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Background   Stevia rebaudiana  (Bertoni) is considered one of the most valuable plants because of the steviol glycosides (SGs) that can be extracted from its leaves. Glycosyltransferases (GTs), which can transfer sugar moieties from activated sugar donors onto saccharide and nonsaccharide acceptors, are widely distributed in the genome of  S. rebaudiana  and play important roles in the synthesis of steviol glycosides.    Results  Six stevia genotypes with significantly different concentrations of SGs were obtained by induction through various mutagenic methods, and the contents of seven glycosides (stevioboside, Reb B, ST, Reb A, Reb F, Reb D and Reb M) in their leaves were considerably different. Then, NGS and single-molecule real-time (SMRT) sequencing were combined to analyse leaf tissue from these six different genotypes to generate a full-length transcriptome of  S. rebaudiana . Two phylogenetic trees of glycosyltransferases (SrUGTs) were constructed by the neighbour-joining method and successfully predicted the functions of SrUGTs involved in SG biosynthesis. With further insight into glycosyltransferases (SrUGTs) involved in SG biosynthesis, the weighted gene co-expression network analysis (WGCNA) method was used to characterize the relationships between SrUGTs and SGs, and forty-four potential SrUGTs were finally obtained, including  SrUGT85C2 ,  SrUGT74G1 ,  SrUGT76G1  and  SrUGT91D2,  which have already been reported to be involved in the glucosylation of steviol glycosides, illustrating the reliability of our results.    Conclusion  Combined with the results obtained by previous studies and those of this work, we systematically characterized glycosyltransferases in  S. rebaudiana  and forty-four candidate  SrUGTs  involved in the glycosylation of steviol glucosides were obtained. Moreover, the full-length transcriptome obtained in this study will provide valuable support for further research investigating  S. rebaudiana .    Supplementary Information  The online version contains supplementary material available at 10.1186/s12864-020-07195-5.

Characterizing glycosyltransferases by a combination of sequencing platforms applied to the leaf tissues of Stevia rebaudiana