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 to obtain a high-quality male genome. Comparative analysis of the sex chromosomes with their homologs in outgroups showed that the Y is highly rearranged and degenerated. Recombination suppression between X and Y extended in several steps and triggered a massive accumulation of repeats on the Y as well as in the nonrecombining pericentromeric region of the X, leading to giant sex chromosomes. Using sex phenotype mutants, we identified candidate sex-determining genes on the Y in locations consistent with their favoring recombination suppression events 11 and 5 million years ago.

Traditional agave spirits such as mezcal or tequila are produced all over Mexico using different species of Agave. Amongst them, A. angustifolia is the most popular given its agricultural extension. A. angustifolia is a wild species extensively distributed from North to Central America, and previous studies show that it is highly related to the tequila agave A. tequilana. In different regions of Mexico, A. angustifolia is cultivated under different types and levels of management, and although traditional producers identify several landraces, for the non-trained eye there are no perceivable differences. After interviews with producers from different localities in Jalisco, Mexico, we sampled A. angustifolia plants classified as different landraces, measured several morphological traits, and characterized their genetic differentiation and diversity at the genome-wide level. We included additional samples identified as A. tequilana and A. rhodacantha to evaluate their relationship with A. angustifolia. In contrast with previous studies, our pool of ca 20K high quality unlinked SNPs provided more information and helped us to distinguish different genetic groups that are congruent with the ethnobotanical landraces. We found no evidence to genetically delimitate A. tequilana, A. rhodacantha and A. angustifolia. Our large genome level dataset allows a better understanding of the genetic identity of important A. angustifolia traditional and autochthonous landraces.

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. Using mutants for sexual phenotype, we identified candidate sex-determining genes on the Y. Comparative analysis of the sex chromosomes with outgroups showed the Y is surprisingly rearranged and degenerated for a ∼11 MY-old system. Recombination suppression between X and Y extended in a stepwise process, and triggered a massive accumulation of repeats on the Y, as well as in the non-recombining pericentromeric region of the X, leading to giant sex chromosomes. One-Sentence Summary: This work uncovers the structure, function, and evolution of one of the largest giant Y chromosomes, that of the model plant Silene latifolia , which is almost 10 times larger than the human Y, despite similar genome sizes.

The selection of Arabidopsis as a model organism played a pivotal role in advancing genomic science, firmly establishing the cornerstone of today ‘s plant molecular biology. Competing frameworks to select an agricultural- or ecological-based model species, or to decentralize plant science and study a multitude of diverse species, were selected against in favor of building core knowledge in a species that would facilitate genome-enabled research that could assumedly be transferred to other plants. Here, we examine the ability of models based on Arabidopsis gene expression data to predict tissue identity in other flowering plant species. Comparing different machine learning algorithms, models trained and tested on Arabidopsis data achieved near perfect precision and recall values using the K-Nearest Neighbor method, whereas when tissue identity is predicted across the flowering plants using models trained on Arabidopsis data, precision values range from 0.69 to 0.74 and recall from 0.54 to 0.64, depending on the algorithm used. Below-ground tissue is more predictable than other tissue types, and the ability to predict tissue identity is not correlated with phylogenetic distance from Arabidopsis . This suggests that gene expression signatures rather than marker genes are more valuable to create models for tissue and cell type prediction in plants. Our data-driven results highlight that, in hindsight, the assertion that knowledge from Arabidopsis is translatable to other plants is not always true. Considering the current landscape of abundant sequencing data and computational resources, it may be prudent to reevaluate the scientific emphasis on Arabidopsis and to prioritize the exploration of plant diversity.

Background and Aims: Tequila agave (Agave tequilana var. azul) sustains one of the world’s most valuable spirit industries, yet its domestication history and genetic status remain incompletely understood. Historical and ethnobotanical evidence indicates that tequila was once produced from multiple A. tequilana landraces that have been largely replaced by a single clonal cultivar. We used genome-wide data to reconstruct the domestication history of tequila agave, quantify genetic diversity across cultivated, landrace and wild relatives, and determine whether independent clonal propagation generated genetic differentiation within the modern cultivar. Methods: We combined extensive field surveys across the Tequila Denomination of Origin with genotyping-by-sequencing of 92 accessions, including tequila agave, remnant A. tequilana landraces, and wild and managed taxa from the Agave angustifolia complex. Genome-wide SNPs were used to assess population structure, genetic diversity, domestication relationships and differentiation among lines maintained by different tequila producers. Key Results: Genome-wide analyses confirmed that A. tequilana is a domesticated derivative within the A. angustifolia complex. Modern tequila agave forms a highly homogeneous but not invariant lineage, retaining genetic variation likely preserved through long-term clonal propagation. Traditional landraces exhibited substantially greater genetic diversity and occupied intermediate positions along a domestication continuum from wild A. angustifolia to tequila agave. Despite extensive fieldwork, landraces were found to persist only as isolated ornamental individuals. We detected subtle genetic differentiation among tequila agave lineages maintained by different producers. Conclusions: Tequila agave represents an extreme example of clonal domestication where industrial production and regulatory frameworks have driven profound genetic and biocultural erosion. Although clonal propagation buffered the complete loss of genetic variation, the near disappearance of traditional landraces eliminated unique domestication-associated diversity. Rescuing remnant landraces and wild relatives is essential to preserve evolutionary potential, enhance crop resilience, and support the long-term sustainability of tequila production.