The <i>Silene latifolia</i> genome and its giant Y chromosome
In many species with sex chromosomes, the Y is a tiny chromosome. However, the dioecious plant <i>Silene latifolia</i> 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.
Authors
- Oushadee A. J. Abeyawardana (ORCID: https://orcid.org/0000-0002-1149-3010)
- Mohammed‐Amin Madoui (ORCID: https://orcid.org/0000-0003-4809-2971)
- Quentin Rougemont (ORCID: https://orcid.org/0000-0003-2987-3801)
- Aline Muyle (ORCID: https://orcid.org/0000-0002-2200-2336)
- Alex Di Genova (ORCID: https://orcid.org/0000-0002-3120-9283)
- L Weingärtner (ORCID: https://orcid.org/0000-0003-0820-3980)
- Karine Labadie (ORCID: https://orcid.org/0000-0001-7467-8509)
- Manuela Krüger (ORCID: https://orcid.org/0000-0001-9223-3570)
- Petr Cápal (ORCID: https://orcid.org/0000-0002-8888-9101)
- Eddy Mendoza-Galindo (ORCID: https://orcid.org/0000-0001-7991-6270)
- Gabriele Adam
- Jérôme Briolay (ORCID: https://orcid.org/0000-0001-9251-4903)
- Paris Veltsos (ORCID: https://orcid.org/0000-0002-8872-6281)
- Vinciane Mossion (ORCID: https://orcid.org/0000-0002-8429-1014)
- Éric Tannier (ORCID: https://orcid.org/0000-0002-3681-7536)
- Cécile Fruchard
- Pavel Jedlička (ORCID: https://orcid.org/0000-0001-9324-5151)
- Caroline Belser (ORCID: https://orcid.org/0000-0002-8108-9910)
- Adil El Filali (ORCID: https://orcid.org/0000-0001-5183-0010)
- Stéphane Delmotte
- Amine Chebbi
- Zuzana Tulpová (ORCID: https://orcid.org/0000-0002-4403-9367)
- Melissa Hanique
- Amandine Velt (ORCID: https://orcid.org/0000-0003-2368-839X)
- B. Spataro (ORCID: https://orcid.org/0000-0002-3036-2657)
- Djivan Prentout (ORCID: https://orcid.org/0000-0002-3088-3954)
- Adnane Boualem (ORCID: https://orcid.org/0000-0003-4428-6496)
- Deborah Charlesworth (ORCID: https://orcid.org/0000-0002-3939-9122)
- Corinne Cruaud (ORCID: https://orcid.org/0000-0002-4752-7278)
- Lynda F. Delph (ORCID: https://orcid.org/0000-0003-3257-2698)
- Raquel Linheiro (ORCID: https://orcid.org/0000-0003-2659-0910)
- Roman Hobza (ORCID: https://orcid.org/0000-0003-3062-2962)
- Raquel Tavares
- Tatiana Giraud (ORCID: https://orcid.org/0000-0002-2685-6478)
- Gabriel Marais (ORCID: https://orcid.org/0000-0003-2134-5967)
- Ricardo C. Rodŕıguez de la Vega (ORCID: https://orcid.org/0000-0002-9852-6654)
- Radim Čegan (ORCID: https://orcid.org/0000-0002-6789-6564)
- Richard Cordaux (ORCID: https://orcid.org/0000-0003-4997-735X)
- Sophie Karrenberg (ORCID: https://orcid.org/0000-0002-7146-588X)
- Abdelhafid Bendahmane (ORCID: https://orcid.org/0000-0003-3246-868X)
- Catarina Branco (ORCID: https://orcid.org/0000-0002-6669-2519)
- Diane E. Taylor (ORCID: https://orcid.org/0000-0002-2568-140X)
- Helena Toegelová (ORCID: https://orcid.org/0000-0001-6983-0609)
- Daniel B. Sloan (ORCID: https://orcid.org/0000-0002-3618-0897)
- Carol Moraga (ORCID: https://orcid.org/0000-0002-7659-1287)
- Claire Lemaitre (ORCID: https://orcid.org/0000-0001-8675-170X)
- Peter D. Fields (ORCID: https://orcid.org/0000-0003-2959-2524)
- Helena Štorchová (ORCID: https://orcid.org/0000-0001-6701-179X)
- Matthew S. Olson (ORCID: https://orcid.org/0000-0002-0798-145X)
- Xiaodong Liu (ORCID: https://orcid.org/0000-0001-8839-2659)
- Sylvain Santoni (ORCID: https://orcid.org/0000-0002-4537-7982)
- Hana Šimková (ORCID: https://orcid.org/0000-0003-4159-7619)
Institutions
- Université Claude Bernard Lyon 1 (FR)
- Texas Tech University (US)
- Uppsala University (SE)
- University of Copenhagen (DK)
- Centre National de la Recherche Scientifique (FR)
- Centre de Coopération Internationale en Recherche Agronomique pour le Développement (FR)
- Vrije Universiteit Brussel (BE)
- University of Louisville (US)
- École Pratique des Hautes Études (FR)
- Universidade do Porto (PT)
- Université de Montpellier (FR)
- Commissariat à l'Énergie Atomique et aux Énergies Alternatives (FR)
- Université Paris-Saclay (FR)
- Institut de Recherche en Informatique et Systèmes Aléatoires (FR)
- Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement (FR)
- Centre d'Écologie Fonctionnelle et Évolutive (FR)
- Czech Academy of Sciences, Institute of Biophysics (CZ)
- Institut des Sciences des Plantes de Paris Saclay (FR)
- Ecologie, Société, Evolution (FR)
- Communauté urbaine de Lyon (FR)
- Santé et Agroécologie du Vignoble (FR)
- Évolution, Génomes, Comportement, Écologie (FR)
- Genoscope (FR)
- Indiana University Bloomington (US)
- Amélioration Génétique et Adaptation des Plantes méditerranéennes et tropicales (FR)
- Santé de la Vigne et Qualité du Vin (FR)
- CEA Paris-Saclay (FR)
- Centre for Immunity, Infection and Evolution (GB)
- Institut de Biologia Evolutiva (ES)
- Laboratoire de Biométrie et Biologie Evolutive (FR)
- University of O'Higgins (CL)
- Institute of Mathematics and Mathematical Modeling (KZ)
- Miguel de Cervantes University (CL)
- Czech Academy of Sciences, Institute of Experimental Botany (CZ)
- Institut de Recherche pour le Développement (FR)
- University of Virginia (US)
- Columbia University (US)
- International Space Science Institute (CH)
- Colorado State University (US)
Publication Details
- Journal
- Science
- Published
- 2025-02-06
- DOI
- https://doi.org/10.1126/science.adj7430
- Citations
- 27
- Primary Topic
- Plant Reproductive Biology
- Type
- article
- Field-Weighted Citation Impact
- 21.76
Funders
- Agence Nationale de la Recherche
- Grantová Agentura České Republiky
- Université de Lyon