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Preprints, Working Papers, ... Year : 2023

The Silene latifolia genome and its giant Y chromosome

Carol Moraga (1, 2, 3) , Catarina Branco (1, 4, 5) , Quentin Rougemont (6) , Paris Veltsos (7) , Pavel Jedlička (8) , Aline Muyle (9) , Melissa Hanique (10) , Eric Tannier (1) , Xiaodong Liu (11) , Eddy Mendoza-Galindo (9) , Claire Lemaitre (12) , Peter Fields (13) , Corinne Cruaud (14) , Karine Labadie (14) , Caroline Belser (15) , Jerome Briolay (16) , Sylvain Santoni (17) , Radim Cegan (7) , Raquel Linheiro (4, 5, 18) , Ricardo de la Vega (6) , Gabriele Adam (10) , Adil El Filali (1, 2, 3) , Vinciane Mossion (19) , Adnane Boualem (10) , Raquel Tavares (4, 5) , Amine Chebbi (20) , Richard Cordaux (21) , Cécile Fruchard (1) , Djivan Prentout (22) , Amandine Velt (23) , Bruno Spataro (1) , Stephane Delmotte (1) , Laura Weingartner (24) , Helena Toegelová (25) , Zuzana Tulpová (25) , Petr Cápal (25) , Hana Šimková (25) , Helena Štorchová (25) , Manuela Krüger (25) , Oushadee Abeyawardana (25) , Douglas Taylor (26) , Matthew Olson (27) , Daniel Sloan (13) , Sophie Karrenberg (28) , Lynda Delph (29) , Deborah Charlesworth (30) , Tatiana Giraud (6) , Abdelhafid Bendahmane (10) , Alex Di Genova (2) , Amin Madoui (14, 29) , Roman Hobza (8) , Gabriel Marais (1, 4, 31)
1 LBBE - Laboratoire de Biométrie et Biologie Evolutive - UMR 5558
2 ICIn - UOH - Instituto de Ciencias de la Ingenieria
3 iBio - Instituto Milenio de Biología Integrativa = Millennium Institute for Integrative Biology
4 CIBIO - Centro de Investigação em Biodiversidade e Recursos Genéticos [Vairao]
5 FCUP - Faculdade de Ciências da Universidade do Porto
6 ESE - Ecologie Systématique et Evolution
7 VUB - Vrije Universiteit Brussel [Bruxelles]
8 IBP / CAS - Institute of Biophysics of the Czech Academy of Sciences
9 CEFE - Centre d’Ecologie Fonctionnelle et Evolutive
10 IPS2 (UMR_9213 / UMR_1403) - Institut des Sciences des Plantes de Paris-Saclay
11 UCPH - University of Copenhagen = Københavns Universitet
12 GenScale - Scalable, Optimized and Parallel Algorithms for Genomics
13 CSU - Colorado State University [Fort Collins]
14 GENOSCOPE - Genoscope - Centre national de séquençage [Evry]
15 LBGB - Laboratoire de Bioinformatique pour la Génomique et la Biodiversité
16 DTAMB - Développement de Techniques et Analyse Moléculaire de la Biodiversité [Lyon]
17 UMR AGAP - Amélioration génétique et adaptation des plantes méditerranéennes et tropicales
18 Département écologie évolutive [LBBE]
19 EBC - Department of Ecology and Genetics [Uppsala]
20 EFOR Group
21 EGCE - Evolution, génomes, comportement et écologie
22 Columbia University [New York]
23 SVQV - Santé de la vigne et qualité du vin
24 University of Louisville School of Medicine [Louisville]
25 IEB / CAS - Institute of Experimental Botany of the Czech Academy of Sciences
26 University of Virginia
27 TTU - Texas Tech University [Lubbock]
28 Uppsala Universitet [Uppsala]
29 JACOB - Institut de Biologie François JACOB
30 CEA - Commissariat à l'énergie atomique et aux énergies alternatives
31 Universidade do Porto = University of Porto
Carol Moraga
  • Function : Author
Laboratoire de Biométrie et Biologie Evolutive - UMR 5558
Instituto de Ciencias de la Ingenieria
Instituto Milenio de Biología Integrativa = Millennium Institute for Integrative Biology
Catarina Branco
  • Function : Author
Laboratoire de Biométrie et Biologie Evolutive - UMR 5558
Centro de Investigação em Biodiversidade e Recursos Genéticos [Vairao]
Faculdade de Ciências da Universidade do Porto
Quentin Rougemont
  • Function : Author
Ecologie Systématique et Evolution
Paris Veltsos
Vrije Universiteit Brussel [Bruxelles]
Pavel Jedlička
Institute of Biophysics of the Czech Academy of Sciences
Aline Muyle
  • Function : Author
Centre d’Ecologie Fonctionnelle et Evolutive
Melissa Hanique
  • Function : Author
Institut des Sciences des Plantes de Paris-Saclay
Eric Tannier
  • Function : Author
Laboratoire de Biométrie et Biologie Evolutive - UMR 5558
Xiaodong Liu
University of Copenhagen = Københavns Universitet
Eddy Mendoza-Galindo
Centre d’Ecologie Fonctionnelle et Evolutive
Claire Lemaitre
Scalable, Optimized and Parallel Algorithms for Genomics
CV
Peter Fields
Colorado State University [Fort Collins]
Corinne Cruaud
Genoscope - Centre national de séquençage [Evry]
Karine Labadie
Genoscope - Centre national de séquençage [Evry]
Caroline Belser
Laboratoire de Bioinformatique pour la Génomique et la Biodiversité
CV
Jerome Briolay
  • Function : Author
Développement de Techniques et Analyse Moléculaire de la Biodiversité [Lyon]
Sylvain Santoni
  • Function : Author
Amélioration génétique et adaptation des plantes méditerranéennes et tropicales
Radim Cegan
Vrije Universiteit Brussel [Bruxelles]
Raquel Linheiro
  • Function : Author
Centro de Investigação em Biodiversidade e Recursos Genéticos [Vairao]
Faculdade de Ciências da Universidade do Porto
Département écologie évolutive [LBBE]
Ricardo de la Vega
Ecologie Systématique et Evolution
Gabriele Adam
  • Function : Author
Institut des Sciences des Plantes de Paris-Saclay
Adil El Filali
Laboratoire de Biométrie et Biologie Evolutive - UMR 5558
Instituto de Ciencias de la Ingenieria
Instituto Milenio de Biología Integrativa = Millennium Institute for Integrative Biology
Vinciane Mossion
Department of Ecology and Genetics [Uppsala]
Adnane Boualem
Institut des Sciences des Plantes de Paris-Saclay
CV
Raquel Tavares
  • Function : Author
Centro de Investigação em Biodiversidade e Recursos Genéticos [Vairao]
Faculdade de Ciências da Universidade do Porto
Amine Chebbi
  • Function : Author
EFOR Group
Richard Cordaux
  • Function : Author
Evolution, génomes, comportement et écologie
Cécile Fruchard
  • Function : Author
Laboratoire de Biométrie et Biologie Evolutive - UMR 5558
Djivan Prentout
Columbia University [New York]
Amandine Velt
  • Function : Author
Santé de la vigne et qualité du vin
Bruno Spataro
  • Function : Author
Laboratoire de Biométrie et Biologie Evolutive - UMR 5558
Stephane Delmotte
  • Function : Author
Laboratoire de Biométrie et Biologie Evolutive - UMR 5558
Laura Weingartner
University of Louisville School of Medicine [Louisville]
Helena Toegelová
  • Function : Author
Institute of Experimental Botany of the Czech Academy of Sciences
Zuzana Tulpová
  • Function : Author
Institute of Experimental Botany of the Czech Academy of Sciences
Petr Cápal
  • Function : Author
Institute of Experimental Botany of the Czech Academy of Sciences
Hana Šimková
Institute of Experimental Botany of the Czech Academy of Sciences
Helena Štorchová
Institute of Experimental Botany of the Czech Academy of Sciences
Manuela Krüger
  • Function : Author
Institute of Experimental Botany of the Czech Academy of Sciences
Oushadee Abeyawardana
  • Function : Author
Institute of Experimental Botany of the Czech Academy of Sciences
Douglas Taylor
  • Function : Author
University of Virginia
Matthew Olson
Texas Tech University [Lubbock]
Daniel Sloan
Colorado State University [Fort Collins]
Sophie Karrenberg
Uppsala Universitet [Uppsala]
Lynda Delph
Institut de Biologie François JACOB
Deborah Charlesworth
Commissariat à l'énergie atomique et aux énergies alternatives
Tatiana Giraud
Ecologie Systématique et Evolution
Abdelhafid Bendahmane
Institut des Sciences des Plantes de Paris-Saclay
Alex Di Genova
Instituto de Ciencias de la Ingenieria
Amin Madoui
Genoscope - Centre national de séquençage [Evry]
Institut de Biologie François JACOB
Roman Hobza
  • Function : Author
Institute of Biophysics of the Czech Academy of Sciences
Gabriel Marais
Laboratoire de Biométrie et Biologie Evolutive - UMR 5558
Centro de Investigação em Biodiversidade e Recursos Genéticos [Vairao]
Universidade do Porto = University of Porto

