Plant genera Cannabis and Humulus share the same pair of well‐differentiated sex chromosomes

Summary We recently described, in Cannabis sativa , the oldest sex chromosome system documented so far in plants (12–28 Myr old). Based on the estimated age, we predicted that it should be shared by its sister genus Humulus , which is known also to possess XY chromosomes. Here, we used transcriptome sequencing of an F 1 family of H. lupulus to identify and study the sex chromosomes in this species using the probabilistic method SEX‐DET ector . We identified 265 sex‐linked genes in H. lupulus , which preferentially mapped to the C. sativa X chromosome. Using phylogenies of sex‐linked genes, we showed that a region of the sex chromosomes had already stopped recombining in an ancestor of both species. Furthermore, as in C. sativa , Y‐linked gene expression reduction is correlated to the position on the X chromosome, and highly Y degenerated genes showed dosage compensation. We report, for the first time in Angiosperms, a sex chromosome system that is shared by two different genera. Thus, recombination suppression started at least 21–25 Myr ago, and then (either gradually or step‐wise) spread to a large part of the sex chromosomes ( c. 70%), leading to a degenerated Y chromosome.