The Silene latifolia genome and its giant Y chromosome

Carol Moraga^#^{1

2

3}, Catarina Branco^#^{1

4

5

6}, Quentin Rougemont^#⁷, Pavel Jedlička⁸, Eddy Mendoza-Galindo⁹, Paris Veltsos¹⁰, Melissa Hanique¹¹, Ricardo C Rodríguez de la Vega⁷, Eric Tannier^{1

12}, Xiaodong Liu¹³, Claire Lemaitre¹⁴, Peter D Fields¹⁵, Corinne Cruaud¹⁶, Karine Labadie¹⁶, Caroline Belser¹⁶, Jerome Briolay¹⁷, Sylvain Santoni¹⁸, Radim Cegan⁸, Raquel Linheiro^{1

4

5

6}, Gabriele Adam¹¹, Adil El Filali¹, Vinciane Mossion¹⁹, Adnane Boualem¹¹, Raquel Tavares^{4

5

6}, Amine Chebbi²⁰, Richard Cordaux²¹, Cécile Fruchard¹, Djivan Prentout²², Amandine Velt²³, Bruno Spataro¹, Stephane Delmotte¹, Laura Weingartner²⁴, Helena Toegelová²⁵, Zuzana Tulpová²⁵, Petr Cápal²⁵, Hana Šimková²⁵, Helena Štorchová²⁶, Manuela Krüger²⁶, Oushadee A J Abeyawardana²⁶, Douglas R Taylor²⁷, Matthew S Olson²⁸, Daniel B Sloan¹⁵, Sophie Karrenberg¹⁹, Lynda F Delph²⁹, Deborah Charlesworth³⁰, Aline Muyle^{1

9}, Tatiana Giraud⁷, Abdelhafid Bendahmane¹¹, Alex Di Genova^{2

3

31}, Mohammed-Amin Madoui^{15

32}, Roman Hobza⁸, Gabriel A B Marais^{1

4

5

6

33}

Affiliations

¹ Laboratoire Biométrie et Biologie Evolutive (LBBE), CNRS/Université Claude Bernard Lyon 1, Villeurbanne, France.
² Instituto de Ciencias de la Ingeniería, Universidad de O'Higgins, Rancagua, Chile.
³ Centro UOH de Bioingenieria (CUBI), Universidad de O'Higgins, Rancagua, Chile.
⁴ CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO, Laboratório Associado, Campus de Vairão, Universidade do Porto, Vairão, Portugal.
⁵ Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Porto, Portugal.
⁶ BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, Vairão, Portugal.
⁷ Université Paris-Saclay, CNRS, AgroParisTech, Laboratoire Ecologie Systématique et Evolution, UMR 8079, Bâtiment 680, Gif-sur-Yvette, France.
⁸ Department of Plant Developmental Genetics, Institute of Biophysics of the Czech Academy of Sciences, Brno, Czech Republic.
⁹ Centre d'Ecologie Fonctionnelle et Evolutive (CEFE), University of Montpellier, CNRS, EPHE, IRD, Montpellier, France.
¹⁰ Ecology, Evolution and Genetics Research Group, Biology Department, Vrije Universiteit Brussel, Brussels, Belgium.
¹¹ Institute of Plant Sciences Paris-Saclay (IPS2), Université Paris-Saclay, CNRS, INRAE, Université d'Évry, Gif-sur-Yvette, France.
