For the facultative species, clonal reproduction is beneficial for short-term competition in a relatively stable environment, while sexual reproduction promotes genomic diversity for adaptation in a changing environment. Thus, the alteration between the two reproductive modes might affect fitness. However, what causes the alteration from sexual reproduction to asexual mode remains largely unknown. Here, we investigate 228 genomes of the giant duckweed (Spirodela polyrhiza) that were collected worldwide. Four populations were observed and named according to their geographic distribution: America, Southeast Asia (SE-Asia), India, and Europe populations. Substantial differences were observed among those four populations, including genomic diversity, recombination rate, decay of linkage disequilibrium, and selection efficiency. However, different sexual reproduction rates might be the initiator. Further investigation suggests that the changes in sexual reproduction rate are associated with two structure variations that involved MADS-box genes. In addition, genome-wide scans revealed that multiple genes involved in flowering and embryogenesis were under positive selection, consistent with the hypothesis that natural selection drove the evolution of asexuality during the recent habitat expansions in this plant. Together, these results provide new insights into the evolution of plant reproductive systems and suggest that natural selection can drive the evolutionary changes of asexuality, which in turn alters the levels of genomic diversity.
Population genomics provide insights into the evolution of facultative asexuality in plants