the Hz32 control library. The third column is the RPM of Hz32 at 4 h treatment library. The last column is the relative change. Chi- square test is applied to the relative change and * denotes the p value ,0.01. (XLSX) Table S4 Novel mature miRNA and their precursor with genome coordinates. The table gives the information of the predicted novel miRNA such as genome coordinate, mature sequence and pre-miRNA sequence. (XLSX) Table S5 Targets of novel miRNAs with interpro annotation. List of novel miRNA targets with interpro id and description. MM: miss match. (XLSX) Table S6 miRNA SLRT-PCR primers and their target function. The first column is the miRNA id. The second column is the gene specific forward primer for the SLRT-PCR. The third column is the stem loop primer for the first strand cDNA amplification. The last column is the predicted miRNA targets annotation. Universal reverse primer is for the SLRT-PCR reaction. (XLSX) Table S7 qRT-PCR internal control primers. Maize 18s ribosome RNA gene was used as the internal control to normalize the qRT-PCR results. (XLSX) Table S8 miRNA targets qRT-PCR primers. The first column is the miRNA id. The second column is the target gene id. The third column is the gene specific forward primer for the qRT- PCR. The fourth column is the gene specific reverse primer for the qRT-PCR. The fifth column is the designed product size (around 200 bp). The last column is the targets annotation. (XLSX) Table S9 5’RLM-RACE validation of the miRNA targets nested PCR primers. The first column is the miRNA id. The second column is the target gene id. The third column is the gene specific outer primer for the PCR. The fourth column is the gene specific inner primer for the PCR. The fifth column is the designed product size. The last column is the targets annotation. 59RLM- RACE adapter is the adapter used for the 59RACE analysis. References 1. Maltby E (1991) Wetlands-their status and role in the biosphere. 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Lopez-Barneo J, del Toro R, Levitsky KL, Chiara MD, Ortega-Saenz P (2004) Regulation of oxygen sensing by ion channels. Journal of Applied Physiology 96: 1187–1195. 8. Waypa GB, Schumacker PT (2005) Hypoxic pulmonary vasoconstriction: redox events in oxygen sensing. Journal of Applied Physiology 98: 404–414. 9. Bartel DP (2004) MicroRNAs: genomics, biogenesis, mechanism, and function. Cell 116: 281–297. Characterization of Hypoxia Induced Maize miRNAs 59RACE outer primer is the universal outer primer for the PCR. 59RACE inner primer is the universal inner primer for the PCR. (XLSX) Table S10 Mapping of intragenic hypoxia responsive miRNAs with B73 maize genome. Out of 64 differentially expressed miRNA genes representing 22 known mature miRNA signatures, 30 miRNA genes belonging to 13 miRNA families could be mapped to the transcription start site (TSS). (XLSX) Table S11 Brief description of the list of transcription Factors from JASPAR Core Plantae whose binding sites were found on miRNA promoter region. The first column is the TF id. The second column is the TF family. The third column is the TF class. The fourth column is the plant species for that TF annotated in JASPER. The fifth column is the reference. (XLSX) Table S12 List of transcription factors that have been used for motifs predictions for probable TF-miRNA interactions for upstream analysis of miRNA-mediated gene regulatory sub-network. The first column is the miRNA id. The second column is the TF that bind to the miRNA promoter. The third column is the TF family. The fourth column is the description of the TF family. (XLSX) Table S13 List of miRNA targets that have been used for miRNA-TF interactions for downstream analysis of probable miRNA-mediated gene regulatory sub-net- work. The first column is the miRNA id. The second column is the TF family of the miRNA targets. 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