The Silene latifolia genome and its giant Y chromosome

Carol Moraga; Catarina Branco; Quentin Rougemont; Paris Veltsos; Pavel Jedlička; Aline Muyle; Mélissa Hanique; Eric Tannier; Xiaodong Liu; Eddy Mendoza-Galindo; Claire Lemaitre; Peter D. Fields; Corinne Cruaud; Karine Labadie; Caroline Belser; Jérôme Briolay; Sylvain Santoni; Radim Cegan; Raquel Linheiro; Ricardo C. Rodríguez de la Vega; Gabriele Adam; Adil El Filali; Vinciane Mossion; Adnane Boualem; Raquel Tavares; Amine Chebbi; Richard Cordaux; Cécile Fruchard; Djivan Prentout; Amandine Velt; Bruno Spataro; Stephane Delmotte; Laura Weingartner; Helena Toegelová; Zuzana Tulpová; Petr Cápal; Hana Šimková; Helena Štorchová; Manuela Krüger; Oushadee A. J. Abeyawardana; Douglas R. Taylor; Matthew S. Olson; Daniel B. Sloan; Sophie Karrenberg; Lynda F. Delph; Deborah Charlesworth; Tatiana Giraud; Abdelhafid Bendahmane; Alex Di Genova; Mohammed‐Amin Madoui; Roman Hobza; Gabriel Marais

doi:10.1126/science.adj7430

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The Silene latifolia genome and its giant Y chromosome

Journal article

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The Silene latifolia genome and its giant Y chromosome

Carol Moraga, Catarina Branco, Quentin Rougemont, Paris Veltsos, Pavel Jedlička, Aline Muyle, Mélissa Hanique, Eric Tannier, Xiaodong Liu, Eddy Mendoza-Galindo, …

Science, Vol.387(6734), pp.630-636

06/02/2025

DOI: https://doi.org/10.1126/science.adj7430

PMID: 39913565

Abstract

plant genome

Y chromosome

evolutionary genomics

candidate gene

sexual phenotype

phenotypic sex

SRY

testis determining factor

TDF

SRY gene

sex-determining region of the Y chromosome

gonosome

sex chromosome

molecular evolution

gene function

plant model

transposon

mobile element

jumping gene

transposable element

major sex determining gene

major sex-determining gene

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.

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Title: The Silene latifolia genome and its giant Y chromosome
Creators - without role: Carol Moraga - Université Claude Bernard Lyon 1
Catarina Branco - Laboratoire de Biométrie et Biologie Evolutive
Quentin Rougemont - AgroParisTech
Paris Veltsos - Vrije Universiteit Brussel
Pavel Jedlička - Czech Academy of Sciences, Institute of Biophysics
Aline Muyle - Université de Montpellier, Centre d'Ecologie Fonctionnelle et Evolutive - CEFE
Mélissa Hanique - Université Paris-Saclay
Eric Tannier - Université Claude Bernard Lyon 1
Xiaodong Liu - University of Copenhagen
Eddy Mendoza-Galindo - Université de Montpellier, Centre d'Ecologie Fonctionnelle et Evolutive - CEFE
Claire Lemaitre - Université de Rennes
Peter D. Fields - Colorado State University
Corinne Cruaud - Centre National de la Recherche Scientifique
Karine Labadie - Centre National de la Recherche Scientifique
Caroline Belser - Centre National de la Recherche Scientifique
Jérôme Briolay - Université Claude Bernard Lyon 1
Sylvain Santoni - Université de Montpellier, Institut Amélioration Génétique & Adaptation des Plantes méditerranéennes & tropicales-AGAP
Radim Cegan - Czech Academy of Sciences, Institute of Biophysics
Raquel Linheiro - Laboratoire de Biométrie et Biologie Evolutive
Ricardo C. Rodríguez de la Vega - Écologie, Systématique et Évolution
Gabriele Adam - Université Paris-Saclay
Adil El Filali - Laboratoire de Biométrie et Biologie Evolutive
Vinciane Mossion - Uppsala University
Adnane Boualem - Université Paris-Saclay
Raquel Tavares - Universidade do Porto
Amine Chebbi - EFOR Group
Richard Cordaux - Université Paris-Saclay
Cécile Fruchard - Laboratoire de Biométrie et Biologie Evolutive
Djivan Prentout - Columbia University
Amandine Velt - Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement
Bruno Spataro - Laboratoire de Biométrie et Biologie Evolutive
Stephane Delmotte - Laboratoire de Biométrie et Biologie Evolutive
Laura Weingartner - University of Louisville
Helena Toegelová - Czech Academy of Sciences, Institute of Experimental Botany
Zuzana Tulpová - Czech Academy of Sciences, Institute of Experimental Botany
Petr Cápal - Czech Academy of Sciences, Institute of Experimental Botany
Hana Šimková - Czech Academy of Sciences, Institute of Experimental Botany
Helena Štorchová - Czech Academy of Sciences, Institute of Experimental Botany
Manuela Krüger - Czech Academy of Sciences, Institute of Experimental Botany
Oushadee A. J. Abeyawardana - Czech Academy of Sciences, Institute of Experimental Botany
Douglas R. Taylor - University of Virginia
Matthew S. Olson - Texas Tech University
Daniel B. Sloan - Colorado State University
Sophie Karrenberg - Uppsala University
Lynda F. Delph - Indiana University Bloomington
Deborah Charlesworth - University of Edinburgh
Tatiana Giraud - AgroParisTech
Abdelhafid Bendahmane - Université Paris-Saclay
Alex Di Genova - Center for Mathematical Modeling
Mohammed‐Amin Madoui - Colorado State University
Roman Hobza - Czech Academy of Sciences, Institute of Biophysics
Gabriel Marais - Laboratoire de Biométrie et Biologie Evolutive
Publication Details: Science, Vol.387(6734), pp.630-636
Grant note: The Czech Science Foundation grants 21-00580S and 22-00364
Identifiers: 9934128809311
Academic Unit: Institut Amélioration Génétique & Adaptation des Plantes méditerranéennes & tropicales-AGAP; Centre d'Ecologie Fonctionnelle et Evolutive - CEFE
Language: English
Resource Type: Journal article
Local Fields: hal-04293712