Molecular basis of dioeciousness in palm trees. Supervised by F. Aberlenc / J. Kafer
Sex chromosomes have evolved several times in living organisms, particularly in plants, due to a large number of independent transitions to separate sexes (dioeciousness). Although sex chromosomes are characterized by a non-recombining region subject to the same processes in each species, recent advances have shown that there is a wide variety of size, divergence, degeneration, and gene content, particularly in plants. Here, we use the palm family, which has undergone several transitions to dioeciousness, to study the dynamics of sex chromosome evolution. We have developed a comparative genomics approach based on exome sequencing that allows genes to be compared at an intermediate evolutionary scale in non-model organisms. Sex chromosomes and sex-linked genes are detected using a probabilistic method based on population genetics combined with heterozygosity rates, coverage bias, and synonymous divergence. Using the genome of the model species of dioecious palm (Phoenix dactylifera, date palm) as a reference, we then characterize non-recombining syntenic regions, their level of divergence, and gene loss. We identified XY chromosomes in four species belonging to lineages that evolved into dioecious plants independently of the date palm. Our results reveal a case of convergent evolution of sex chromosomes in Kerriodoxa elegans, which to our knowledge is the first such case described in plants. In Trachycarpus fortunei, Borassus aethiopum, and Borassus flabellifer, different genomic regions gave rise to sex chromosomes, suggesting that different sets of genes can lead to dioeciousness. The non-recombining regions are generally old, small in size, not very divergent, and appear to be relatively undegenerated. Several non-recombining genes have homologies with genes involved in multiple pathways of floral unisexuality in angiosperms. It is currently unknown whether frequent changes in sexual systems in palms limit the divergence of sex chromosomes or whether this is due to other mechanisms (e.g., turnovers, selection), but further studies on palms could shed additional light on the evolution of sex and sex chromosomes.
