Abstract Sex determination is poorly understood in plants. Amborella trichopoda is a well-known plant model for evo-devo studies, which is also dioecious (has male and female individuals), with an unknown sex determination mechanism. A. trichopoda is a “sex switcher”, which points to possible environmental factors that act on sex, but populations grown from seed under greenhouse conditions exhibit a 50:50 sex ratio, which indicates the operation of genetic factors. Here, we use a new method ( SDpop ) to identify sex-linked genes from genotyping data of male and female individuals sampled in the field, and find that A. trichopoda has a ZW sex-chromosome system. The sex-linked genes map to a 4 Mb sex-determining region on chromosome 9. The low extent of ZW divergence suggests these sex chromosomes are of recent origin, which is consistent with dioecy being derived character in the A. trichopoda lineage. Our work has uncovered clearly formed sex chromosomes in a species in which both genetic and environmental factors can influence sex. One Sentence Summary Amborella trichopoda , a dioecious species in which both genetics and the environment influence sex, possesses a pair of quite recently evolved ZW chromosomes.

A derived ZW chromosome system in Amborella trichopoda, the sister species to all other extant flowering plants