygen species and the inositol polyphosphate 1-phosphatase (SAL1) and 3′-phosphoadenosine-5′-phosphate (PAP) pathways inducing gene expression and accumulation of specific metabolites. Systems used by both Chlorophyta and Embryophyta were activated such as the xanthophyll cycle with an accumulation of zeaxanthin and protein folding and repair mechanisms constituted by NADPH-dependent thioredoxin reductases, thioredoxin-disulfide reductases and peroxiredoxins. Similarly, cyclic electron flow, specifically the pathway dependent on Proton Gradient Regulation 5, was strongly activated under high light. We detected a simultaneous co-activation of the non-photochemical quenching mechanisms based on LHC-like Stress Related protein and the photosystem II subunit S that are specific to Chlorophyta and Embryophyta respectively. Exclusive Embryophyta systems for the synthesis, sensing and response to the phytohormone auxin were also activated under high light in Klebsormidium leading to an increase in auxin content with the concomitant accumulation of amino acids such as tryptophan, histidine and phenylalanine.
2022-04-29 | GSE198330 | GEO
Project description:CAGE-seq of Klebsormidium nitens NIES-2285
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Project description:Plant nitrate, phosphate, and sucrose responses create a complex molecular network fine-tuned for growth and survival. This triangular interplay, crucial for the adaptability of terrestrial plants, allows the availability of one nutrient to influence plant responses to others. However, the origins and functional repurposing of this complex network for plant terrestrialization remain scarcely understood. By delving into the time-series transcriptome responses to nitrate, phosphate, and sucrose in the bryophyte Marchantia polymorpha and its streptophycean algal relatives Klebsormidium nitens, we observed convergent yet largely species-specific regulatory circuits in nutrient response. A key gene regulatory network (GRN) module centered on MpCSD, MpERF20, and MpHD9 was found to govern the hierarchical responses and crosstalk among the three nutrients in M. polymorpha. In K. nitens, these transcription factors were involved in nutrient responses but were co-opted during phytoterrestrialization to serve additional functions. Further network perturbation experiments validated the extensive evolution of transcriptional targets of these regulatory circuits, with cytokinin responsive genes being recruited exclusively into macronutritional GRNs in M. polymorpha thus optimizing nutrient response. Our findings illuminate the evolutionary strategies employed to redeploy the triad of nutrient interactions during the adaptation of ancestral green plants to terrestrial habitats.
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Project description:Transposable elements are entangled in a constant evolutionary arms race with their host genomes, constantly evolving ways to evade host silencing mechanisms. One silencing mechanism used by many distantly related eukaryotes is dependent on cytosine methylation, an epigenetic mark deposited by C5 cytosine methyltransferases (CMTs). Therefore, it is expected transposable elements would acquire mechanisms to escape from being targeted by cytosine methylation. Here we report how two distantly related eukaryotic lineages have incorporated CMTs into the coding regions of distinct retrotransposon classes. Three of these events have occurred in the dinoflagellates of the genus Symbiodinium, where these CMT-encoding retrotransposons show hundreds of insertions. In a case of convergent evolution, the charophyte Klebsormidium nitens shows an independent expansion of CMT encoding retrotransposons. Concomitantly, we find that Symbiodinium genomes show cytosine methylation patterns unlike any other eukaryote with most of the genome hypermethylated in CpGs, while targeted CH methylation accumulates on transposable elements. Similarly, K. nitens shows CHH and CHG targeted methylation on repressed transposable elements, while CpG methylation is concentrated in gene bodies and transposable elements. Furthermore, we demonstrate the ability of retrotransposon CMTs to de novo methylate CpGs, indicating a putative role in mimicking retrotranscribed DNA as host active genomic DNA. Our results show an unprecedented example of how retrotransposons incorporate host-derived genes involved in DNA methylation as a source of adaptation to their host epigenomic environments.
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Project description:Purpose: To understand the dynamic heat-sress response in M. polymorpha and K. nitens
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Project description:High-density kinetic analysis of the metabolomic and transcriptomic response of Arabidopsis to temperature and light
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