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Article

Bioinformatic Exploration of the Targets of Xylem Sap miRNAs in Maize under Cadmium Stress

1
Lianyungang Institute of Agricultural Sciences in Jiangsu Xuhuai Region, Jiangsu Academy of Agricultural Sciences, Lianyungang 222000, China
2
National Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
*
Author to whom correspondence should be addressed.
These authors contributed equally to this work.
Int. J. Mol. Sci. 2019, 20(6), 1474; https://doi.org/10.3390/ijms20061474
Received: 11 February 2019 / Revised: 12 March 2019 / Accepted: 14 March 2019 / Published: 23 March 2019
(This article belongs to the Special Issue Transcriptional and Post-transcriptional Gene Regulation in Plants)
Cadmium (Cd) has the potential to be chronically toxic to humans through contaminated crop products. MicroRNAs (miRNAs) can move systemically in plants. To investigate the roles of long-distance moving xylem miRNAs in regulating maize response to Cd stress, three xylem sap small RNA (sRNA) libraries were constructed for high-throughput sequencing to identify potential mobile miRNAs in Cd-stressed maize seedlings and their putative targets in maize transcriptomes. In total, about 199 miRNAs (20–22 nucleotides) were identified in xylem sap from maize seedlings, including 97 newly discovered miRNAs and 102 known miRNAs. Among them, 10 miRNAs showed differential expression in xylem sap after 1 h of Cd treatment. Two miRNAs target prediction tools, psRNAtarget (reporting the inhibition pattern of cleavage) and DPMIND (discovering Plant MiRNA-Target Interaction with degradome evidence), were used in combination to identify, via bioinformatics, the targets of 199 significantly expressed miRNAs in maize xylem sap. The integrative results of these two bioinformatic tools suggested that 27 xylem sap miRNAs inhibit 34 genes through cleavage with degradome evidence. Moreover, nearly 300 other genes were also the potential miRNAs cleavable targets without available degradome data support, and the majority of them were enriched in abiotic stress response, cell signaling, transcription regulation, as well as metal handling. These approaches and results not only enhanced our understanding of the Cd-responsive long-distance transported miRNAs from the view of xylem sap, but also provided novel insights for predicting the molecular genetic mechanisms mediated by miRNAs. View Full-Text
Keywords: xylem sap; miRNAs; target gene; cadmium; maize xylem sap; miRNAs; target gene; cadmium; maize
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MDPI and ACS Style

Wang, B.; Cheng, D.; Chen, Z.; Zhang, M.; Zhang, G.; Jiang, M.; Tan, M. Bioinformatic Exploration of the Targets of Xylem Sap miRNAs in Maize under Cadmium Stress. Int. J. Mol. Sci. 2019, 20, 1474. https://doi.org/10.3390/ijms20061474

AMA Style

Wang B, Cheng D, Chen Z, Zhang M, Zhang G, Jiang M, Tan M. Bioinformatic Exploration of the Targets of Xylem Sap miRNAs in Maize under Cadmium Stress. International Journal of Molecular Sciences. 2019; 20(6):1474. https://doi.org/10.3390/ijms20061474

Chicago/Turabian Style

Wang, Baoxiang, Dan Cheng, Ziyan Chen, Manman Zhang, Guoqiang Zhang, Mingyi Jiang, and Mingpu Tan. 2019. "Bioinformatic Exploration of the Targets of Xylem Sap miRNAs in Maize under Cadmium Stress" International Journal of Molecular Sciences 20, no. 6: 1474. https://doi.org/10.3390/ijms20061474

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