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Background  Compared with white-fleshed sweetpotato (WFSP), purple-fleshed sweetpotato (PFSP) is a desirable resource for functional food development because of the abundant anthocyanin accumulation in its tuberous roots. Some studies have shown that the expression regulation mediated by miRNA plays an important role in anthocyanin biosynthesis in plants. However, few miRNAs and their corresponding functions related to anthocyanin biosynthesis in tuberous roots of sweetpotato have been known.    Results  In this study, small RNA (sRNA) and degradome libraries from the tuberous roots of WFSP (Xushu-18) and PFSP (Xuzishu-3) were constructed, respectively. Totally, 191 known and 33 novel miRNAs were identified by sRNA sequencing, and 180 target genes cleaved by 115 known ib-miRNAs and 5 novel ib-miRNAs were identified by degradome sequencing. Of these, 121 miRNAs were differently expressed between Xushu-18 and Xuzishu-3. Integrated analysis of sRNA, degradome sequencing, GO, KEGG and qRT-PCR revealed that 26 differentially expressed miRNAs and 36 corresponding targets were potentially involved in the anthocyanin biosynthesis. Of which, an inverse correlation between the expression of ib-miR156 and its target  ibSPL  in WFSP and PFSP was revealed by both qRT-PCR and sRNA sequencing. Subsequently, ib-miR156 was over-expressed in  Arabidopsis . Interestingly, the ib-miR156 over-expressing plants showed suppressed abundance of  SPL  and a purplish phenotype. Concomitantly, upregulated expression of four anthocyanin pathway genes was detected in transgenic  Arabidopsis  plants. Finally, a putative ib-miRNA-target model involved in anthocyanin biosynthesis in sweetpotato was proposed.    Conclusions  The results represented a comprehensive expression profiling of miRNAs related to anthocyanin accumulation in sweetpotato and provided important clues for understanding the regulatory network of anthocyanin biosynthesis mediated by miRNA in tuberous crops.    Electronic supplementary material  The online version of this article (10.1186/s12870-019-1790-2) contains supplementary material, which is available to authorized users.

Uncovering anthocyanin biosynthesis related microRNAs and their target genes by small RNA and degradome sequencing in tuberous roots of sweetpotato