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Dioecy is generally associated with the evolution of sexual dimorphism. In this study, we tested whether small RNAs (sRNAs) play a role in sexual dimorphism and sex chromosome evolution in Silene latifolia. We generated new data for female and male sRNAs and DNA methylation. We showed that sRNAs are most of the time female-biased in S. latifolia, suggesting that the presence of the Y chromosome globally impacts the epigenome by diluting sRNAs genome-wide in males. We found limited evidence for the regulation of sex-biased genes by sRNAs, but we nonetheless identified a male-biased transcription factor that may potentially be regulated by sex-biased RNA-directed DNA methylation. This transcription factor might contribute to male traits through the regulation of key factors in sex determination and phenotypic sexual dimorphism. Finally, we compared female and male sRNA mapping along the S. latifolia sex chromosomes. We found that X and Y genes are targeted by significantly more sRNAs in males compared to females and pseudoautosomal region genes. Our results suggest that Y genes silencing following Y degeneration leads to the formation of sRNAs that can interact with both X and Y genes in males due to X-Y sequence homology. Our work calls for future investigation of the impact of these sRNAs generated from the Y chromosome on X gene expression in males.<\/jats:p>","DOI":"10.1093\/jeb\/voaf051","type":"journal-article","created":{"date-parts":[[2025,5,4]],"date-time":"2025-05-04T06:11:33Z","timestamp":1746339093000},"page":"952-967","source":"Crossref","is-referenced-by-count":1,"title":["The contribution of small RNAs to the evolution of separate sexes and sex chromosomes in the plant <i>Silene latifolia<\/i>"],"prefix":"10.1093","volume":"38","author":[{"given":"Eddy","family":"Mendoza-Galindo","sequence":"first","affiliation":[{"name":"CEFE, Univ Montpellier, CNRS, EPHE, IRD , Montpellier ,","place":["France"]},{"name":"Erasmus Mundus Master Programme in Evolutionary Biology MEME, Montpellier, France"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2200-2336","authenticated-orcid":false,"given":"Aline","family":"Muyle","sequence":"additional","affiliation":[{"name":"CEFE, Univ Montpellier, CNRS, EPHE, IRD , Montpellier ,","place":["France"]},{"name":"Laboratoire Biom\u00e9trie et Biologie Evolutive (LBBE), CNRS\/INRIA\/Univ. 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