Genome-wide Identification of microRNAs that Respond to Drought Stress in Seedlings of Tertiary Relict Ammopiptanthus mongolicus

microRNAs (miRNAs) are important post-transcriptional regulators of gene expression in plant abiotic stress responses. Ammopiptanthus mongolicus is a typical evergreen woody xerophyte, which makes it an ideal model system for studying drought tolerance in woody plants. The response of miRNAs to drought stress is still unknown in this plant. In this research, we obtained 34 695 665 raw reads from two small RNA libraries constructed from control and drought-treated A. mongolicus seedlings by the Illumina deep sequencing technology. Length analysis revealed that reads of 20, 21, and 24 nucleotides accounted for the majority of the small RNAs in the two libraries. Sequence analyses identified 65 conserved miRNA sequences from 190 members of 31 miRNA families and 20 potential novel miRNAs from 17 families that were differentially expressed between the two libraries. The expression patterns of 25 of these miRNAs were significantly different in the two libraries, but only am-miR4a-c was downregulated during drought stress, the other 24 were upregulated. The expression trends determined by the HiSeq sequencing and by qRT-PCR were similar. Furthermore, 35 target genes for the conserved miRNA were markedly changed and 52 target genes for the potential novel miRNAs were predicted and their functions were annotated by computational analysis. Our results provide new molecular evidence for understanding the molecular mechanisms of drought response and tolerance in A. mongolicus.