Biology subjects

Guyot, R.

Publications and source records attributed to Guyot, R..

11 recordsLinked to original sources

bioRxiv2026

Genomic insights into sex-linked regions and dioecy in the ivory palm (Phytelephas aequatorialis)

Background and Aims: Dioecy has evolved independently multiple times in Palms, yet the genetic mechanisms underlying sex determination remain poorly understood across the family. Current knowledge is limited to genera from the subfamily Coryphoideae, in which Phoenix and Kerriodoxa independently recruited the same genomic region as the sex determining locus, suggesting a potentially convergent evolutionary pathway. Whether this pattern extends across the family remains unknown. Here, we investigate the genetic basis of sex determination in Phytelephas aequatorialis, from the Ceroxyloideaea palm subfamily, to identify its sex chromosome system, sex-linked genomic region, and candidate sex-determining genes. Methods: Using exon capture sequencing data from male and female individuals of P. aequatorialis, we analyzed genome wide sequence polymorphisms to detect signatures of sex linkage. Key Results: Our analyses reveal an XY sex chromosome system in Phytelephas, similar to that reported in the few dioecious palm species investigated to date. However, sex linkage maps to a distinct genomic region, indicating an independent origin of the sex-determining locus. We further identified 16 high confidence sex-linked genes with key roles in developmental processes and hormone signaling pathways, making them key candidates for involvement in sex determination. Sex-specific genetic markers were successfully developed from a subset of these genes. Conclusions: Our study suggests that in P. aequatorialis, the independent evolution of sex separation has relied on distinct genomic regions and genes, highlighting multiple evolutionary pathways leading to dioecy across the palm family. Comparative genomic analyses across additional lineages will be essential to reconstruct the evolutionary history of sex chromosomes and sex separation in this family.

plant biology↗

bioRxiv2024

Architectural singularities in wild Coffea (Baracoffea) species: integrated morphological perspectives for climate-resilient coffee cultivation

Global coffee production faces increasing threats from climate change, including rising temperatures, prolonged droughts, and spreads of diseases. Wild coffee species, notably those growthing in highly constrained environments in Madagascar, offer a critical genetic resource to address these challenges. Understanding adaptive traits allowing these species to establish into arid environments is essential to implement guid breeding strategies into create resilient coffee varieties. Here, we hypothesize that these wild Coffee species display unique traits compared to other Coffea species, reflecting adaptations to arid and seasonally dry environments. We used the architectural analysis to describe three Baracoffea species and compare them to known cultivated Coffee. Field studies were conducted in two contrasting sites in Madagascar, focusing on three wild coffee species, natively growing into arid environments: Coffea ambongensis, C. bissetiae, and C. boinensis. Structural traits at the whole plant scale were measured across developmental stages using morphological and architectural analyses. Our results suggest that unique traits characterize Barracoffea species, such as rhythmic growth, terminal flowering on short shoots, and species-specific developmental strategies. These findings highlight the architectural diversity of Baracoffea, identify potential key drivers of ecological adaptation and therefore highlights the potential of this group of species for breeding climate- resilient coffee varieties.

ecology↗

bioRxiv2024

Thyroid hormones act as a timer for the postnatal maturation of parvalbumin neurons in mouse neocortex

Thyroid hormones (THs) are required for proper maturation of parvalbumin-expressing GABAergic interneurons in the mouse neocortex, which function is essential to maintain a proper balance between neuronal excitation and inhibition. However, the timeline of this TH action has yet to be elucidated. Here, we used several mouse models expressing dominant negative mutations of the TH nuclear receptor 1 (TR1), to better define the time window during which THs promote the maturation of parvalbumin neurons. The action of THs during the first three postnatal weeks appears to be necessary to initiate the elaboration of a specialized extracellular matrix called the perineuronal net. Transcriptome analysis identified a small set of putative target genes for TR1, which are at the origin of the postnatal remodeling of the repertoire of ions channels and the elaboration of perineuronal nets. These data suggest that THs act as a timer to define the temporal boundaries of the critical period of heightened cortical plasticity, which plays a fundamental role in the development of neuronal circuits. Significance statementThyroid hormones exert a major influence on late neurodevelopment, acting directly on gene expression by binding to nuclear receptors present in all cell types. This study reports the discovery of a direct link between the transcriptional regulation exerted by the thyroid hormones in GABAergic neurons and the timing of the critical period of heightened plasticity. This provides a general framework to understand the pathology associated with altered thyroid hormone signaling.

