Files
Abstract
Sex chromosomes exhibit evolutionary innovations such as reduced recombination, sex-specific gene content/expression, and size differences. The growing interest in the origin and evolution of sex chromosomes is fueled by availability of new sequencing technologies enabling accurate phasing of XY (or ZW) haplotypes in assemblies. However, investigations of the early evolution of sex chromosomes are intractable in groups with ancient sex-determination systems, including placental mammals. In angiosperms, the recent and repeated evolution of separate sexes (dioecy) offers great opportunity to make strong inferences regarding the mechanisms driving the earliest stages of sex chromosome evolution. A better understanding of variation in sex chromosome structure and gene content is necessary to elucidate common themes in plant sex chromosome evolution. The dioecious garden asparagus (Asparagus officinalis L.) is an emergent model for studying sex chromosomes in plants. Yet, little is known regarding sex-determination in the other ~57 dioecious species of Asparagus. In this dissertation, I use phylogenomics and comparative genome analyses to further develop a foundational framework for studying sex chromosomes in Asparagus. Inferences from phylogenomic and ancestral biogeography analysis support two young origins of dioecy in Asparagus, independently arising ~2.78–3.78 million years ago (Ma) and in association with range expansion out of Africa, in two clades. Whereas A. officinalis is a representative of the Eurasian dioecy clade, genomic resources are lacking for the other dioecy clade which is restricted to the Mediterranean Basin. I present an assembly of an XY male genome for A. horridus – a species in the Medit. Basin clade – and found that the Y evolved from a different ancestral autosome and exhibits no homology with that of the A. officinalis Y. Evolutionary analyses suggest that reduced recombination on the A. horridus Y evolved ~1.1–1.8 Ma via an ~2-Mb inversion, which later expanded to ~10-Mb largely due to accumulation of retrotransposons in the nonrecombining region. Altogether, my results suggest that two novel XY systems evolved between independent, yet closely related lineages of Asparagus and will contribute to a deeper understanding of sex chromosome evolution across the tree of life.