Plant sex chromosome evolution in the phylogenomic era

<jats:p>Plants harbor a tremendous diversity of sexual systems, including various forms of chromosomal sex determination that have arisen repeatedly across major clades, especially in angiosperms. The causes and consequences of sex chromosome evolution are far-reaching, with implications for sexual system, mating system, and life history evolution, genome architecture, and speciation, extinction, and diversification across lineages. With advances in sequencing, it is now possible to generate high-quality, chromosome-scale genome assemblies for many non-model plant species, ushering in a “golden age” for phylogenomic research. In this review, we argue that the time is ripe for a phylogenomic perspective on the evolution of plant sex chromosomes; the repeated origins of these systems, availability of hermaphroditic close relatives, and access to high quality genomic data will enable new approaches to testing classic models for the initiation, progression, and consequences of sex chromosome evolution. We conduct a clade-level survey of documented plant sex chromosome systems, revealing remarkable variation in the size, age, and degree of differentiation across sex-linked regions, revealing the need for renewed consideration of alternate models. Identifying key questions for future research, we highlight how phylogenomic approaches can be used to test hypotheses across a wide range of models, paving the way for a more robust understanding of how sex chromosomes arise and persist across lineages.</jats:p>