Preferential Retention of Circadian Clock Genes during Diploidization following Whole Genome Triplication in Brassica rapa

Much has been learned about the architecture and function of the circadian clock of Arabidopsis thaliana, a model for plant circadian rhythms. Circadian rhythms contribute to evolutionary fitness, suggesting that circadian rhythmicity may also contribute to agricultural productivity. Therefore, we extend our study of the plant circadian clock to Brassica rapa, an agricultural crop. Since its separation from Arabidopsis, B. rapa has undergone whole genome triplication and subsequent diploidization that has involved considerable gene loss. We find that circadian clock genes are preferentially retained relative to comparison groups of their neighboring genes, a set of randomly chosen genes, and a set of housekeeping genes broadly conserved in eukaryotes. The preferential retention of clock genes is consistent with the gene dosage hypothesis, which predicts preferential retention of highly networked or dose-sensitive genes. Two gene families encoding transcription factors that play important roles in the plant core oscillator—the PSEUDO-RESPONSE REGULATORS, including TIMING OF CAB EXPRESSION1, and the REVEILLE family, including CIRCADIAN CLOCK ASSOCIATED1 and LATE ELONGATED HYPOCOTYL—exhibit preferential retention consistent with the gene dosage hypothesis, but a third gene family, including ZEITLUPE, that encodes F-Box proteins that regulate posttranslational protein stability offers an exception.