Biology subjects

Marais, G. A.

Publications and source records attributed to Marais, G. A..

13 recordsLinked to original sources

bioRxiv2025

Exploring the role of transposable elements to sex gap in longevity in Drosophila species

In Drosophila, like in many other animal species, females tend to live longer than males, a phenomenon known as sex gap in longevity (SGL). One possible explanation for this phenomenon could be related to the activity of transposable elements (TE), which may be present at higher levels in the heterogametic sex. TE activity is normally repressed by epigenetic mechanisms, but this regulation weakens with age. Sex chromosomes, such as the Y chromosome, are enriched in TEs, and age-related TE activity may therefore be more pronounced in older males than in older females, likely affecting longevity patterns. Using three Drosophila species, we show that SGL varies naturally among wild-type populations, reflecting both intra-and inter-species differences. Transcriptomic data revealed increased age-related TE expression in D. melanogaster and D. suzukii flies, but not in D. simulans. Moreover, we observed a higher number of upregulated TE copies in older males compared to older females across all the three species tested. Additionally, we detected an increase in TE-chimeric transcript generation in some aged samples, particularly in D. suzukii males. Finally, the replacement of the Y chromosome between strains with different SGL led to a progressive reduction in male lifespan and increased TE transcriptional release over generations, suggesting a Y chromosome important role in male longevity. Our work highlights the importance of investigating the role of TEs to better understand differences in longevity between sexes and across different species.

genomics↗

bioRxiv2023

Evolution of sex-biased gene expression during transitions to separate sexes in the Silene genus

Sexual dimorphism is widespread among species with separate sexes and its extent is thought to be governed by the differential expression of thousands of genes between males and females (known as Sex-Biased Genes, hereafter SBGs). SBGs have been studied in numerous species, but rarely in a comparative way, which curtails our understanding of their evolution, especially during multiple independent transitions to separate sexes. We sequenced the transcriptomes of nine dioecious species, two gynodioecious species (separate females and hermaphrodites) and two hermaphrodite species from the Silene genus. Our dataset provides access to three independent transitions to dioecy (dating from less than 1 Myo to about 11 Myo). We demonstrated that male-biased expression emerges first during a transition to separate sexes, later followed by female-biased genes. Furthermore, we showed that, despite a mixture of selective regimes, positive selection significantly affects the evolution of some SBGs. Overall, this study provides new insights on the causes of SBG evolution during transitions to separate sexes. TeaserThis study describes the evolution of sex-biased gene expression during a transition to separate sexes in plants.

evolutionary biology↗

bioRxiv2023

Transposable element expression with variation in gonosome number supports a toxic Y effect on human longevity

AO_SCPLOWBSTRACTC_SCPLOWWhy women live longer than men is still an open question in human biology. Sex chromosomes have been proposed to play a role in the observed sex gap in longevity, and the Y male chromosome has been suspected of having a potential toxic genomic impact on male longevity. It has been hypothesized that in aging individuals, TE repression is diminished, which could lead to detrimental effects (e.g. somatic mutations, perturbed gene expression) and to an acceleration of the aging process. As the Y chromosome is typically enriched in transposable elements (TE), this could explain why the presence of a Y chromosome is associated with shorter longevity. Using transcriptomic data from humans with atypical karyotypes, we found an association between TE expression and the presence and number of Y chromosomes. These findings are consistent with the existence of a toxic Y effect on men's longevity.

