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.

BIOPOLIS Program in Genomics Biodiversity and Land Planning CIBIO Campus de Vairão Vairão Portugal

Center for Mathematical Modeling UMI CNRS 2807 Santiago Chile

Centre d'Ecologie Fonctionnelle et Evolutive University of Montpellier CNRS EPHE IRD Montpellier France

Centro UOH de Bioingenieria Universidad de O'Higgins Rancagua Chile

CIBIO Centro de Investigação em Biodiversidade e Recursos Genéticos InBIO Laboratório Associado Campus de Vairão Universidade do Porto Vairão Portugal

Departamento de Biologia Faculdade de Ciências Universidade do Porto Porto Portugal

Department of Biological Sciences Columbia University New York NY USA

Department of Biological Sciences Texas Tech University Lubbock TX USA

Department of Biology Colorado State University Fort Collins CO USA

Department of Biology Indiana University Bloomington IN USA

Department of Biology University of Copenhagen Copenhagen Denmark

Department of Biology University of Virginia Charlottesville VA USA

Department of Ecology and Genetics Division of Plant Ecology and Evolution Uppsala University Uppsala Sweden

Department of Plant Developmental Genetics Institute of Biophysics of the Czech Academy of Sciences Brno Czech Republic

Développement de Techniques et Analyse Moléculaire de la Biodiversité Université Claude Bernard Lyon 1 Campus de la Doua Villeurbanne France

Ecology Evolution and Genetics Research Group Biology Department Vrije Universiteit Brussel Brussels Belgium

Efor Grosspeter Tower Basel Switzerland

Évolution Génomes Comportement Écologie Université Paris Saclay CNRS IRD Gif sur Yvette France

Genomic Platform Amélioration Génétique et Adaptation des Plantes Méditerranéennes et Tropicales Université de Montpellier CIRAD INRAE Montpellier France

Genoscope Institut François Jacob CEA CNRS Université d'Évry Université Paris Saclay Évry France

GreenUPorto Sustainable Agrifood Production Research Centre Departamento de Biologia Faculdade de Ciências Universidade do Porto Vairão Portugal

Inria Lyon Research Center Villeurbanne France

Institut de Recherche en Informatique et Systèmes Aléatoires Université de Rennes Inria CNRS Rennes France

Institute of Ecology and Evolution School of Biological Sciences University of Edinburgh Ashworth Laboratories Edinburgh UK

Institute of Experimental Botany of the Czech Academy of Sciences Olomouc Czech Republic

Institute of Plant Sciences Paris Saclay Université Paris Saclay CNRS INRAE Université d'Évry Gif sur Yvette France

Instituto de Ciencias de la Ingeniería Universidad de O'Higgins Rancagua Chile

Laboratoire Biométrie et Biologie Evolutive CNRS Université Claude Bernard Lyon 1 Villeurbanne France

Plant Reproduction Laboratory Institute of Experimental Botany Czech Academy of Sciences Prague Czech Republic

Santé de la Vigne et Qualité du Vin INRAE Colmar France

Service d'Etude des Prions et des Infections Atypiques Université Paris Saclay Fontenay aux Roses France

Université Paris Saclay CNRS AgroParisTech Laboratoire Ecologie Systématique et Evolution UMR 8079 Bâtiment 680 Gif sur Yvette France

University of Louisville School of Medicine Undergraduate Medical Education Louisville KY USA

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