Aline Muyle
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View article: Evolution of Sex-Biased Gene Expression During Transitions to Separate Sexes in the <i>Silene</i> Genus
Evolution of Sex-Biased Gene Expression During Transitions to Separate Sexes in the <i>Silene</i> Genus Open
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 (SBGs). SBGs have been stu…
View article: The <i>Silene latifolia</i> genome and its giant Y chromosome
The <i>Silene latifolia</i> genome and its giant Y chromosome Open
In many species with sex chromosomes, the Y is a tiny chromosome. However, the dioecious plant Silene latifolia has a giant ~550-megabase Y chromosome, which has remained unsequenced so far. We used a long- and short-read hybrid approach t…
View article: Sex Chromosome Evolution: Hallmarks and Question Marks
Sex Chromosome Evolution: Hallmarks and Question Marks Open
Sex chromosomes are widespread in species with separate sexes. They have evolved many times independently and display a truly remarkable diversity. New sequencing technologies and methodological developments have allowed the field of molec…
View article: Phased gap-free genome assembly of octoploid cultivated strawberry illustrates the genetic and epigenetic divergence among subgenomes
Phased gap-free genome assembly of octoploid cultivated strawberry illustrates the genetic and epigenetic divergence among subgenomes Open
The genetic and epigenetic mechanisms underlying the coexistence and coordination of the four diverged subgenomes (ABCD) in octoploid strawberries (Fragaria × ananassa) remains poorly understood. In this study, we have assembled a haplotyp…
View article: miRNA-like secondary structures in maize ( <i>Zea mays</i> ) genes and transposable elements correlate with small RNAs, methylation, and expression
miRNA-like secondary structures in maize ( <i>Zea mays</i> ) genes and transposable elements correlate with small RNAs, methylation, and expression Open
RNA molecules carry information in their primary sequence and also their secondary structure. Secondary structure can confer important functional information, but it is also a signal for an RNAi-like host epigenetic response mediated by sm…
View article: Evolution of sex-biased gene expression during transitions to separate sexes in the<i>Silene</i>genus
Evolution of sex-biased gene expression during transitions to separate sexes in the<i>Silene</i>genus Open
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 hav…
View article: The<i>Silene latifolia</i>genome and its giant Y chromosome
The<i>Silene latifolia</i>genome and its giant Y chromosome Open
In some species, the Y is a tiny chromosome but the dioecious plant Silene latifolia has a giant ∼550 Mb Y chromosome, which has remained unsequenced so far. Here we used a hybrid approach to obtain a high-quality male S. latifolia genome.…
View article: Diverse patterns of secondary structure across genes and transposable elements are associated with siRNA production and epigenetic fate
Diverse patterns of secondary structure across genes and transposable elements are associated with siRNA production and epigenetic fate Open
RNA molecules carry information in their primary sequence and also their secondary structure. Secondary structure can confer important functional information, but it is also a potential signal for an RNAi-like host epigenetic response medi…
View article: Dosage compensation evolution in plants: theories, controversies and mechanisms
Dosage compensation evolution in plants: theories, controversies and mechanisms Open
In a minority of flowering plants, separate sexes are genetically determined by sex chromosomes. The Y chromosome has a non-recombining region that degenerates, causing a reduced expression of Y genes. In some species, the lower Y expressi…
View article: Gene Body Methylation in Plants: Mechanisms, Functions, and Important Implications for Understanding Evolutionary Processes
Gene Body Methylation in Plants: Mechanisms, Functions, and Important Implications for Understanding Evolutionary Processes Open
Gene body methylation (gbM) is an epigenetic mark where gene exons are methylated in the CG context only, as opposed to CHG and CHH contexts (where H stands for A, C, or T). CG methylation is transmitted transgenerationally in plants, open…
View article: Gene body methylation is under selection in <i>Arabidopsis thaliana</i>
Gene body methylation is under selection in <i>Arabidopsis thaliana</i> Open
In plants, mammals and insects, some genes are methylated in the CG dinucleotide context, a phenomenon called gene body methylation (gbM). It has been controversial whether this phenomenon has any functional role. Here, we took advantage o…
View article: Epigenetics drive the evolution of sex chromosomes in animals and plants
Epigenetics drive the evolution of sex chromosomes in animals and plants Open
We review how epigenetics affect sex chromosome evolution in animals and plants. In a few species, sex is determined epigenetically through the action of Y-encoded small RNAs. Epigenetics is also responsible for changing the sex of individ…
View article: Plant epigenetics: phenotypic and functional diversity beyond the DNA sequence
Plant epigenetics: phenotypic and functional diversity beyond the DNA sequence Open
Phenotypic variation determines the capacity of plants to adapt to changing environments and to colonize new habitats. Deciphering the mechanisms contributing to plant phenotypic variation and their effects on plant ecological interactions…