¹² Inria Lyon Research Center, Villeurbanne, France.
¹³ Department of Biology, University of Copenhagen, Copenhagen, Denmark.
¹⁴ Institut de Recherche en Informatique et Systèmes Aléatoires (IRISA), Université de Rennes, Inria, CNRS, Rennes, France.
¹⁵ Department of Biology, Colorado State University, Fort Collins, CO, USA.
¹⁶ Genoscope, Institut François Jacob, CEA, CNRS, Université d'Évry, Université Paris-Saclay, Évry, France.
¹⁷ Développement de Techniques et Analyse Moléculaire de la Biodiversité (DTAMB), Université Claude Bernard Lyon 1, Campus de la Doua, Villeurbanne, France.
¹⁸ Genomic Platform, Amélioration Génétique et Adaptation des Plantes Méditerranéennes et Tropicales (AGAP), Université de Montpellier, CIRAD, INRAE, Montpellier, France.
¹⁹ Department of Ecology and Genetics, Division of Plant Ecology and Evolution, Uppsala University, Uppsala, Sweden.
²⁰ Efor, Grosspeter Tower (Spaces), Basel, Switzerland.
²¹ Évolution Génomes Comportement Écologie, Université Paris-Saclay, CNRS, IRD, Gif-sur-Yvette, France.
²² Department of Biological Sciences, Columbia University, New York, NY, USA.
²³ Santé de la Vigne et Qualité du Vin (SVQV), INRAE, Colmar, France.
²⁴ University of Louisville School of Medicine, Undergraduate Medical Education, Louisville, KY, USA.
²⁵ Institute of Experimental Botany of the Czech Academy of Sciences, Olomouc, Czech Republic.
²⁶ Plant Reproduction Laboratory, Institute of Experimental Botany, Czech Academy of Sciences, Prague, Czech Republic.
²⁷ Department of Biology, University of Virginia, Charlottesville, VA, USA.
²⁸ Department of Biological Sciences, Texas Tech University, Lubbock, TX, USA.
²⁹ Department of Biology, Indiana University, Bloomington, IN, USA.
³⁰ Institute of Ecology and Evolution, School of Biological Sciences, University of Edinburgh, Ashworth Laboratories, Edinburgh, UK.
³¹ Center for Mathematical Modeling, UMI-CNRS 2807, Santiago, Chile.
³² Service d'Etude des Prions et des Infections Atypiques (SEPIA), Institut François Jacob, Commissariat à l'Energie Atomique et aux Energies Alternatives (CEA), Université Paris Saclay, Fontenay-aux-Roses, France.
³³ GreenUPorto-Sustainable Agrifood Production Research Centre, Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Vairão, Portugal.

