Integration of small RNAs, degradome and transcriptome sequencing in hyperaccumulator Sedum alfredii uncovers a complex regulatory network and provides insights into cadmium phytoremediation

Summary

The hyperaccumulating ecotype of Sedum alfredii Hance is a cadmium (Cd)/zinc/lead co‐hyperaccumulating species of Crassulaceae. It is a promising phytoremediation candidate accumulating substantial heavy metal ions without obvious signs of poisoning. However, few studies have focused on the regulatory roles of mi RNAs and their targets in the hyperaccumulating ecotype of S. alfredii. Here, we combined analyses of the transcriptomics, sRNAs and the degradome to generate a comprehensive resource focused on identifying key regulatory mi RNA‐target circuits under Cd stress. A total of 87 721 unigenes and 356 mi RNAs were identified by deep sequencing, and 79 mi RNAs were differentially expressed under Cd stress. Furthermore, 754 target genes of 194 mi RNAs were validated by degradome sequencing. A gene ontology ( GO) enrichment analysis of differential mi RNA targets revealed that auxin, redox‐related secondary metabolism and metal transport pathways responded to Cd stress. An integrated analysis uncovered 39 pairs of mi RNA targets that displayed negatively correlated expression profiles. Ten mi RNA‐target pairs also exhibited negative correlations according to a real‐time quantitative PCR analysis. Moreover, a coexpression regulatory network was constructed based on profiles of differentially expressed genes. Two hub genes, ARF4 (auxin response factor 4) and AAP3 (amino acid permease 3), which might play central roles in the regulation of Cd‐responsive genes, were uncovered. These results suggest that comprehensive analyses of the transcriptomics, sRNAs and the degradome provided a useful platform for investigating Cd hyperaccumulation in S. alfredii, and may provide new insights into the genetic engineering of phytoremediation.