molecular biology↗

bioRxiv2021

Sex chromosomes, sex ratios and sex gaps in longevity in plants

In animals, males and females can display markedly different longevity (also called sex gap in longevity, SGLs). Recent work has revealed that sex chromosomes contribute to establishing these SGLs. X-hemizygosity and toxicity of the Y chromosomes are two mechanisms that have been suggested to reduce male longevity (Z-hemizygosity and W toxicity in females in ZW systems). In plants, SGLs are known to exist but the role of sex chromosomes remains to be established. Here, by using adult sex ratio as a proxy for measuring SGLs, we explored the relationship between sex chromosome and SGLs across 43 plant species. Based on the knowledge recently accumulated in animals, we specifically asked whether: (i) species with XY systems tend to have female-biased sex ratios (reduced male longevity) and species with ZW ones tend to have male-biased sex ratios (reduced female longevity), and (ii) this patterns was stronger in heteromorphic systems compared to homomorphic ones. Our results tend to support these predictions although we lack statistical power because of a small number of ZW systems and the absence of any heteromorphic ZW system in the dataset. We discuss the implications of these findings, which we hope will stimulate further research on sex-differences in lifespan and ageing across plants.

plant biology↗

bioRxiv2021

Plant genera Cannabis and Humulus share the same pair of well-differentiated sex chromosomes.

O_LIWe recently described, in Cannabis sativa, the oldest sex chromosome system documented so far in plants. Based on our estimate of its age, we predicted that it should be shared by its sister genus Humulus, which is known to also possess XY sex chromosomes. C_LIO_LIHere, we used transcriptome sequencing of a F1 family of Humulus lupulus to identify and study the sex chromosomes in this species using the probabilistic method SEX-DETector. C_LIO_LIWe identified 265 sex-linked genes in H. lupulus, located on the chromosome that is also the C. sativa sex chromosome pair. Using phylogenies of sex-linked genes, we show that a region of these chromosomes had already stopped recombining in the common ancestor of the two species. Furthermore, as in C. sativa, Y gene expression was reduced in correlation to the position on the X chromosome, and strongly Y degenerated genes showed dosage compensation. C_LIO_LIHere we report, for the first time in the Angiosperms, a sex chromosome system that is shared by two different genera. Recombination suppression started at least 21-25 My ago, and then (either gradually or step-wise) spread to a large part of the sex chromosomes, leading to a strongly degenerated Y. C_LI

evolutionary biology↗

bioRxiv2020

A derived ZW chromosome system in Amborella trichopoda, the sister species to all other extant flowering plants

Sex determination is poorly understood in plants. Amborella trichopoda is a well-known plant model for evo-devo studies, which is also dioecious (has male and female individuals), with an unknown sex determination mechanism. A. trichopoda is a "sex switcher", which points to possible environmental factors that act on sex, but populations grown from seed under greenhouse conditions exhibit a 50:50 sex ratio, which indicates the operation of genetic factors. Here, we use a new method (SDpop) to identify sex-linked genes from genotyping data of male and female individuals sampled in the field, and find that A. trichopoda has a ZW sex-chromosome system. The sex-linked genes map to a 4 Mb sex-determining region on chromosome 9. The low extent of ZW divergence suggests these sex chromosomes are of recent origin, which is consistent with dioecy being derived character in the A. trichopoda lineage. Our work has uncovered clearly formed sex chromosomes in a species in which both genetic and environmental factors can influence sex. One Sentence SummaryAmborella trichopoda, a dioecious species in which both genetics and the environment influence sex, possesses a pair of quite recently evolved ZW chromosomes.

plant biology↗

bioRxiv2020

Development of genetic markers for sexing Cannabis sativa seedlings

Cannabis sativa is a dioecious plant with a XY system. Only females produce cannabinoids in large amount. Efficient male removal is an important issue for the cannabis industry. We have recently identified the sex chromosomes of C. sativa, which opens opportunities for developing universal genetic markers for early sexing of C. sativa plants. Here we selected six Y-linked markers and designed PCR primers, which were tested on five hemp cultivars both dioecious and monoecious. We obtained promising results, which need to be extended using a larger number of individuals and a more diverse set of cultivars, including THC producing ones.

plant biology↗

bioRxiv2020

Evidence for dosage compensation in Coccinia grandis, a plant with a highly heteromorphic XY system

