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Comparative Transcriptome Profiling Under Cadmium Stress Reveals the Uptake and Tolerance Mechanism in Brassica juncea

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Abstract

Cadmium (Cd) is a biologically non-essential and phytotoxic heavy metal pollutant. In this study, we estimated the Cd accumulation potential of Indian mustard and identified factors responsible for Cd uptake, tolerance, and detoxification. Eight transcriptomic libraries were sequenced and ≈ 230 million good quality reads were generated. The alignment rate against B. juncea reference genome V1.5 varied in the range of 85.03–90.06%. Comparative expression analysis using DESeq2 revealed 11,294 genes to be significantly differentially expressed under Cd treatment. The agriGO singular enrichment analysis revealed genes related to response to chemical, oxidative stress, transport, and secondary metabolic process were upregulated, whereas multicellular organismal development, developmental process, and photosynthesis were downregulated by Cd treatment. Furthermore, 616 membrane transport proteins were found to be significantly differentially expressed. Cd-related transporters such as metal transporter (Nramp1), metal tolerance protein (MTPC2, MTP11), cadmium-transporting ATPase, and plant cadmium resistance protein (PCR2, PCR6) were upregulated whereas cadmium/zinc-transporting ATPase (HMA2, HMA3, HMA4), high-affinity calcium antiporter (CAX1), and iron transport protein (IRT1) were downregulated by Cd treatment. A total of 332 different gene-networks affected by Cd stress were identified using KAAS analysis. Various plant hormones signaling cascades were modulated suggesting their role in Cd stress tolerance. The regulation overview using MapMan analysis also revealed gene expression related to plant hormones, calcium regulation, and MAP kinases were altered under Cd stress.

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Data Availability

The raw sequence data of the libraries are available from the NCBI SRA under the study with Accession Nos.: SRP152398 and SRP126203.

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Acknowledgements

This work was supported by the Council for Scientific and Industrial Research, India under Grant No. 38(1403)/15/EMR-II. ST and SC acknowledge the fellowship received from ICMR towards Ph.D.

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Authors and Affiliations

  1. Molecular Genetics Laboratory, Department of Plant Sciences, Central University of Punjab, City Campus, Mansa Road, Bathinda, 151001, India

    Sapna Thakur, Shruti Choudhary & Pankaj Bhardwaj

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  1. Sapna Thakur
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  2. Shruti Choudhary
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  3. Pankaj Bhardwaj
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Contributions

PB designed and conceived of the study. ST analyzed and interpreted data, drafted the manuscript. SC helped in the acquisition of data and data analysis. PB and SC coordinated further in improving the manuscript. All the authors have read and approved the final manuscript.

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Correspondence to Pankaj Bhardwaj.

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Electronic supplementary material

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Supplementary material 1 (DOCX 17 KB)

Supplementary material 2 (DOCX 14 KB)

Online Resource 3

: Details of BLASTx analysis against the transporter classification database. (XLSX 510 KB)

Details of Gene ontology (GO) analysis (XLSX 19 KB)

Online Resource 5

: KAAS summary and details of metabolic and regulatory pathways. (XLSX 22 KB)

Online Resource 6

: MAPK signaling pathway (The boxes in green represent transcripts with significant differential expression under Cd stress) (PNG 37 KB)

Online Resource 7

: Calcium signaling pathway (The boxes in green represent transcripts with significant differential expression under Cd stress) (PNG 27 KB)

Online Resource 8

: Glutathione metabolism pathway (The boxes in green represent transcripts with significant differential expression under Cd stress) (PNG 30 KB)

Online Resource 9

: Plant hormone signal transduction pathway (The boxes in green represent transcripts with significant differential expression under Cd stress) (PNG 32 KB)

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Thakur, S., Choudhary, S. & Bhardwaj, P. Comparative Transcriptome Profiling Under Cadmium Stress Reveals the Uptake and Tolerance Mechanism in Brassica juncea. J Plant Growth Regul 38, 1141–1152 (2019). https://doi.org/10.1007/s00344-019-09919-8

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