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

Abstract

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.

High-throughput deep sequencing reveals the important role that microRNAs play in the salt response in sweet potato (Ipomoea batatas L.)

“…The x-axis represents the name of the GO sub-categories and the novel miRNAs are mainly 21 and 24 nt in length ( Fig. 3 and Additional file 10: Figure S3), which is consistent with the report of sRNA in sweet potato [42]. And the sRNA length distribution pattern in sweet potato is very similar to the typical pattern of sRNAs reported in Betula luminifera [43].…”

Integrated transcriptome, small RNA and degradome sequencing approaches proffer insights into chlorogenic acid (CGA) biosynthesis in leafy sweet potato

“…For instance, SPLs played important roles in plant growth and development. The miR156/SPL module was reported to participate in the biosynthesis of phenylpropanoids by destabilizing the MYB-bHLH-WD (MBW) complex and directly preventing the expression of anthocyanin biosynthetic genes in Litchi chinensis [51]; as HD-ZIP TFs played crucial roles in shoot apical meristem and organ polarity, the blockage of miRNA165/166 caused the upregulation of HD-ZIP TFs and increased IAA content accompanied by enhanced anthocyanin [41]. In this research, the analyses of degradome sequencing demonstrated that SPLs were targeted by miR156, HD-ZIP by miR166, MYB by miR159.…”

Integrated transcriptome, small RNA and degradome sequencing approaches proffer insights into chlorogenic acid (CGA) biosynthesis in leafy sweet potato

“…For instance, SPLs played important roles in plant growth and development. The miR156/SPL module was reported to participate in the biosynthesis of phenylpropanoids by destabilizing the MYB-bHLH-WD (MBW) complex and directly preventing the expression of anthocyanin biosynthetic genes in Litchi chinensis [51]; as HD-ZIP TFs played crucial roles in shoot apical meristem and organ polarity, the blockage of miRNA165/166 caused the upregulation of HD-ZIP TFs and increased IAA content accompanied by enhanced anthocyanin [41]. In this research, the analyses of degradome sequencing demonstrated that SPLs were targeted by miR156, HD-ZIP by miR166, MYB by miR159.…”

“…7d). miR156, miR166, miR167 and miR858 were found in different comparisons, which had been reported to be involved in phenylpropanoid pathway [41].…”