Some ~15.000 angiosperms are dioecious, but mechanisms of sex determination in plants remain poorly understood. In particular, how Y chromosomes evolve and degenerate, and whether dosage compensation evolves as a response, are matters of debate. Here we focus on Coccinia grandis, a dioecious cucurbit with the highest level of X/Y heteromorphy recorded so far. We identified sex-linked genes using RNA sequences from a cross and a model-based method termed SEX-DETector. Parents and F1 individuals were genotyped and the transmission patterns of SNPs then analysed. In the >1300 sex-linked genes studied, X-Y divergence was 0.13 - 0.17, and substantial Y degeneration is implied by an average Y/X expression ratio of 0.63 and an inferred gene loss on the Y of ~40%. We also found reduced Y gene expression being compensated by elevated expression of corresponding genes on the X and an excess of sex-biased genes on the sex chromosomes. Molecular evolution of sex-linked genes in C. grandis is thus comparable to that in Silene latifolia, another dioecious plant with a strongly heteromorphic XY system, and cucurbits are the fourth plant family in which dosage compensation is described, suggesting it might be common in plants.

plant biology↗

bioRxiv2020

Detecting sex-linked genes using genotyped individuals sampled in natural populations

We propose a method, SDpop, able to infer sex-linkage caused by recombination suppression typical of sex chromosomes. The method is based on the modeling of the allele and genotype frequencies of individuals of known sex in natural populations. It is implemented in a hierarchical probabilistic framework, accounting for different sources of error. It allows to statistically test for the presence or absence of sex chromosomes, and to infer sex-linked genes based on the posterior probabilities in the model. Furthermore, for gametologous sequences, the haplotype and level of nucleotide polymorphism of each copy can be inferred, as well as the divergence between both. We test the method using simulated and human sequencing data, and show that, for most cases, robust predictions are obtained with 5 to 10 individuals per sex.

genomics↗

bioRxiv2020

The wild grape genome sequence provides insights into the transition from dioecy to hermaphroditism during grape domestication

Grapevine has a major economical and cultural importance since antiquity. A key step in domestication was the transition from separate sexes (dioecy) in wild Vitis vinifera ssp. sylvestris (V. sylvestris) to hermaphroditism in cultivated Vitis vinifera ssp. vinifera. While the grapevine sex locus is known to be small, its precise boundaries, gene content and the sex-determining genes are unknown. Here we obtained a high-quality de novo reference genome for V. sylvestris and whole-genome resequencing data of a cross. Studying SNP segregation patterns, gene content and expression in wild and cultivated accessions allowed us to build a model for sex determination in grapevine. In this model, up- and down-regulation of a cytokinin regulator is sufficient to cause female sterility and reversal to hermaphroditism, respectively. This study highlights the importance of neo-functionalization of Y alleles in sex determination and provides a resource for studying genetic diversity in V. sylvestris and the genomic processes of grapevine domestication.

plant biology↗

bioRxiv2019

A high-throughput segregation analysis identifies the sex chromosomes of Cannabis sativa

Cannabis sativa-derived tetrahydrocannabinol (THC) production is increasing very fast worldwide. C. sativa is a dioecious plant with XY chromosomes, and only females (XX) are useful for THC production. The C. sativa sex chromosomes sequence would improve early sexing and better management of this crop; however, the C. sativa genome projects failed to identify the sex chromosomes so far. Moreover, dioecy in the Cannabaceae family is ancestral, C. sativa sex chromosomes are potentially old and thus very interesting to study as little is known about the last steps of sex chromosome evolution in plants. Here we RNA-sequenced a C. sativa family (2 parents and 10 male and female offspring) and performed a segregation analysis for all C. sativa genes using the probabilistic method SEX-DETector. We identified >500 sex-linked genes. Mapping of these sex-linked genes to a C. sativa genome assembly identified a single chromosome pair with a large non-recombining region. Further analysis of the >500 sex-linked genes revealed that C. sativa has a strongly degenerated Y chromosome and represents the oldest plant sex chromosome system documented so far. Our study revealed that old plant sex chromosomes can have large non-recombining regions and be very differentiated and still be of similar size (homomorphic).

genomics↗

bioRxiv2018

Dioecy in plants: an evolutionary dead end? Insights from a population genomics study in the Silene genus

