Presented here are two comparative genomic vignettes in clades emerging as sex chromosome evolution models - Humulus-Cannabis and Chiroptera. A complete picture of how sex chromosome evolution progresses across the tree of life requires a reservoir of knowledge, both molecular and genomic in nature. The Humulus-Cannabis clade is a monophyletic clade within the broader Cannabaceae. This clade is characterized by relatively old well defined heteromorphic sex chromosomes with one member, Humulus japonicus, possessing a derived XYY system. In my first two chapters I present the first draft genome for Humulus japonicus, generated from an invasive population of Japanese hops from New Paltz, New York using a combination of Oxford Nanopore long-read and Illumina short-read sequencing. Leveraging this new assembly for H. japonicus, I explore the genotypic similarities and differences between H. japonicus and its close relatives. There is broad synteny at the macro-level between H. japonicus and Humulus lupulus. Within this largely conserved genomic structure, differential gene family expansions may partially account for the variation in important secondary metabolites characteristic of each species. Finally, I propose interruption of the final prenyltransferase genes in H. japonicus as a putative cause for the absence of bitter acids that are important secondary metabolites of H. lupulus. In my final chapter I investigate the sexualization of a X-chromosome linked autosomal translocation in the neotropical leaf-nosed bat, Artibeus jamaicensis. Sexualization is measured by comparative gene loss relative to Phyllostomus discolor another neotropical leaf-nosed bat whose chromosome 15 is homologous to the X-chromosome linked autosomal translocation in A. jamaicensis. Based on a lack of significant gene loss I propose that a section of heterochromatin found at the tip of chromosome 15 in P. discolor and at the junction of the X-chromosome linked autosomal translocation represents an array of immunoglobulin genes that acts as a genomic seawall preventing the sexualization of the homologous X-chromosome linked autosomal translocation in A. jamaicensis.