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

item TORRES, M - Weill Medical College - Cornell
item MATHEW, L - Weill Medical College - Cornell
item AHMED, I - Weill Medical College - Cornell
item AL-AZWANI, A - Weill Medical College - Cornell
item Krueger, Robert
item RIVERA, D - Universidad De Murcia
item MOHAMOUD, Y - Weill Medical College - Cornell
item SUHRE, K - Weill Medical College - Cornell
item MALEK, J - Weill Medical College - Cornell
item CLARK, A - Cornell University - New York

Submitted to: Nature Communications
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 9/3/2018
Publication Date: 9/28/2018
Citation: Torres, M.F., Mathew, L.S., Ahmed, I., Al-Azwani, A., Krueger, R., Rivera, D., Mohamoud, Y.A., Suhre, K., Malek, J.A., Clark, A.G. 2018. Genus-wide sequencing supports a two-locus model for sex-determination in Phoenix. Nature Communications. 9:3969. doi: 10.1038/s41467-018-06375-y.

Interpretive Summary: The genus Phoenix includes 14 species, of which Phoenix dactylifera (date palm) is of the economic importance. Phoenix species are dioecious, having male and female plants. A region of the genome had previously been identified as being linked to sex determination. The development of dioecy likely occurred before the ancestral Phoenix species evolved into the 14 species currently present. The current work involved sequencing the genomes of 28 trees representing all 14 species of Phoenix and identifying male-specific sequences. The sequences conserved in all males were found in 4 genes, which likely represent the changes leading from monoecy to dioecy. The data suggest that genes critical to make flower formation disappeared from female Phoenix individuals but are retained in male Phoenix individuals. Overall, it appears that the evolution from monoecy to dioecy occurred in two steps, each associated with a distinct mutation.

Technical 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.