Transcriptome analysis of Cd-treated switchgrass root revealed novel transcripts and the importance of HSF/HSP network in switchgrass Cd tolerance
Transcriptome analysis of Cd-treated switchgrass roots not only revealed novel switchgrass transcripts and gene structures but also highlighted the indispensable role of HSF/HSP network in switchgrass Cd tolerance.
Switchgrass (Panicum virgatum L.), a C4 perennial tall grass, can be used for revegetation of Cd-contaminated soil. In the present study, a comparative transcriptome analysis of Cd-treated switchgrass roots was conducted. The result revealed a total of 462 novel transcripts and refined gene structures of 2337 transcripts. KEGG pathway and Gene Ontology analyses of the differentially expressed genes (DEGs) suggested that activation of redox homeostasis and oxidation-related metabolic processes were the primary response to Cd stress in switchgrass roots. In particular, 21 out of 23 differentially expressed shock transcription factor genes (HSFs), and 22 out of 23 differentially expressed heat shock protein genes (HSPs) had increased expression levels after Cd treatment. Furthermore, over-expressing one HSP-encoding gene in Arabidopsis significantly improved plant Cd tolerance. The result highlighted the activation of the redox homeostasis and the involvement of the HSF/HSP network in re-establishing normal protein conformation and thus cellular homeostasis in switchgrass upon Cd stress. These DEGs, especially those of the HSF/HSP network, could be used as candidate genes for further functional studies toward improved plant Cd tolerance in switchgrass and related species.
KeywordsSwitchgrass Cadmium RNA-Seq Novel transcripts Chaperone
We thank Dr. Chuansheng Mei at Virginia Tech and Dr. Linkai Huang at Sichuan Agricultural University for their assistance with materials and technical suggestions.
The project was funded by Grants 31372359 and 31572455 from the National Natural Science Foundation of China and by the Priority Academic Program Development of Jiangsu Higher Education Institutions.
Compliance with ethical standards
Conflict of interest
The authors declare that they have no competing interests.
Availability of data and materials
The dataset supporting the conclusions of this article is available in the NCBI SRA repository ‘SRR5838951’ in http://www.ncbi.nlm.nih.gov/sra/?term=SRR5838951. The dataset supporting the conclusions of this article is included in the article and its supplementary material.
- Fan JL, Wei XZ, Wan LC, Zhang LY, Zhao XQ, Liu WZ, Hao HQ, Zhang HY (2011) Disarrangement of actin filaments and Ca²+ gradient by CdCl2 alters cell wall construction in Arabidopsis thaliana root hairs by inhibiting vesicular trafficking. J Plant Physiol 168:157–1167Google Scholar
- Kolde R (2015) “pheatmap: Pretty Heatmaps. R package version 1.0.2”Google Scholar