Transcriptome Profiling of Radish (<i>Raphanus sativus</i> L.) Root and Identification of Genes Involved in Response to Lead (Pb) Stress with Next Generation Sequencing

<div><p>Lead (Pb), one of the most toxic heavy metals, can be absorbed and accumulated by plant roots and then enter the food chain resulting in potential health risks for human beings. The radish (<i>Raphanus sativus</i> L.) is an important root vegetable crop with fleshy taproots as the edible parts. Little is known about the mechanism by which radishes respond to Pb stress at the molecular level. In this study, Next Generation Sequencing (NGS)–based RNA-seq technology was employed to characterize the <i>de novo</i> transcriptome of radish roots and identify differentially expressed genes (DEGs) during Pb stress. A total of 68,940 assembled unique transcripts including 33,337 unigenes were obtained from radish root cDNA samples. Based on the assembled <i>de novo</i> transcriptome, 4,614 DEGs were detected between the two libraries of untreated (CK) and Pb-treated (Pb1000) roots. Gene Ontology (GO) and pathway enrichment analysis revealed that upregulated DEGs under Pb stress are predominately involved in defense responses in cell walls and glutathione metabolism-related processes, while downregulated DEGs were mainly involved in carbohydrate metabolism-related pathways. The expression patterns of 22 selected genes were validated by quantitative real-time PCR, and the results were highly accordant with the Solexa analysis. Furthermore, many candidate genes, which were involved in defense and detoxification mechanisms including signaling protein kinases, transcription factors, metal transporters and chelate compound biosynthesis related enzymes, were successfully identified in response to heavy metal Pb. Identification of potential DEGs involved in responses to Pb stress significantly reflected alterations in major biological processes and metabolic pathways. The molecular basis of the response to Pb stress in radishes was comprehensively characterized. Useful information and new insights were provided for investigating the molecular regulation mechanism of heavy metal Pb accumulation and tolerance in root vegetable crops.</p></div

COG function classification of assembled transcripts.

<p>COG function classification of assembled transcripts.</p

The identified genes involved in glutathione metabolism of the <i>de novo</i> transcriptome.

<p>KO (KEGG Orthology), a classification of ortholog and paralog groups based on highly confident sequence similarity scores, and the reaction classification system for biochemical reaction classification, along with other classifications for compounds and drug.</p

Validation of the RNA-Seq expression profiles of selected DEGs by qRT-PCR.

<p>Validation of the RNA-Seq expression profiles of selected DEGs by qRT-PCR.</p

Enriched pathways of the up-regulated DEGs.

<p>Enriched pathways of the up-regulated DEGs.</p

Enriched pathways of the down-regulated DEGs.

<p>Enriched pathways of the down-regulated DEGs.</p

The length distribution of the assembled transcripts.

<p>The length distribution of the assembled transcripts.</p

Gene ontology classification of assembled transcripts.

<p>Gene ontology classification of assembled transcripts.</p