The Silene latifolia genome and its giant Y chromosome

Carol Moraga; Catarina Branco; Quentin Rougemont; Pavel Jedlička; Eddy Mendoza-Galindo; Paris Veltsos; Melissa Hanique; Ricardo C. Rodríguez de la Vega; Eric Tannier; Xiaodong Liu; Claire Lemaitre; Peter D. Fields; Corinne Cruaud; Karine Labadie; Caroline Belser; Jerome Briolay; Sylvain Santoni; Radim Cegan; Raquel Linheiro; 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; Aline Muyle; Tatiana Giraud; Abdelhafid Bendahmane; Alex Di Genova; Mohammed Amin Madoui; Roman Hobza; Gabriel A.B. Marais

doi:10.1126/science.adj7430

The Silene latifolia genome and its giant Y chromosome

Carol Moraga, Catarina Branco, Quentin Rougemont, Pavel Jedlička, Eddy Mendoza-Galindo, Paris Veltsos, Melissa Hanique, Ricardo C. Rodríguez de la Vega, Eric Tannier, Xiaodong Liu, Claire Lemaitre, Peter D. Fields, Corinne Cruaud, Karine Labadie, Caroline Belser, Jerome Briolay, Sylvain Santoni, Radim Cegan, Raquel Linheiro, Gabriele AdamAdil 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, Aline Muyle, Tatiana Giraud, Abdelhafid Bendahmane, Alex Di Genova, Mohammed Amin Madoui, Roman Hobza, Gabriel A.B. Marais

Computational and RNA Biology

Research output: Contribution to journal › Journal article › Research › peer-review

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.

Original language	English
Journal	Science (New York, N.Y.)
Volume	387
Issue number	6734
Pages (from-to)	630-636
Number of pages	7
ISSN	0036-8075
DOIs	https://doi.org/10.1126/science.adj7430
Publication status	Published - 2025

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10.1126/science.adj7430

Cite this

Moraga, C., Branco, C., Rougemont, Q., Jedlička, P., Mendoza-Galindo, E., Veltsos, P., Hanique, M., Rodríguez de la Vega, R. C., Tannier, E., Liu, X., Lemaitre, C., Fields, P. D., Cruaud, C., Labadie, K., Belser, C., Briolay, J., Santoni, S., Cegan, R., Linheiro, R., ... Marais, G. A. B. (2025). The Silene latifolia genome and its giant Y chromosome. Science (New York, N.Y.), 387(6734), 630-636. https://doi.org/10.1126/science.adj7430

Moraga, C, Branco, C, Rougemont, Q, Jedlička, P, Mendoza-Galindo, E, Veltsos, P, Hanique, M, Rodríguez de la Vega, RC, Tannier, E, Liu, X, Lemaitre, C, Fields, PD, Cruaud, C, Labadie, K, Belser, C, Briolay, J, Santoni, S, Cegan, R, Linheiro, R, Adam, G, El Filali, A, Mossion, V, Boualem, A, Tavares, R, Chebbi, A, Cordaux, R, Fruchard, C, Prentout, D, Velt, A, Spataro, B, Delmotte, S, Weingartner, L, Toegelová, H, Tulpová, Z, Cápal, P, Šimková, H, Štorchová, H, Krüger, M, Abeyawardana, OAJ, Taylor, DR, Olson, MS, Sloan, DB, Karrenberg, S, Delph, LF, Charlesworth, D, Muyle, A, Giraud, T, Bendahmane, A, Di Genova, A, Madoui, MA, Hobza, R & Marais, GAB 2025, 'The Silene latifolia genome and its giant Y chromosome', Science (New York, N.Y.), vol. 387, no. 6734, pp. 630-636. https://doi.org/10.1126/science.adj7430