^# Contributed equally.

PMID: 39913565
PMCID: PMC11890086 (available on 2026-02-07)
DOI: 10.1126/science.adj7430

The Silene latifolia genome and its giant Y chromosome

Carol Moraga et al. Science. 2025.

. 2025 Feb 7;387(6734):630-636.

doi: 10.1126/science.adj7430. Epub 2025 Feb 6.

Authors

Affiliations

¹ Laboratoire Biométrie et Biologie Evolutive (LBBE), CNRS/Université Claude Bernard Lyon 1, Villeurbanne, France.
² Instituto de Ciencias de la Ingeniería, Universidad de O'Higgins, Rancagua, Chile.
³ Centro UOH de Bioingenieria (CUBI), Universidad de O'Higgins, Rancagua, Chile.
⁴ CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO, Laboratório Associado, Campus de Vairão, Universidade do Porto, Vairão, Portugal.
⁵ Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Porto, Portugal.
⁶ BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, Vairão, Portugal.
⁷ Université Paris-Saclay, CNRS, AgroParisTech, Laboratoire Ecologie Systématique et Evolution, UMR 8079, Bâtiment 680, Gif-sur-Yvette, France.
⁸ Department of Plant Developmental Genetics, Institute of Biophysics of the Czech Academy of Sciences, Brno, Czech Republic.
⁹ Centre d'Ecologie Fonctionnelle et Evolutive (CEFE), University of Montpellier, CNRS, EPHE, IRD, Montpellier, France.
¹⁰ Ecology, Evolution and Genetics Research Group, Biology Department, Vrije Universiteit Brussel, Brussels, Belgium.
¹¹ Institute of Plant Sciences Paris-Saclay (IPS2), Université Paris-Saclay, CNRS, INRAE, Université d'Évry, Gif-sur-Yvette, France.
¹² Inria Lyon Research Center, Villeurbanne, France.
¹³ Department of Biology, University of Copenhagen, Copenhagen, Denmark.
¹⁴ Institut de Recherche en Informatique et Systèmes Aléatoires (IRISA), Université de Rennes, Inria, CNRS, Rennes, France.
¹⁵ Department of Biology, Colorado State University, Fort Collins, CO, USA.
¹⁶ Genoscope, Institut François Jacob, CEA, CNRS, Université d'Évry, Université Paris-Saclay, Évry, France.
¹⁷ Développement de Techniques et Analyse Moléculaire de la Biodiversité (DTAMB), Université Claude Bernard Lyon 1, Campus de la Doua, Villeurbanne, France.
¹⁸ Genomic Platform, Amélioration Génétique et Adaptation des Plantes Méditerranéennes et Tropicales (AGAP), Université de Montpellier, CIRAD, INRAE, Montpellier, France.
¹⁹ Department of Ecology and Genetics, Division of Plant Ecology and Evolution, Uppsala University, Uppsala, Sweden.
²⁰ Efor, Grosspeter Tower (Spaces), Basel, Switzerland.
²¹ Évolution Génomes Comportement Écologie, Université Paris-Saclay, CNRS, IRD, Gif-sur-Yvette, France.
²² Department of Biological Sciences, Columbia University, New York, NY, USA.
²³ Santé de la Vigne et Qualité du Vin (SVQV), INRAE, Colmar, France.
²⁴ University of Louisville School of Medicine, Undergraduate Medical Education, Louisville, KY, USA.
²⁵ Institute of Experimental Botany of the Czech Academy of Sciences, Olomouc, Czech Republic.
²⁶ Plant Reproduction Laboratory, Institute of Experimental Botany, Czech Academy of Sciences, Prague, Czech Republic.
²⁷ Department of Biology, University of Virginia, Charlottesville, VA, USA.
²⁸ Department of Biological Sciences, Texas Tech University, Lubbock, TX, USA.
²⁹ Department of Biology, Indiana University, Bloomington, IN, USA.
³⁰ Institute of Ecology and Evolution, School of Biological Sciences, University of Edinburgh, Ashworth Laboratories, Edinburgh, UK.
³¹ Center for Mathematical Modeling, UMI-CNRS 2807, Santiago, Chile.
³² Service d'Etude des Prions et des Infections Atypiques (SEPIA), Institut François Jacob, Commissariat à l'Energie Atomique et aux Energies Alternatives (CEA), Université Paris Saclay, Fontenay-aux-Roses, France.
³³ GreenUPorto-Sustainable Agrifood Production Research Centre, Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Vairão, Portugal.

^# Contributed equally.

PMID: 39913565
PMCID: PMC11890086 (available on 2026-02-07)
DOI: 10.1126/science.adj7430

Abstract

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.

PubMed Disclaimer

Conflict of interest statement

Competing interests: The authors declare that they have no competing interests.

References

1. Charlesworth D, Charlesworth B, Marais G, Heredity 95, 118–128 (2005). - PubMed
1. Bachtrog D et al., PLOS Biol. 12, e1001899 (2014). - PMC - PubMed
1. Ming R, Bendahmane A, Renner SS, Annu. Rev. Plant Biol. 62, 485–514 (2011). - PubMed
1. Rosolen LAM, Vicari MR, Almeida MC, Cytogenet. Genome Res. 156, 215–222 (2018). - PubMed
1. Muyle A, Shearn R, Marais GA, Genome Biol. Evol. 9, 627–645 (2017). - PMC - PubMed

MeSH terms

Actions
Actions
Actions
Actions
Actions
Actions
Actions

Grants and funding

R35 GM148134/GM/NIGMS NIH HHS/United States

LinkOut - more resources

Full Text Sources

Save citation to file

Email citation

Add to Collections

Add to My Bibliography

Your saved search

Create a file for external citation management software

Your RSS Feed

The Silene latifolia genome and its giant Y chromosome

Affiliations

The Silene latifolia genome and its giant Y chromosome

Authors

Affiliations

Abstract

Conflict of interest statement

References

MeSH terms

Grants and funding

LinkOut - more resources

Full Text Sources