This study presents an evolutionary model that simulates gene and genome duplication dynamics in eukaryotes, considering both continuous and large-scale duplication events. The model is applied to the Arabidopsis genome, which has evidence of three whole-genome duplications. The results show that gene loss is significantly different between large-scale and small-scale duplication events, with a strong bias toward certain functional classes. The study provides evidence that some gene categories were almost exclusively expanded through large-scale duplication events. In particular, the three whole-genome duplications in Arabidopsis are responsible for more than 90% of the increase in transcription factors, signal transducers, and developmental genes over the last 350 million years. The model is widely applicable and can be used to evaluate different assumptions about small- and large-scale gene duplication events in eukaryotic genomes. The study also shows that gene decay rates differ significantly between large-scale and small-scale duplication events, with large-scale duplication events leading to lower gene decay rates and higher retention of genes involved in regulatory functions. The results suggest that large-scale gene duplication events have been of major importance for evolution, as they have contributed significantly to the expansion of certain functional categories in the Arabidopsis genome. The study highlights the importance of considering both small- and large-scale duplication events in understanding the evolution of eukaryotic genomes.This study presents an evolutionary model that simulates gene and genome duplication dynamics in eukaryotes, considering both continuous and large-scale duplication events. The model is applied to the Arabidopsis genome, which has evidence of three whole-genome duplications. The results show that gene loss is significantly different between large-scale and small-scale duplication events, with a strong bias toward certain functional classes. The study provides evidence that some gene categories were almost exclusively expanded through large-scale duplication events. In particular, the three whole-genome duplications in Arabidopsis are responsible for more than 90% of the increase in transcription factors, signal transducers, and developmental genes over the last 350 million years. The model is widely applicable and can be used to evaluate different assumptions about small- and large-scale gene duplication events in eukaryotic genomes. The study also shows that gene decay rates differ significantly between large-scale and small-scale duplication events, with large-scale duplication events leading to lower gene decay rates and higher retention of genes involved in regulatory functions. The results suggest that large-scale gene duplication events have been of major importance for evolution, as they have contributed significantly to the expansion of certain functional categories in the Arabidopsis genome. The study highlights the importance of considering both small- and large-scale duplication events in understanding the evolution of eukaryotic genomes.