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Background  The cytochrome P450 monooxygenases (CYP450, CYP, P450) catalyze numerous monooxygenation/hydroxylation reactions in biochemical pathways. Although CYP superfamily has been systematically studied in a few species, the genome-scale research about it in rice has not been done.    Results  In this study, a total of 355 CYPs encoded by 326 genes were identified in  japonica  genome. The  OsCYP  genes are classified into 10 clans including 45 families according to phylogenetic analysis. More than half of the genes are distributed in 53 tandem duplicated gene clusters. Intron-exon structure of  OsCYP s exhibits highly conserved and specificity within a family, and divergences of duplicate genes in gene structure result in non-functionalization, neo-functionalization or sub-functionalization. Selection pressure analysis showed that rice  CYP s are under purifying selection. The microarray data analysis shows that some genes are tissue-specific expression, such as  OsCYP710A5  and  OsCYP71X14  in endosperm,  OsCYP99A3  and  OsCYP78A16  in root and  OsCYP93G2  and  OsCYP97D7  in leaf. Analysis of RNA-seq data derived from rice leaf developmental gradient indicates that some  OsCYP s exhibit zone-specific expression patterns.  OsCYP87C2, OsCYP96B5 ,  OsCYP96B8  and  OsCYP84A5  were specifically expressed in leaf base and transitional zone. The transcripts of lineages II and IV-1 members were highly abundant in maturing zone. Eighty three  OsCYP s are differentially expressed in response to drought stress, of which  OsCYP51G3 ,  OsCYP709C9 ,  OsCYP709C5 ,  OsCYP81A6 ,  OsCYP72A18  and  OsCYP704A5  are strongly induced and  OsCYP78A16 ,  OsCYP89C9  and  OsCYP704A5  are down-regulated significantly, and some of the results were validated by qPCR. And 23 up-regulated and 17 down-regulated genes are specific to  Osbhlh148  mutation under drought stress. Compared to those in wild type, the changes in transcript levels of several genes are slight in the mutant, such as  OsCYP51G3 ,  OsCYP94C2 ,  OsCYP709C9  and  OsCYP709C5 .    Conclusion  The whole-genomic analysis of rice P450 superfamily provides a clue to understanding biological function of  OsCYP s in development regulation and drought stress response, and is helpful to rice molecular breeding.    Electronic supplementary material  The online version of this article (10.1186/s12864-017-4425-8) contains supplementary material, which is available to authorized users.

Global identification, structural analysis and expression characterization of cytochrome P450 monooxygenase superfamily in rice