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De novo sequencing of root transcriptome reveals complex cadmium-responsive regulatory networks in radish (Raphanus sativus L.)

Xu, Liang, Wang, Yan, Liu, Wei, Wang, Jin, Zhu, Xianwen, Zhang, Keyun, Yu, Rugang, Wang, Ronghua, Xie, Yang, Zhang, Wei, Gong, Yiqin, Liu, Liwang
Plant science 2015 v.236 pp. 313-323
ABC transporters, Raphanus sativus, biosynthesis, cadmium, chronic toxicity, cysteine, gene expression, gene expression regulation, genetic engineering, glucosinolates, glutathione, models, quantitative polymerase chain reaction, radishes, reverse transcriptase polymerase chain reaction, sequence analysis, transcriptome, unigenes, vegetable crops, zinc
Cadmium (Cd) is a nonessential metallic trace element that poses potential chronic toxicity to living organisms. To date, little is known about the Cd-responsive regulatory network in root vegetable crops including radish. In this study, 31,015 unigenes representing 66,552 assembled unique transcripts were isolated from radish root under Cd stress based on de novo transcriptome assembly. In all, 1496 differentially expressed genes (DEGs) consisted of 3579 transcripts were identified from Cd-free (CK) and Cd-treated (Cd200) libraries. Gene Ontology and pathway enrichment analysis indicated that the up- and down-regulated DEGs were predominately involved in glucosinolate biosynthesis as well as cysteine and methionine-related pathways, respectively. RT-qPCR showed that the expression profiles of DEGs were in consistent with results from RNA-Seq analysis. Several candidate genes encoding phytochelatin synthase (PCS), metallothioneins (MTs), glutathione (GSH), zinc iron permease (ZIPs) and ABC transporter were responsible for Cd uptake, accumulation, translocation and detoxification in radish. The schematic model of DEGs and microRNAs-involved in Cd-responsive regulatory network was proposed. This study represents a first comprehensive transcriptome-based characterization of Cd-responsive DEGs in radish. These results could provide fundamental insight into complex Cd-responsive regulatory networks and facilitate further genetic manipulation of Cd accumulation in root vegetable crops.