In the modern era of plant biology, high-quality reference genome assemblies represent a foundational first step to many studies. They allow chromosome level structural analysis, characterization of various types of repetitive sequence, and identification of cis regulatory elements. Additionally, they improve many other types of research including functional annotation of genes and gene family analysis. The proliferation of relatively cheap high throughput sequencing and powerful computational resources has resulted in a surge of such assemblies being produced across the tree of life. However, the majority of this effort has been restricted to a relatively narrow range of phylogenetic diversity, focusing on a handful of agriculturally important groups. This has resulted in a significant bias in our understanding of many fundamental concepts and processes such as plant genome structure and organization, regulation of gene expression, and whole genome duplication, to name a few. My doctoral research seeks to expand our understanding of plant biology using a combination of genomic and transcriptomic data from ferns and lycophytes. I have utilized high quality genome assemblies from multiple species of ferns and lycophytes to gain unprecedented insight into processes and downstream effects of whole genome duplication and subsequent diploidization in seed-free plants. In addition, I have studied the convergent evolution of aquatic CAM in the lycophyte genus Isoetes using a combination of genomic and transcriptomic data. Lastly, I conducted species and population level phylogenetic analysis of Isoetes appalachiana, a widespread allopolyploid, to investigate the establishment of polyploid lineages and quantify subsequent gene flow between them. My research is diverse, spanning multiple disciplines as well as multiple phylogenetic lineages and ultimately represents a valuable resource for future forays into comparative genomics and transcriptomics of vascular plants.