View article: Chromosome‐scale assembly of the genome of <i>Salix</i> <i>dunnii</i> reveals a male‐heterogametic sex determination system on chromosome 7
Chromosome‐scale assembly of the genome of <i>Salix</i> <i>dunnii</i> reveals a male‐heterogametic sex determination system on chromosome 7 Open
Sex determination systems in plants can involve either female or male heterogamety (ZW or XY, respectively). Here we used Illumina short reads, Oxford Nanopore Technologies (ONT) long reads and Hi‐C reads to assemble the first chromosome‐s…
View article: Chromosome-scale assembly of the genome of<i>Salix dunnii</i>reveals a male-heterogametic sex determination system on chromosome 7
Chromosome-scale assembly of the genome of<i>Salix dunnii</i>reveals a male-heterogametic sex determination system on chromosome 7 Open
Sex determination systems in plants can involve either female or male heterogamety (ZW or XY, respectively). Here we used Illumina short reads, Oxford Nanopore Technologies (ONT) long reads, and Hi-C reads to assemble the first chromosome-…
View article: Dioecy Is Associated with High Genetic Diversity and Adaptation Rates in the Plant Genus<i>Silene</i>
Dioecy Is Associated with High Genetic Diversity and Adaptation Rates in the Plant Genus<i>Silene</i> Open
About 15,000 angiosperm species (∼6%) have separate sexes, a phenomenon known as dioecy. Why dioecious taxa are so rare is still an open question. Early work reported lower species richness in dioecious compared with nondioecious sister cl…
View article: Evidence for Dosage Compensation in Coccinia grandis, a Plant with a Highly Heteromorphic XY System
Evidence for Dosage Compensation in Coccinia grandis, a Plant with a Highly Heteromorphic XY System Open
About 15,000 angiosperms are dioecious, but the 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 …
View article: The genetic basis of sex determination in grapes
The genetic basis of sex determination in grapes Open
It remains a major challenge to identify the genes and mutations that lead to plant sexual differentiation. Here, we study the structure and evolution of the sex-determining region (SDR) in Vitis species. We report an improved, chromosome-…
View article: Evidence for dosage compensation in<i>Coccinia grandis</i>, a plant with a highly heteromorphic XY system
Evidence for dosage compensation in<i>Coccinia grandis</i>, a plant with a highly heteromorphic XY system Open
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 d…
View article: The genetic basis of sex determination in grapevines (<i>Vitis spp.</i>)
The genetic basis of sex determination in grapevines (<i>Vitis spp.</i>) Open
Sex determination in grapevine evolved through a complex succession of switches in sexual systems. Phased genomes built with single molecule real-time sequencing reads were assembled for eleven accessions of cultivated hermaphrodite grapev…
View article: Early Sex-Chromosome Evolution in the Diploid Dioecious Plant <i>Mercurialis annua</i>
Early Sex-Chromosome Evolution in the Diploid Dioecious Plant <i>Mercurialis annua</i> Open
Suppressed recombination 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…
View article: How different is the evolution of sex-biased gene expression between plants and animals? A commentary on: ‘Sexual dimorphism and rapid turnover in gene expression in pre-reproductive seedlings of a dioecious herb’
How different is the evolution of sex-biased gene expression between plants and animals? A commentary on: ‘Sexual dimorphism and rapid turnover in gene expression in pre-reproductive seedlings of a dioecious herb’ Open
This article comments on: Guillaume G. Cossard, Melissa A. Toups and John R. Pannell. 2019. Sexual dimorphism and rapid turnover in gene expression in pre-reproductive seedlings of a dioecious herb. Annals of Botany 123(7): 1119–1131.
View article: The Genomics of Selfing in Maize (<i>Zea mays</i>ssp.<i>mays</i>): Catching Purging in the Act
The Genomics of Selfing in Maize (<i>Zea mays</i>ssp.<i>mays</i>): Catching Purging in the Act Open
In plants, self-fertilization is both an important reproductive strategy and a valuable genetic tool. In theory, selfing increases homozygosity at a rate of 0.50 per generation. Increased homozygosity can uncover recessive deleterious vari…
View article: Evolution of Young Sex Chromosomes in Two Dioecious Sister Plant Species with Distinct Sex Determination Systems
Evolution of Young Sex Chromosomes in Two Dioecious Sister Plant Species with Distinct Sex Determination Systems Open
In the last decade, progress has been made in methods to identify the sex determination system in plants. This gives the opportunity to study sex chromosomes that arose independently at different phylogenetic scales, and thus allows the di…
View article: Loss of Gene Body Methylation in<i>Eutrema salsugineum</i>Is Associated with Reduced Gene Expression
Loss of Gene Body Methylation in<i>Eutrema salsugineum</i>Is Associated with Reduced Gene Expression Open
Gene body methylation (gbM) is typically characterized by DNA methylation in the CG context within coding regions and is associated with constitutive genes that have moderate to high expression levels. A recent study discovered the loss of…
View article: Dioecy in plants: an evolutionary dead end? Insights from a population genomics study in the <i>Silene</i> genus
Dioecy in plants: an evolutionary dead end? Insights from a population genomics study in the <i>Silene</i> genus Open
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 …