developmental biology↗

bioRxiv2024

Thyroid hormones maintain parvalbumin neuron functions in mouse neocortex

Parvalbumin-expressing GABAergic interneurons play a key role in maintaining the excitation-inhibition balance in the mammalian neocortex. While postnatal maturation of parvalbumin neurons is highly sensitive to thyroid hormone deficiency, the role of these hormones in mature parvalbumin neurons remains poorly understood. Here, we addressed the possibility that thyroid hormones are also required to maintain the function of mature parvalbumin neurons in the mouse neocortex. To this end, Cre/loxP recombination system was used to express a dominant-negative mutated receptor of thyroid hormones to selectively eliminate thyroid hormone signaling in parvalbumin neurons after the onset of parvalbumin expression. We analyzed the neocortical phenotype of these mice by combining genomics, histology, electrophysiology, sleep recordings and behavioral analysis. In the mutant mice, gene expression analysis revealed a decreased expression of key perineuronal net components. parvalbumin neuron excitability was decreased and mice displayed behavioral hyperactivity and increased susceptibility to epileptic seizures. Additionally, sleep analysis revealed that mutant mice spent more time awake, and had a delayed transition to sleep. Electrophysiological recordings further demonstrated altered gamma oscillations in the somatosensory cortex. The findings of this study underscore that thyroid hormones are essential not only for the differentiation of parvalbumin interneurons, but also for the maintenance of their inhibitory function after the onset of parvalbumin expression. As a consequence, alterations in thyroid hormone signaling, during development or in adulthood, may contribute to the occurrence of neurological and psychiatric disorders involving altered cortical oscillations.

neuroscience↗

bioRxiv2023

The genome and population genomics of allopolyploid Coffea arabica reveal the diversification history of modern coffee cultivars

Coffea arabica, an allotetraploid hybrid of C. eugenioides and C. canephora, is the source of approximately 60% of coffee products worldwide, and its cultivated accessions have undergone several population bottlenecks. We present chromosome-level assemblies of a di-haploid C. arabica accession and modern representatives of its diploid progenitors, C. eugenioides and C. canephora. The three species exhibit largely conserved genome structures between diploid parents and descendant subgenomes, with no obvious global subgenome dominance. We find evidence for a founding polyploidy event 350,000-610,000 years ago, followed by several pre-domestication bottlenecks, resulting in narrow genetic variation. A split between wild accessions and cultivar progenitors occurred [~]30.5 kya, followed by a period of migration between the two populations. Analysis of modern varieties, including lines historically introgressed with C. canephora, highlights their breeding histories and loci that may contribute to pathogen resistance, laying the groundwork for future genomics-based breeding of C. arabica.

genomics↗

bioRxiv2022

An atlas of thyroid hormone receptors target genes in mouse tissues

We gathered in a single database available RNA-seq and ChIP-seq data to better characterize the target genes of the thyroid hormone receptors in several cell types. This database can serve as a resource to analyze the mode of action of the hormone. Also, it is an easy-handling convenient tool to obtain information on specific genes in regards to T3 regulation, or extract larger list of genes of interest based on the users criteria. Overall, this atlas is a unique compilation of recent sequencing data focusing on thyroid hormones, their receptors, mode of action, targets and roles which may profit researchers within the field. A preliminary analysis indicates extensive variations in the repertoire of target genes which transcription is upregulated by chromatin-bound nuclear receptor. Although it has a major influence, chromatin accessibility is not the only parameter that determines the cellular selectivity of hormonal response.

genomics↗

bioRxiv2022

Brown adipocytes local response to thyroid hormone is required for adaptive thermogenesis in adult male mice

Thyroid hormone (T3) and its nuclear receptors (TR) are important regulators of energy expenditure and adaptive thermogenesis, notably through their action in the brown adipose tissue (BAT). However, T3 acts in many other peripheral and central tissues which are also involved in energy expenditure. The general picture of how T3 regulates BAT thermogenesis is currently not fully established, notably due to the absence of extensive omics analyses and the lack of specific mice model. Here, we first used transcriptome and cistrome analyses to establish the list of T3/TR direct target genes in brown adipocytes. We then developed a novel model of transgenic mice, in which T3-signaling is specifically suppressed in brown adipocytes at adult stage. We addressed the capacity of these mice to mount a thermogenic response when challenged by either a cold exposure or a high-fat diet, and analyzed the associated changes in BAT transcriptome. We conclude that T3 plays a crucial role in the thermogenic response of the BAT, controlling the expression of genes involved in lipid and glucose metabolism and regulating BAT proliferation. The resulting picture provides an unprecedented view on the pathways by which T3 activates energy expenditure through an efficient adaptive thermogenesis in the BAT. Significance StatementThyroid hormones (TH) increase energy expenditure by regulating the expression of target genes in many metabolic tissues. Among them, brown adipose tissue (BAT) dissipates biochemical energy into heat production to notably prevent hypothermia during cold exposure. Hypothyroid mice display inefficient BAT thermogenesis suggesting that TH are crucial for this process. Here, we eliminated TH signaling specifically in brown adipocytes and expose the mice to different physiological stressors. We showed that TH signaling is crucial for BAT thermogenesis as it controls the expression of genes involved in proliferation and in the metabolism of lipids and glucose, the main energy resources for BAT thermogenesis. This study provides an unprecedented view on the pathways by which T3 activates energy expenditure the BAT.

