Abstract
The date palm tree is a commercially important member of the genus Phoenix whose 14 species are dioecious with separate male and female individuals. To identify sex determining genes we sequenced the genomes of 15 female and 13 male Phoenix trees representing all 14 species. We identified male-specific sequences and extended them using phased single-molecule sequencing or BAC clones. We observed that only four genes contained sequences conserved in all analyzed Phoenix males. Most of these sequences showed similarity to a single genomic locus in the closely related monoecious oil palm. CYP703 and GPAT3, two single copy genes present in males and critical for male flower development in other monocots, were absent in females. A LOG-like gene appears translocated into the Y-linked region and is suggested to play a role in suppressing female flowers. Our data are consistent with a two-mutation model for the evolution of dioecy in Phoenix.
Highlights
The female date palm (Phoenix dactylifera) is another important dioecious crop, producing edible dates and having high agricultural value in North Africa, the Middle East, and South East Asia
The study is based on the hypothesis that genes for male function and female organ suppression in the ancestral Phoenix would be maintained on the Y chromosome in present-day species
No kmers were unique to all females; kmers present in females but absent in males were not shared by more than eight species of the genus, consistent with an XY sex determination system (Fig. 1a)
Summary
The female date palm (Phoenix dactylifera) is another important dioecious crop, producing edible dates and having high agricultural value in North Africa, the Middle East, and South East Asia. Phylogenetic analysis of one sex-linked gene suggested that dioecy evolved before speciation in the genus Phoenix[18] consistent with the fact that all members of the genus Phoenix are dioecious, unlike related genera in the palm family[19]. Hypothesizing a single origin of dioecy, we designed a study that combines de novo whole-genome sequencing and comparative genomics across all 14 members of Phoenix with the aim of identifying the genes responsible for sex determination in the genus. The study is based on the hypothesis that genes for male function and female organ suppression in the ancestral Phoenix would be maintained on the Y chromosome in present-day species. We identify four candidate genes, of which three are completely absent in all female Phoenix individuals, but present in two closely related hermaphroditic palms.
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