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

Plant Biotechnology Journal
Xiaojiao HanRenying Zhuo

Abstract

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 miRNAs 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 miRNA-target circuits under Cd stress. A total of 87 721 unigenes and 356 miRNAs were identified by deep sequencing, and 79 miRNAs were differentially expressed under Cd stress. Furthermore, 754 target genes of 194 miRNAs were validated by degradome sequencing. A gene ontology (GO) enrichment analysis of differential miRNA targets revealed that auxin, redox-related secondary metabolism and metal transport pathways responded to Cd stress. An integrated analysis uncovered 39 pairs of miRNA targets that displayed negatively correlated expression profiles. Ten miRNA-target pairs also exhibited negative correlations according to a real-time quantitative PCR analysis. Moreover, a coexpression regulatory netw...Continue Reading

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Citations

Apr 15, 2016·International Journal of Molecular Sciences·Xiang LiYonggen Lu
Jun 29, 2017·Journal of Agricultural and Food Chemistry·Yanfei DingCheng Zhu
Mar 15, 2018·Scientific Reports·Meng LuoShiping Wang
May 20, 2020·Frontiers in Plant Science·An YanZhong Chen
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Apr 21, 2018·International Journal of Molecular Sciences·Shuang-Shuang ChenRen-Ying Zhuo
Mar 27, 2019·International Journal of Molecular Sciences·Baoxiang WangMingpu Tan
Dec 29, 2020·Plant Biotechnology Journal
Feb 3, 2021·International Journal of Molecular Sciences·Dong XuRenying Zhuo
Feb 1, 2020·Journal of Agricultural and Food Chemistry·Yanfei DingCheng Zhu

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Datasets Mentioned

BETA
SRP058333

Methods Mentioned

BETA
heavy metal stress
degradome sequencing
GTPase
PCR
electrophoresis
cDNA

Software Mentioned

CleaveLand
Bowtie
WGCNA
reviGO
Mfold
CleaveL
ggplot2
Illumina Genome Analyzer Pipeline
BLAST
BLASTX

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