Epigenetic Control of Diatom Genomes: An Overview from In Silico Characterization to Functional Studies

Zhao, Xue; Hoguin, Antoine; Chaumier, Timothée; Tirichine, Leïla

doi:10.1007/978-3-030-92499-7_7

Cited by 4 publications

(4 citation statements)

References 85 publications

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“…DNMRT players in P. multistriata were determined by searching in the PLAZA Diatoms 1.0 platform ( Osuna-Cruz et al, 2020 ) the gene IDs based on Table 1 in Zhao et al, 2022 , which summarizes putative methylation players (proteins to set, maintain or remove cytosine methylation) in three different diatom species.…”

Section: Methodsmentioning

confidence: 99%

DNA methylation is linked to the monoallelic expression ofMRP3, a diatom mating type determining gene

Ruggiero,

Mager,

Manfellotto

et al. 2023

Preprint

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Diatoms are unicellular microalgae widely distributed in aquatic ecosystems. In diatoms, sexual reproduction is needed to counteract cell miniaturization imposed by the rigid silica shell, and only small cells, below a species-specific size threshold, are competent for sex. We performed a genome-wide Enzymatic Methyl-seq analysis in the heterothallic diatom Pseudo-nitzschia multistriata comparing cells of different size and opposite mating type (MT) to investigate potential epigenetic controls in life cycle transitions. We found an imprinting-like pattern of methylation at the sex locus: alleles of the gene responsible for the specification of the MT+, MRP3, are hypermethylated in MT- and differentially methylated in MT+, with transcription occurring only on the MT+ hypomethylated variant. The methylation pattern is overall stable over the P. multistriata life cycle. Absence of methylation in MRP3 is necessary for its expression but not sufficient, since large non-sexual cells have the same methylation profile of small sexual cells but do not express MRP3, suggesting that additional controls are involved in the mechanism of sex determination.

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Section: Methodsmentioning

confidence: 99%

DNA methylation is linked to the monoallelic expression ofMRP3, a diatom mating type determining gene

Ruggiero,

Mager,

Manfellotto

et al. 2023

Preprint

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“…Phaeodactylum tricornutum is also helping us to understand diatom genome structure and evolution, thanks to the improved genomic resources and information about genetic and epigenetic mechanisms controlling gene expression (Zhao et al., 2022). Moreover, as a powerful genetic model, P. tricornutum is allowing researchers to clarify the mechanisms underlying the extensive intraspecific variability (at the level of SNV) observed within diatom populations by metagenomic analysis.…”

Section: Insight Into the Biology Of Diatomsmentioning

confidence: 99%

Phaeodactylum tricornutum: An established model species for diatom molecular research and an emerging chassis for algal synthetic biology

Russo,

Rogato,

Jaubert

et al. 2023

Journal of Phycology

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Diatoms are prominent and highly diverse microalgae in aquatic environments. Compared with other diatom species, Phaeodactylum tricornutum is an “atypical diatom” displaying three different morphotypes and lacking the usual silica shell. Despite being of limited ecological relevance, its ease of growth in the laboratory and well‐known physiology, alongside the steady increase in genome‐enabled information coupled with effective tools for manipulating gene expression, have meant it has gained increased recognition as a powerful experimental model for molecular research on diatoms. We here present a brief overview of how over the last 25 years P. tricornutum has contributed to the unveiling of fundamental aspects of diatom biology, while also emerging as a new tool for algal process engineering and synthetic biology.

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“…Today, the most common approach to infer algal gene function relates to acclimation processes in many marine algae, based on the analysis of transcriptomic data. It is however reasonable to expect that post-transcriptional and epigenetic modifications, as well as complex metabolic and cell signaling networks, also contribute to alga-environment relationships, as already demonstrated in land plants [13,14] and currently under scrutiny in a few algal species [9,13,15,16].…”

Section: Introductionmentioning

confidence: 98%

“…Néanmoins, les mécanismes épigénétiques, ainsi que les réseaux métaboliques ou de signalisation cellulaire contribuent également aux interactions algues-environnement. Cela a été bien étudié chez les plantes terrestres [14], mais n'a encore été abordé que sur un faible nombre d'espèces de microalgues [9,13,15,16,55].…”

Section: Introductionunclassified

Light-driven processes: key players of the functional biodiversity in microalgae

Falciatore¹,

Bailleul²,

Boulouis³

et al. 2022

Comptes Rendus. Biologies

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Microalgae are prominent aquatic organisms, responsible for about half of the photosynthetic activity on Earth. Over the past two decades, breakthroughs in genomics and ecosystem biology, as well as the development of genetic resources in model species, have redrawn the boundaries of our knowledge on the relevance of these microbes in global ecosystems. However, considering their vast biodiversity and complex evolutionary history, our comprehension of algal biology remains limited. As algae rely on light, both as their main source of energy and for information about their environment, we focus here on photosynthesis, photoperception, and chloroplast biogenesis in the green alga Chlamydomonas reinhardtii and marine diatoms. We describe how the studies of lightdriven processes are key to assessing functional biodiversity in evolutionary distant microalgae. We also emphasize that integration of laboratory and environmental studies, and dialogues between different scientific communities are both timely and essential to understand the life of phototrophs in complex ecosystems and to properly assess the consequences of environmental changes on aquatic environments globally.

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Epigenetic Control of Diatom Genomes: An Overview from In Silico Characterization to Functional Studies

Cited by 4 publications

References 85 publications

DNA methylation is linked to the monoallelic expression ofMRP3, a diatom mating type determining gene

DNA methylation is linked to the monoallelic expression ofMRP3, a diatom mating type determining gene

Phaeodactylum tricornutum: An established model species for diatom molecular research and an emerging chassis for algal synthetic biology

Light-driven processes: key players of the functional biodiversity in microalgae

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