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1. Two independent origins of XY sex chromosomes in Asparagus

   https://doi.org/10.1101/2025.09.05.674532  

   Bentz, Philip C; Carey, Sarah B; Mercati, Francesco; Hale, Haley; Ricciardi, Valentina; Sunseri, Francesco; Harkess, Alex; Leebens-Mack, Jim (September 2025, bioRxiv)

   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,Asparagusis a model taxon for studying genetic sex-determination and sex chromosome evolution. Dioecy first evolved inAsparagus~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 includingAsparagus 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 andA. horridus, to elucidate the sex chromosomes ofA. horridusand explore how dioecy evolved between these two closely related lineages. Analysis of theA. horridusgenome 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 inA. 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 inAsparagus. Moreover, this work implicates alternative molecular mechanisms for two separate shifts to dioecy in a model taxon important for investigating young sex chromosome evolution. 

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2. Bursts of Rapid Diversification, Dispersals Out of Southern Africa, and Two Origins of Dioecy Punctuate the Evolution of Asparagus

   https://doi.org/10.1093/gbe/evae200  

   Bentz, Philip C; Burrows, John E; Burrows, Sandra M; Mizrachi, Eshchar; Liu, Zhengjie; Yang, Junbo; Mao, Zichao; Popecki, Margot; Seberg, Ole; Petersen, Gitte; et al (October 2024, Genome Biology and Evolution)

   Sloan, Daniel (Ed.)

   Abstract The genus Asparagus arose ∼9 to 15 million years ago (Ma), and transitions from hermaphroditism to dioecy (separate sexes) occurred ∼3 to 4 Ma. Roughly 27% of extant Asparagus species are dioecious, while the remaining are bisexual with monoclinous flowers. As such, Asparagus is an ideal model taxon for studying the early stages of dioecy and sex chromosome evolution in plants. Until now, however, understanding of diversification and shifts from hermaphroditism to dioecy in Asparagus has been hampered by the lack of robust species tree estimates for the genus. In this study, a genus-wide phylogenomic analysis including 1,726 nuclear loci and comprehensive species sampling supports two independent origins of dioecy in Asparagus—first in a widely distributed Eurasian clade and then in a clade restricted to the Mediterranean Basin. Modeling of ancestral biogeography indicates that both dioecy origins were associated with range expansion out of southern Africa. Our findings also reveal several bursts of diversification across the phylogeny, including an initial radiation in southern Africa that gave rise to 12 major clades in the genus, and more recent radiations that have resulted in paraphyly and polyphyly among closely related species, as expected given active speciation processes. Lastly, we report that the geographic origin of domesticated garden asparagus (Asparagus officinalis L.) was likely in western Asia near the Mediterranean Sea. The presented phylogenomic framework for Asparagus is foundational for ongoing genomic investigations of diversification and functional trait evolution in the genus and contributes to its utility for understanding the origin and early evolution of dioecy and sex chromosomes. 

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3. Young evolutionary origins of dioecy in the genus Asparagus

   https://doi.org/10.1002/ajb2.16276  

   Bentz, Philip C.; Liu, Zhengjie; Yang, Jun‐Bo; Zhang, Le; Burrows, Sandra; Burrows, John; Kanno, Akira; Mao, Zichao; Leebens‐Mack, Jim (February 2024, American Journal of Botany)

   Abstract PremiseDioecy (separate sexes) has independently evolved numerous times across the angiosperm phylogeny and is recently derived in many lineages. However, our understanding is limited regarding the evolutionary mechanisms that drive the origins of dioecy in plants. The recent and repeated evolution of dioecy across angiosperms offers an opportunity to make strong inferences about the ecological, developmental, and molecular factors influencing the evolution of dioecy, and thus sex chromosomes. The genusAsparagus(Asparagaceae) is an emerging model taxon for studying dioecy and sex chromosome evolution, yet estimates for the age and origin of dioecy in the genus are lacking. MethodsWe use plastome sequences and fossil time calibrations in phylogenetic analyses to investigate the age and origin of dioecy in the genusAsparagus. We also review the diversity of sexual systems present across the genus to address contradicting reports in the literature. ResultsWe estimate that dioecy evolved once or twice approximately 2.78−3.78 million years ago inAsparagus, of which roughly 27% of the species are dioecious and the remaining are hermaphroditic with monoclinous flowers. ConclusionsOur findings support previous work implicating a young age and the possibility of two origins of dioecy inAsparagus, which appear to be associated with rapid radiations and range expansion out of Africa. Lastly, we speculate that paleoclimatic oscillations throughout northern Africa may have helped set the stage for the origin(s) of dioecy inAsparagusapproximately 2.78−3.78 million years ago. 

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4. ZW sex chromosome structure in Amborella trichopoda

   https://doi.org/10.1038/s41477-024-01858-x  

   Carey, Sarah B; Aközbek, Laramie; Lovell, John T; Jenkins, Jerry; Healey, Adam L; Shu, Shengqiang; Grabowski, Paul; Yocca, Alan; Stewart, Ada; Jones, Teresa; et al (December 2024, Nature Plants)

   Sex chromosomes have evolved hundreds of times across the flowering plant tree of life; their recent origins in some members of this clade can shed light on the early consequences of suppressed recombination, a crucial step in sex chromosome evolution. Amborella trichopoda, the sole species of a lineage that is sister to all other extant flowering plants, is dioecious with a young ZW sex determination system. Here we present a haplotype-resolved genome assembly, including highly contiguous assemblies of the Z and W chromosomes. We identify a ~3-megabase sex-determination region (SDR) captured in two strata that includes a ~300-kilobase inversion that is enriched with repetitive sequences and contains a homologue of the Arabidopsis METHYLTHIOADENOSINE NUCLEOSIDASE (MTN1-2) genes, which are known to be involved in fertility. However, the remainder of the SDR does not show patterns typically found in non-recombining SDRs, such as repeat accumulation and gene loss. These findings are consistent with the hypothesis that dioecy is derived in Amborella and the sex chromosome pair has not significantly degenerated. 

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5. The Diversity and Evolution of Sex Chromosomes in Frogs

   https://doi.org/10.3390/genes12040483  

   Ma, Wen-Juan; Veltsos, Paris (April 2021, Genes)

   Frogs are ideal organisms for studying sex chromosome evolution because of their diversity in sex chromosome differentiation and sex-determination systems. We review 222 anuran frogs, spanning ~220 Myr of divergence, with characterized sex chromosomes, and discuss their evolution, phylogenetic distribution and transitions between homomorphic and heteromorphic states, as well as between sex-determination systems. Most (~75%) anurans have homomorphic sex chromosomes, with XY systems being three times more common than ZW systems. Most remaining anurans (~25%) have heteromorphic sex chromosomes, with XY and ZW systems almost equally represented. There are Y-autosome fusions in 11 species, and no W-/Z-/X-autosome fusions are known. The phylogeny represents at least 19 transitions between sex-determination systems and at least 16 cases of independent evolution of heteromorphic sex chromosomes from homomorphy, the likely ancestral state. Five lineages mostly have heteromorphic sex chromosomes, which might have evolved due to demographic and sexual selection attributes of those lineages. Males do not recombine over most of their genome, regardless of which is the heterogametic sex. Nevertheless, telomere-restricted recombination between ZW chromosomes has evolved at least once. More comparative genomic studies are needed to understand the evolutionary trajectories of sex chromosomes among frog lineages, especially in the ZW systems. 

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