biostudies-literatureWang YSwiss National Science FoundationDeutsche ForschungsgemeinschaftDeutsche Forschungsgemeinschaft (German Research Foundation)581https://www.ebi.ac.uk/biostudies/studies/S-EPMC11099151biostudies-literatureUnknown7(1)Many plants are facultatively asexual, balancing short-term benefits with long-term costs of asexuality. During range expansion, natural selection likely influences the genetic controls of asexuality in these organisms. However, evidence of natural selection driving asexuality is limited, and the evolutionary consequences of asexuality on the genomic and epigenomic diversity remain controversial. We analyzed population genomes and epigenomes of Spirodela polyrhiza, (L.) Schleid., a facultatively asexual plant that flowers rarely, revealing remarkably low genomic diversity and DNA methylation levels. Within species, demographic history and the frequency of asexual reproduction jointly determined intra-specific variations of genomic diversity and DNA methylation levels. Genome-wide scans revCommunications biologyPopulation genomics and epigenomics of Spirodela polyrhiza provide insights into the evolution of facultative asexuality.PMC11099151422213951P400PB_186770186770438887884Sree KSHuber MXu SAppenroth KJChavez AWang YDuchen PHofer MZhao HfalsePopulation genomics and epigenomics of Spirodela polyrhiza provide insights into the evolution of facultative asexuality.Many plants are facultatively asexual, balancing short-term benefits with long-term costs of asexuality. During range expansion, natural selection likely influences the genetic controls of asexuality in these organisms. However, evidence of natural selection driving asexuality is limited, and the evolutionary consequences of asexuality on the genomic and epigenomic diversity remain controversial. We analyzed population genomes and epigenomes of Spirodela polyrhiza, (L.) Schleid., a facultatively asexual plant that flowers rarely, revealing remarkably low genomic diversity and DNA methylation levels. Within species, demographic history and the frequency of asexual reproduction jointly determined intra-specific variations of genomic diversity and DNA methylation levels. Genome-wide scans rev2024-01-01T00:00:00Z2024 May2026-06-01T18:48:29.05Z2026-05-19T03:07:07.074ZS-EPMC110991513875531310.1038/s42003-024-06266-7