The Silene latifolia genome and its giant Y chromosome

Carol Moraga; Catarina Branco; Quentin Rougemont; Paris Veltsos; Pavel Jedlička; Aline Muyle; Melissa Hanique; Eric Tannier; Xiaodong Liu; Eddy Mendoza-Galindo; Claire Lemaitre; Peter D. Fields; Corinne Cruaud; Karine Labadie; Caroline Belser; Jerome 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; Amin Madoui; Roman Hobza; Gabriel A. B. Marais

doi:10.1101/2023.09.21.558754

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.

Competing Interest Statement

The authors have declared no competing interest.

The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.