DISSERTATION RESEARCH: The genomic basis of dioecy in Asparagus (Asparagaceae)

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Dioecy -- where plant populations are comprised of separate male and female individuals -- occurs in an estimated 6% of flowering plant species and has evolved repeatedly. In at least 39 species and 17 flowering plant families, the evolution of dioecy is linked to the evolution of specialized chromosomes called allosomes. However, little is known about the genomic changes that result in the evolution of allosomes in plants, or the genomic changes that occur after the formation of these chromosomes. This research will investigate the origin of allosomes and the subsequent genomic changes during 1-2 million years of divergence in garden asparagus (Asparagus officinalis). By tracking the evolution of genes on equivalent chromosomes in related Asparagus species, this research will elucidate how allosomes have evolved, and how this process may be contributing to the degeneration of one chromosome within the allosome pair. The research will result in the training of one graduate student in diverse systematic methods, and the mentoring of undergraduate students in next-generation sequencing methods, fluorescent microscopy, and bioinformatics. Computer code and analysis pipelines resulting from this research will be disseminated broadly and freely to researchers through open-access websites. The project will also provide asparagus breeders with molecular markers that could lead to significant crop improvements.Asparagus officinalis is an ideal species to investigate factors influencing the evolution of allosomes from ancestral autosomes. Theory predicts that the origin of allosomes in plants involves selection for cessation of recombination between at least two genes: one suppressing the formation of pistils and another promoting the formation of stamens. This prediction, however, has not yet been empirically tested. Recent work has identified non-recombining Y-linked regions of the garden asparagus genome and implicated a single Y-linked gene within this region as a suppressor of pistil development in male flowers. This research will use targeted sequence capture to investigate the evolution of this gene across more than half of Asparagus species, including both hermaphroditic and dioecious taxa. At the same time, coalescent methods will be employed to reconstruct a molecular phylogeny for the Asparagus genus using single copy genes. The resulting phylogeny will provide a historical context for comparative genomic analyses aimed at reconstructing gene content in the ancestral allosomes and testing the prediction that mutations in genes promoting stamen development contributed to the origin of autosomes.