About 15,000 angiosperm species ([~]6%) have separate sexes, a phenomenon known as dioecy. Early work reported a lower species richness in dioecious compared to non-dioecious sister clades, which was taken to suggest that dioecy might be an evolutionary dead end. More recently, phylogenetic analyses using different methodologies have challenged this conclusion. Here, we used a population genomics approach to look for evidence of evolutionary handicaps of dioecy in the Silene genus at the molecular level. We obtained RNA-seq data of individuals from several populations in 13 closely related species with different breeding systems: seven dioecious, three hermaphroditic and three gynodioecious species. We show that dioecy is associated with increased genetic diversity and a higher selection efficacy both against deleterious and for beneficial mutations while controlling for differences in population size. We conclude that, in the Silene genus, dioecious species bear no sign of mutational burden or upcoming extinction. On the contrary, dioecious species harbor a higher potential for adaptation than their non-dioecious relatives. Our results do not support the evolutionary dead end hypothesis and re-open the question why dioecy is rare in angiosperms.\n\nSignificance statementDioecy (=separate sexes) is much rarer in flowering plants compared to animals and other organisms. The \"dead-end hypothesis\" states that dioecious plant populations might experience evolutionary handicaps such as low seed dispersal (as only 50% of the individuals, the females, contribute), which might cause high genetic drift, low adaptation and ultimately extinction. Here we tested this hypothesis by focusing on the genus Silene and by comparing the population genetics of 13 dioecious and non-dioecious species. We found that dioecious Silene species exhibit lower genetic drift and more adaptation compared to their non-dioecious relatives. Our results thus reject the dead-end hypothesis and re-open the question of why dioecy is rare in flowering plants.

evolutionary biology↗

bioRxiv2017

Hallmarks of early sex-chromosome evolution in the dioecious plant Mercurialis annua revealed by de novo genome assembly, genetic mapping and transcriptome analysis

Suppressed recombination around a sex-determining locus allows divergence between homologous sex chromosomes and the functionality of their genes. Here, we reveal patterns of the earliest stages of sex-chromosome evolution in the diploid dioecious herb Mercurialis annua on the basis of cytological analysis, de novo genome assembly and annotation, genetic mapping, exome resequencing of natural populations, and transcriptome analysis. Both genetic mapping and exome resequencing of individuals across the species range independently identified the largest linkage group, LG1, as the sex chromosome. Although the sex chromosomes of M. annua are karyotypically homomorphic, we estimate that about a third of the Y chromosome has ceased recombining, a region containing 568 transcripts and spanning 22.3 cM in the corresponding female map. Patterns of gene expression hint at the possible role of sexually antagonistic selection in having favored suppressed recombination. In total, the genome assembly contained 34,105 expressed genes, of which 10,076 were assigned to linkage groups. There was limited evidence of Y-chromosome degeneration in terms of gene loss and pseudogenization, but sequence divergence between the X and Y copies of many sex-linked genes was higher than between M. annua and its dioecious sister species M. huetii with which it shares a sex-determining region. The Mendelian inheritance of sex in interspecific crosses, combined with the other observed pattern, suggest that the M. annua Y chromosome has at least two evolutionary strata: a small old stratum shared with M. huetii, and a more recent larger stratum that is probably unique to M. annua and that stopped recombining about one million years ago. Article summaryPlants that evolved separate sexes (dioecy) recently are ideal models for studying the early stages of sex-chromosome evolution. Here, we use karyological, whole genome and transcriptome data to characterize the homomorphic sex chromosomes of the annual dioecious plant Mercurialis annua. Our analysis reveals many typical hallmarks of dioecy and sex-chromosome evolution, including sex-biased gene expression and high X/Y sequence divergence, yet few premature stop codons in Y-linked genes and very little outright gene loss, despite 1/3 of the sex chromosome having ceased recombination in males. Our results confirm that the M. annua species complex is a fertile system for probing early stages in the evolution of sex chromosomes.

genomics↗