The Silene latifolia genome and its giant Y chromosome

Moraga, C.; Branco, C.; Rougemont, Q.; Veltsos, P.; Jedlicka, P.; Muyle, A.; Hanique, M.; Tannier, E.; Liu, X.; Mendoza-Galindo, E.; Lemaitre, C.; Fields, P. D.; Cruaud, C.; Labadie, K.; Belser, C.; Briolay, J.; Santoni, S.; Cegan, R.; Linheiro, R.; Rodriguez de la Vega, 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.; Toegelova, H.; Tulpova, Z.; Capal, P.; Simkova, H.; Storchova, H.; Kruger, M.; Abeyawardana, O. A.; Taylor, D.; Olson, M.; Sloan, D. B.; Karrenberg, S.

doi:10.1101/2023.09.21.558754

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bioRxiv · 10.1101/2023.09.21.558754

The Silene latifolia genome and its giant Y chromosome

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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 SummaryThis 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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Moraga, C., Branco, C., Rougemont, Q., Veltsos, P., Jedlicka, P., Muyle, A., Hanique, M., Tannier, E., Liu, X., Mendoza-Galindo, E., Lemaitre, C., Fields, P. D., Cruaud, C., Labadie, K., Belser, C., Briolay, J., Santoni, S., Cegan, R., Linheiro, R., Rodriguez de la Vega, 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., Toegelova, H., Tulpova, Z., Capal, P., Simkova, H., Storchova, H., Kruger, M., Abeyawardana, O. A., Taylor, D., Olson, M., Sloan, D. B., Karrenberg, S.. 2023-09-22. The Silene latifolia genome and its giant Y chromosome. https://doi.org/10.1101/2023.09.21.558754

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