Haplotype-resolved genome assemblies and population resequencing reveal no evidence for genetic sex determination in the dioecious conifer Taxus baccata

Hundreds of plant lineages have independently evolved dioecy, the separation of female and male reproductive organs on different individuals. In all dioecious plants investigated at the molecular level to date, sex is determined genetically through a sex-determining region (SDR). However, SDRs have mostly been characterized in angiosperms, even though dioecy is far more common among gymnosperms. Here, we investigate sex determination in the dioecious conifer Taxus baccata L. (European yew). We generated chromosome-level haplotype-resolved genome assemblies, with a mean size of 10.04 Gb, for both haplotypes of one female and one male tree and resequenced 100 phenotypically sexed individuals at ~20X coverage. Strikingly, reference-free k-mer analyses as well as reference-based coverage and association analyses failed to detect any signal of an SDR. These results raise the intriguing possibility of a non-genetic mechanism of sex determination in T. baccata. As T. baccata is the first species studied among the cupressophytes (conifers II), a large clade comprising Taxaceae, Cupressaceae, Sciadopityaceae, Podocarpaceae and Araucariaceae, such a mechanism might be widespread.