Polyploidy has played a significant role in the long-term evolution of plants, particularly in Arabidopsis thaliana. This study analyzed the functional divergence of duplicated genes formed by ancient polyploidy events in Arabidopsis. The results show that genes retained in duplicate are not evenly distributed among functional categories, indicating a non-random process of gene loss. Genes involved in signal transduction and transcription are preferentially retained, while those involved in DNA repair are preferentially lost. Although the two members of each gene pair originally had identical transcription profiles, less than half of the pairs formed by the most recent polyploidy event still retain significantly correlated profiles. The study also identified several cases where groups of duplicated gene pairs have diverged in concert, forming two parallel networks. In these cases, the expression of each gene is strongly correlated with the other nonhomologous genes in its network but poorly correlated with its paralog in the other network. Additionally, the rate of protein sequence evolution has been significantly asymmetric in more than 20% of duplicate pairs. These results suggest that functional diversification of the surviving duplicated genes is a major feature of the long-term evolution of polyploids. The study also found that genes involved in regulatory functions, such as transcription factors, protein kinases, and protein phosphatases, are overduplicated, while genes involved in DNA repair, apoptosis, and defense are underduplicated. The results indicate that duplicated genes encoding proteins targeted to the nucleus and plasma membrane have been preferentially kept, whereas those targeted to organelles have been preferentially lost. The study also found that the expression profiles of duplicated genes have diverged in many cases, with 57% of young duplicates and 73% of old duplicates showing divergent expression. The results suggest that a large majority of Arabidopsis polyploidy-derived duplicates have acquired divergent functions. The study also found that 21% of recent duplicate pairs have evolved at significantly different rates. These findings highlight the importance of functional divergence in the long-term evolution of polyploids.Polyploidy has played a significant role in the long-term evolution of plants, particularly in Arabidopsis thaliana. This study analyzed the functional divergence of duplicated genes formed by ancient polyploidy events in Arabidopsis. The results show that genes retained in duplicate are not evenly distributed among functional categories, indicating a non-random process of gene loss. Genes involved in signal transduction and transcription are preferentially retained, while those involved in DNA repair are preferentially lost. Although the two members of each gene pair originally had identical transcription profiles, less than half of the pairs formed by the most recent polyploidy event still retain significantly correlated profiles. The study also identified several cases where groups of duplicated gene pairs have diverged in concert, forming two parallel networks. In these cases, the expression of each gene is strongly correlated with the other nonhomologous genes in its network but poorly correlated with its paralog in the other network. Additionally, the rate of protein sequence evolution has been significantly asymmetric in more than 20% of duplicate pairs. These results suggest that functional diversification of the surviving duplicated genes is a major feature of the long-term evolution of polyploids. The study also found that genes involved in regulatory functions, such as transcription factors, protein kinases, and protein phosphatases, are overduplicated, while genes involved in DNA repair, apoptosis, and defense are underduplicated. The results indicate that duplicated genes encoding proteins targeted to the nucleus and plasma membrane have been preferentially kept, whereas those targeted to organelles have been preferentially lost. The study also found that the expression profiles of duplicated genes have diverged in many cases, with 57% of young duplicates and 73% of old duplicates showing divergent expression. The results suggest that a large majority of Arabidopsis polyploidy-derived duplicates have acquired divergent functions. The study also found that 21% of recent duplicate pairs have evolved at significantly different rates. These findings highlight the importance of functional divergence in the long-term evolution of polyploids.