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Background  The cytochrome P450 monooxygenase (P450) superfamily is involved in the biosynthesis of various primary and secondary metabolites. However, little is known about the effects of whole genome duplication (WGD) and tandem duplication (TD) events on the evolutionary history and functional divergence of P450s in  Brassica  after splitting from a common ancestor with  Arabidopsis thaliana .    Results  Using Hidden Markov Model search and manual curation, we detected that  Brassica  species have nearly 1.4-fold as many P450 members as  A. thaliana . Most P450s in  A. thaliana  and  Brassica  species were located on pseudo-chromosomes. The inferred phylogeny indicated that all P450s were clustered into two different subgroups. Analysis of WGD event revealed that different P450 gene families had appeared after evolutionary events of species. For the TD event analyses, the P450s from TD events in  Brassica  species can be divided into ancient and recent parts. Our comparison of influence of WGD and TD events on the P450 gene superfamily between  A. thaliana  and  Brassica  species indicated that the family-specific evolution in the  Brassica  lineage can be attributed to both WGD and TD, whereas WGD was recognized as the major mechanism for the recent evolution of the P450 super gene family. Expression analysis of P450s from  A. thaliana  and  Brassica  species indicated that WGD-type P450s showed the same expression pattern but completely different expression with TD-type P450s across different tissues in  Brassica  species. Selection force analysis suggested that P450 orthologous gene pairs between  A. thaliana  and  Brassica  species underwent negative selection, but no significant differences were found between P450 orthologous gene pairs in  A. thaliana – B. rapa  and  A. thaliana – B. oleracea  lineages, as well as in different subgenomes in  B. rapa  or  B. oleracea  compared with  A. thaliana .    Conclusions  This study is the first to investigate the effects of WGD and TD on the evolutionary history and functional divergence of P450 gene families in  A. thaliana  and  Brassica  species. This study provides a biology model to study the mechanism of gene family formation, particularly in the context of the evolutionary history of angiosperms, and offers novel insights for the study of angiosperm genomes .Electronic supplementary material  The online version of this article (10.1186/s12864-017-4094-7) contains supplementary material, which is available to authorized users.

bmc genomics

Evolutionary history and functional divergence of the cytochrome P450 gene superfamily between Arabidopsis thaliana and Brassica species uncover effects of whole genome and tandem duplications