Fungal genomes undergo duplication events such as Whole Genome Duplication (WGD), which contribute to rapid adaptation and increased genetic diversity. The results provide insights into genome integrity, completeness, evolutionary patterns, and functional conservation observed across different fungal species. Highly conserved synteny patterns underscore the significance of cell membrane proteins, proteolytic capabilities, dynein motor proteins, and endocytosis processes in Basidiomycota, supporting the essential roles these processes play in their development throughout evolution. This research establishes the groundwork for further exploration of genomic diversity and potential applications of synteny analysis in elucidating evolutionary patterns and ecological relationships among fungal species.