@article{91903c123b85429fb4f23fe0587b2993,

title = "The Silene latifolia genome and its giant Y chromosome",

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.",

author = "Carol Moraga and Catarina Branco and Quentin Rougemont and Pavel Jedli{\v c}ka and Eddy Mendoza-Galindo and Paris Veltsos and Melissa Hanique and {Rodr{\'i}guez de la Vega}, {Ricardo C.} and Eric Tannier and Xiaodong Liu and Claire Lemaitre and Fields, {Peter D.} and Corinne Cruaud and Karine Labadie and Caroline Belser and Jerome Briolay and Sylvain Santoni and Radim Cegan and Raquel Linheiro and Gabriele Adam and {El Filali}, Adil and Vinciane Mossion and Adnane Boualem and Raquel Tavares and Amine Chebbi and Richard Cordaux and C{\'e}cile Fruchard and Djivan Prentout and Amandine Velt and Bruno Spataro and Stephane Delmotte and Laura Weingartner and Helena Toegelov{\'a} and Zuzana Tulpov{\'a} and Petr C{\'a}pal and Hana {\v S}imkov{\'a} and Helena {\v S}torchov{\'a} and Manuela Kr{\"u}ger and Abeyawardana, {Oushadee A.J.} and Taylor, {Douglas R.} and Olson, {Matthew S.} and Sloan, {Daniel B.} and Sophie Karrenberg and Delph, {Lynda F.} and Deborah Charlesworth and Aline Muyle and Tatiana Giraud and Abdelhafid Bendahmane and {Di Genova}, Alex and Madoui, {Mohammed Amin} and Roman Hobza and Marais, {Gabriel A.B.}",

year = "2025",

doi = "10.1126/science.adj7430",

language = "English",

volume = "387",

pages = "630--636",

journal = "Science (New York, N.Y.)",

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TY - JOUR

T1 - The Silene latifolia genome and its giant Y chromosome

AU - Moraga, Carol

AU - Branco, Catarina

AU - Rougemont, Quentin

AU - Jedlička, Pavel

AU - Mendoza-Galindo, Eddy

AU - Veltsos, Paris

AU - Hanique, Melissa

AU - Rodríguez de la Vega, Ricardo C.

AU - Tannier, Eric

AU - Liu, Xiaodong

AU - Lemaitre, Claire

AU - Fields, Peter D.

AU - Cruaud, Corinne

AU - Labadie, Karine

AU - Belser, Caroline

AU - Briolay, Jerome

AU - Santoni, Sylvain

AU - Cegan, Radim

AU - Linheiro, Raquel

AU - Adam, Gabriele

AU - El Filali, Adil

AU - Mossion, Vinciane

AU - Boualem, Adnane

AU - Tavares, Raquel

AU - Chebbi, Amine

AU - Cordaux, Richard

AU - Fruchard, Cécile

AU - Prentout, Djivan

AU - Velt, Amandine

AU - Spataro, Bruno

AU - Delmotte, Stephane

AU - Weingartner, Laura

AU - Toegelová, Helena

AU - Tulpová, Zuzana

AU - Cápal, Petr

AU - Šimková, Hana

AU - Štorchová, Helena

AU - Krüger, Manuela

AU - Abeyawardana, Oushadee A.J.

AU - Taylor, Douglas R.

AU - Olson, Matthew S.

AU - Sloan, Daniel B.

AU - Karrenberg, Sophie

AU - Delph, Lynda F.

AU - Charlesworth, Deborah

AU - Muyle, Aline

AU - Giraud, Tatiana

AU - Bendahmane, Abdelhafid

AU - Di Genova, Alex

AU - Madoui, Mohammed Amin

AU - Hobza, Roman

AU - Marais, Gabriel A.B.

PY - 2025

Y1 - 2025

N2 - 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.

AB - 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.

U2 - 10.1126/science.adj7430

DO - 10.1126/science.adj7430

M3 - Journal article

C2 - 39913565

AN - SCOPUS:85218290628

SN - 0036-8075

VL - 387

SP - 630

EP - 636

JO - Science (New York, N.Y.)

JF - Science (New York, N.Y.)

IS - 6734

ER -