Genus-wide sequencing supports a two-locus model for sex-determination in Phoenix

The date palm tree is a commercially important member of the genus Phoenix whose 14 species are all dioecious with separate male and female individuals. Previous studies identified a multi-megabase region of the date palm genome linked to sex and showed that dioecy likely developed in Phoenix prior to speciation. To identify genes critical to sex determination we sequenced the genomes of 28 Phoenix trees representing all 14 species. Male-specific sequences were identified and extended using phased single molecule sequencing or BAC clones to distinguish X and Y alleles. Here we show that only four genes contain sequences conserved in all analyzed males, likely identifying the changes foundational to dioecy in Phoenix . The majority of these sequences show similarity to a single genomic locus in the closely related oil palm. CYP703 and GPAT3 , two genes critical to male flower development in other monocots, appear fully deleted in females while maintained as single copy in males. A LOG-like gene appears translocated into the Y chromosome and a cytidine deaminase-like appears at the border of a chromosomal rearrangement. Our data supports a two-mutation model for the evolution from hermaphroditism to dioecy through a gynodioecious intermediate.