genomics↗

bioRxiv2022

Functional definition of thyroid hormone response elements based on a synthetic STARR-seq screen

When bound to thyroid hormone, the nuclear receptor TR1 activates the transcription of a number of genes in many cell types. It mainly acts by binding DNA as an heterodimer with RXRs at specific response elements related to the DR4 consensus sequence. However, the number of DR4-like elements in the genome exceed by far the number of occupied sites, indicating that minor variations in nucleotides composition deeply influence the DNA-binding capacity and transactivation activity of TR1. An improved protocol of synthetic STARR-seq was used to quantitatively assess the transcriptional activity of thousands of synthetic sites in parallel. This functional screen highlights a strong correlation between the affinity of the heterodimers for DNA and their capacity to mediate the thyroid hormone response.

molecular biology↗

bioRxiv2020

In vitro assessment of the capacity of pesticides to act as agonists/antagonists of the thyroid hormone nuclear receptors.

Several in vitro tests, including transcriptome analysis of neural cells, were performed to assess the capacity of 33 pesticides to act as thyroid hormone disruptors (THD). Although some pesticides elicit a cellular response, which interferes with thyroid hormone signaling, we found no evidence that they can act as receptor agonists or antagonists. We conclude that the nuclear receptors of thyroid hormone are not common targets of THD, and that pesticide neurodevelopmental toxicity is not explained by a general alteration of neural cell response to thyroid hormone.

pharmacology and toxicology↗

bioRxiv2019

Genome sequence of the cluster root forming white lupin

White lupin (Lupinus albus L.) is a legume that produces seeds recognized for their high protein content and good nutritional value (lowest glycemic index of all grains, high dietary fiber content, and zero gluten or starch)1-5. White lupin can form nitrogen-fixing nodules but has lost the ability to form mycorrhizal symbiosis with fungi6. Nevertheless, its root system is well adapted to poor soils: it produces cluster roots, constituted of dozens of determinate lateral roots that improve soil exploration and phosphate remobilization7. As phosphate is a limited resource that comes from rock reserves8, the production of cluster roots is a trait of interest to improve fertilizers efficiency. Using long reads sequencing technologies, we provide a high-quality genome sequence of a modern variety of white lupin (2n=50, 451 Mb), as well as de novo assemblies of a landrace and a wild relative. We describe how domestication impacted soil exploration capacity through the early establishment of lateral and cluster roots. We identify the APETALA2 transcription factor LaPUCHI-1, homolog of the Arabidopsis morphogenesis coordinator9, as a potential regulator of this trait. Our high-quality genome and companion genomic and transcriptomic resources enable the development of modern breeding strategies to increase and stabilize yield and to develop new varieties with reduced allergenic properties (caused by conglutins10), which would favor the deployment of this promising culture.

genomics↗

bioRxiv2019

A pivotal genetic program controlled by thyroid hormone during the maturation of GABAergic neurons in mice

In mammals, brain development is critically dependent on proper thyroid hormone signaling, via the TR1 nuclear receptor. However, the downstream mechanisms by which TR1 impacts brain development are currently unknown, notably because this receptor is expressed ubiquitously from early stages of development. In order to better define the function of TR1 in the developing brain, we used mouse genetics to induce the expression of a dominant-negative mutation of the receptor specifically in GABAergic neurons, the main inhibitory neurons in the brain, which were previously identified as sensitive to hypothyroidism. This triggered post-natal epileptic seizures, reflecting a profound impairment of GABAergic neuron maturation in different brain areas. Analysis of transcriptome and TR1 cistrome also allowed us to identify a small set of genes, the transcription of which is upregulated by TR1 in GABAergic neurons during post-natal maturation of the striatum and which probably play an important role during neurodevelopment. Thus, our results point to GABAergic neurons as direct targets of thyroid hormone during brain development and suggest that many defects seen in hypothyroid brains may be secondary to GABAergic neuron malfunction.

developmental biology↗