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Background  Gibberellin (GA), a classical phytohormone, plays significant roles in plant growth and development. It shares the important intermediate diphosphate precursor, GGPP, with the main lipophilic bioactive components, diterpenoid tanshinones in  Salvia miltiorrhiza  Bunge, one of the most important Traditional Chinese Medicine materials and an emerging model medicinal plant. Analysis of GA metabolism and regulation may help to demonstrate the biological functions of GAs and the crosstalk between GA metabolism and tanshinone biosynthesis in  S. miltiorrhiza . However, genes involved in the conversion of  ent -kaurene to GAs have not been systematically studied.    Results  Through genome-wide prediction and molecular cloning, twenty two candidate gibberellin metabolism pathway genes were systematically identified for the first time. It includes a  SmKO , two  SmKAOs , six  SmGA20oxs , two  SmGA3oxs  and eleven  SmGA2oxs , of which twenty genes are novel. The deduced proteins showed sequence conservation and divergence. Gibberellin metabolism pathway genes exhibited tissue-specific expression patterns and responded differentially to exogenous GA 3  treatment, indicating differential regulation of gibberellin metabolism in different tissue types in  S. miltiorrhiza. SmKAO1 ,  SmKAO2 ,  SmGA2ox2 , and  SmGA2ox4 – SmGA2ox7  were significantly up-regulated;  SmGA20ox2, SmGA3ox1, SmGA2ox1 ,  SmGA2ox8 ,  SmGA2ox10  and  SmGA2ox11  were significantly down-regulated; while the responses of many other genes varied among different tissue-types and time-points of GA 3  treatment, suggesting the complexity of feedback regulation. Tanshinone biosynthesis-related genes, such as  SmCPS1  and  SmKSL1 , were up-regulated in response to GA 3  treatment. Among the 22 identified genes, nine responded to yeast extract and Ag + -treatment in  S. miltiorrhiza  hairy roots. Moreover, tissue-specifically expressed splice variants were identified for  SmKO ,  SmGA20ox3 ,  SmGA2ox3  and  SmGA2ox11 , of which  SmKOv1 ,  SmGA20ox3v  and  SmGA2ox11v1  were GA 3 -responsive, suggesting the importance of alternative splicing in regulating GA metabolism.    Conclusions  The results show tissue-specifically expressed, feedback-regulated, stress-responsive and alternatively spliced novel genes and reveal multiple layer regulation of GA metabolism and crosstalk between gibberellin metabolism and tanshinone biosynthesis in  S. miltiorrhiza .    Electronic supplementary material  The online version of this article (doi:10.1186/s12864-015-2315-5) contains supplementary material, which is available to authorized users.

bmc genomics

Genome-wide analysis, molecular cloning and expression profiling reveal tissue-specifically expressed, feedback-regulated, stress-responsive and alternatively spliced novel genes involved in gibberellin metabolism in Salvia miltiorrhiza