Biology subjects

Ricciardi, V.

Publications and source records attributed to Ricciardi, V..

3 recordsLinked to original sources

bioRxiv2025

Two independent origins of XY sex chromosomes in Asparagus

The relatively young and repeated evolutionary origins of dioecy (separate sexes) in flowering plants enable investigation of molecular dynamics occurring at the earliest stages of sex chromosome evolution. With two independently young origins of dioecy in the genus, Asparagus is a model taxon for studying genetic sex-determination and sex chromosome evolution. Dioecy first evolved in Asparagus [~]3-4 million years ago (Ma) in the ancestor of a now widespread Eurasian clade that includes garden asparagus (Asparagus officinalis), while the second origin occurred in a smaller, geographically restricted, Mediterranean Basin clade including Asparagus horridus. The XY sex chromosomes and sex-determination genes in garden asparagus have been well characterized, but the genetics underlying dioecy in the Mediterranean Basin clade are unknown. We generated new haplotype-resolved reference genomes for garden asparagus and A. horridus, to elucidate the sex chromosomes of A. horridus and explore how dioecy evolved between these two closely related lineages. Analysis of the A. horridus genome revealed an independently evolved XY system derived from different ancestral autosomes (chromosome 3) with different sex-determining genes than documented for garden asparagus (on chromosome 1). We estimate that proto-XY chromosomes evolved around 1-2 Ma in the Mediterranean Basin clade, following an [~]2.1-megabase inversion between the ancestral pair. Recombination suppression and LTR retrotransposon accumulation drove the establishment and expansion of the Y-linked sex-determination region (Y-SDR) that now reaches [~]9.6-megabases in A. horridus. The new garden asparagus genome revealed a Y-SDR that spans [~]1.9-megabases with ten hemizygous genes. Our results evoke hemizygosity as the most probable mechanism responsible for the origin of proto-XY recombination suppression in the Eurasian clade, and that neofunctionalization of one duplicated gene (SOFF) drove the origin of dioecy. These findings support previous inference based on phylogeographic analysis revealing two recent origins of dioecy in Asparagus. Moreover, this work implicates alternative molecular mechanisms for two separate shifts to dioecy in a model taxon important for investigating young sex chromosome evolution. SIGNIFICANCE STATEMENTFlowering plants with separate sexes are ideal systems for investigating genome dynamics underlying the earliest stages of sex chromosome evolution across the tree of life. We use Asparagus as a model to better understand early sex chromosome formation more generally, by investigating how different XY sex chromosomes evolved between two young, closely related clades. Genomic comparisons of garden asparagus and Asparagus horridus (wild related species) revealed distinct evolutionary origins of XY-chromosomes with different sex-determination mechanisms. Whereas the garden asparagus Y-chromosome originally evolved around 3-4 million years ago (Ma), following a small segmental duplication, the Y-chromosome in Asparagus horridus evolved more recently ([~]1-2 Ma) following a large structural inversion between a different chromosome pair. Interestingly, both evolutionary transitions from hermaphroditism to separate sexes occurred as ancestors of garden asparagus and Asparagus horridus independently dispersed northward out of southern Africa.

evolutionary biology↗

bioRxiv2024

Evolutionary history of the grape sex-determining region in angiosperms and emergence of dioecy in Vitaceae

Dioecy, defined by the presence of either female or male flowers on separate individual plants, is rare in angiosperms. However, it has independently evolved multiple times from hermaphroditic ancestors. In Vitis spp., flower sex is determined by a [~]200-kbp region with five genes involved in flower development and sexual identity. This study traces the evolutionary history of the Vitis sex-determining region (SDR) to assess whether it evolved in a conserved flowering-related locus. We analyzed the conservation of the Vitis SDR across 42 plant genomes and found collinearity in all 39 angiosperms, but not in non-flowering plants. The number of collinear genes and their rank-normalized gene conservation score were higher in the Vitis SDR compared to the rest of the genome, indicating its importance for flowering. We further explored SDR conservation within the Vitaceae family by long-read sequencing and haplotype phasing of eight species, including the outgroup Leea coccinea. Similarly, the Vitis SDR was highly conserved across the Vitaceae genomes, although variations in region size, primarily attributed to differences in repetitive elements, were observed. Interestingly, no recombination suppression was found in the dioecious Tetrastigma, suggesting a different sex determination mechanism. In Muscadinia rotundifolia, linkage disequilibrium analysis, haplotype comparison, and gene expression profiling showed that muscadine grapes have similar SDR boundaries and candidate sex-determining genes as Vitis. These results suggest that dioecy emerged in a common ancestor of the two grape genera at a locus associated with flower morphology and fertility, highly conserved in flowering plants.

evolutionary biology↗

bioRxiv2020

The drought-responsive ZmFDL1 gene regulates cuticle biosynthesis and cuticle-dependent leaf permeability

In higher plants, the outer surface of the aerial parts is covered by the cuticle, a complex lipid layer that constitutes a barrier against damages caused by environmental factors and provides protection against non-stomatal water loss. We show in this study that cuticle deposition, during the juvenile phase of in maize (Zea mays) plant development, and cuticle-dependent leaf permeability are controlled by the MYB transcription factor ZmMYB94/FUSED LEAVES1 (ZmFDL1). Biochemical analysis showed that in fdl1-1 mutant seedlings at the coleoptile stage both cutin and wax biosynthesis and deposition were altered. Among cutin compounds, {omega}-hydroxy fatty acids and polyhydroxy-fatty acids were specifically affected, while the reduction of epicuticular waxes, was mainly observed in primary long chain alcohols, and to a minor extent, long-chain wax esters. Transcriptome analysis allowed the identification of novel candidate genes involved in lipid metabolism and the assembly of a proposed pathway for cuticle biosynthesis in maize. Lack of ZmFDL1 affects the expression of genes located in different modules of the pathway and correspondence between gene transcriptional variations and biochemical defects have been highlighted. A decrease in cuticle-dependent leaf permeability was observed in maize seedlings exposed to drought as well as ABA treatment, which implies coordinated changes in the transcript levels of ZmFDL1 and associated genes. Overall, our results suggest that the response to water stress implies the activation of wax biosynthesis and the involvement of by both ZmFDL1 and ABA regulatory pathways. One-Sentence SummaryCuticle biosynthesis and cuticle-mediated drought-response during the juvenile phase of maize plant growth, are regulated by the MYB transcription factor fused leaves1 (ZmFDL1) and influenced by ABA.

plant biology↗