Abstract

Abstract In some species, the Y is a tiny chromosome but the dioecious plant Silene latifolia has a giant ∼550 Mb Y chromosome, which has remained unsequenced so far. Here we used a hybrid approach to obtain a high-quality male S. latifolia genome. Using mutants for sexual phenotype, we identified candidate sex-determining genes on the Y. Comparative analysis of the sex chromosomes with outgroups showed the Y is surprisingly rearranged and degenerated for a ∼11 MY-old system. Recombination suppression between X and Y extended in a stepwise process, and triggered a massive accumulation of repeats on the Y, as well as in the non-recombining pericentromeric region of the X, leading to giant sex chromosomes. One-Sentence Summary This work uncovers the structure, function, and evolution of one of the largest giant Y chromosomes, that of the model plant Silene latifolia , which is almost 10 times larger than the human Y, despite similar genome sizes.

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Life Sciences [q-bio]

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https://hal.science/hal-04293712

Submitted on : Sunday, November 19, 2023-2:04:34 AM

Last modification on : Monday, May 27, 2024-3:16:12 AM

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hal-04293712 , version 1 (19-11-2023)

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Carol Moraga, Catarina Branco, Quentin Rougemont, Paris Veltsos, Pavel Jedlička, et al.. The Silene latifolia genome and its giant Y chromosome. 2023. ⟨hal-04293712⟩

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