y HemI software showing conserved miRNA and corresponding miRNA family expression patterns were also presented. As shown in Fig. [3a](#Fig3){ref-type="fig"}, for miRNA family expression, three samples for CK and three samples for MJ were clustered into one group respectively, while the clustering of each miRNA expression showed a different clustering pattern (CK1, CK2 and MJ2 clustering in one group; CK3, MJ1 and MJ3 clustering in one group) (Fig. [3b](#Fig3){ref-type="fig"}). Furthermore, we performed principal components analysis (PCA) to assess the variability of samples (Additional file [2](#MOESM2){ref-type="media"}: Figure S3). The results showed a similar tendency appeared in Fig. [3b](#Fig3){ref-type="fig"}.Fig. 3Expression analysis of *L.aurea* miRNA. Heatmap showing miRNA family (**a**) and conserved miRNA (**b**) expression patterns

Among the 60 known miRNA families, 20 differentially expressed miRNA families were identified according to the average expression levels between CK and MJ (Additional file [4](#MOESM4){ref-type="media"}: Table S3). Of these, ten miRNA families were up-regulated in MJ100 compared with CK, whereas ten miRNA families showed down-regulated patterns (Additional file [4](#MOESM4){ref-type="media"}: Table S3). MJ has been proven to play a key role in changing small RNA expression profile in plants \[[@CR37], [@CR38], [@CR50]\]. For example, 14 miRNAs from seven different families (miR156, miR168, miR169, miR172, miR396, miR480 and miR1310) were down-regulated whereas three miRNAs from two families (miR164 and miR390) were up regulated in Chinese yew \[[@CR37]\]. Interestingly, among above mentioned miRNAs, we observed no miRNA was induced by MJ (Additional file [4](#MOESM4){ref-type="media"}: Table S3), which exhibit the same expression pattern under MJ treatment in *Arabidopsis* \[[@CR38]\]. In this study, the average expression of miR398 in all the samples was down-regulated by 1.33-fold in MJ treatment when compared with the CK (Additional file [4](#MOESM4){ref-type="media"