The study of microRNAs (miRNAs) in plants has gained significant attention in recent years due to their regulatory role during development and in response to biotic and abiotic stresses. Although cassava (Manihot esculenta Crantz) is tolerant to drought and other adverse conditions, most cassava miRNAs have been predicted using bioinformatics alone or through sequencing of plants challenged by biotic stress. Here, we use high-throughput sequencing and different bioinformatics methods to identify potential cassava miRNAs expressed in different tissues subject to heat and drought conditions. We identified 60？miRNAs conserved in other plant species and 821 potential cassava-specific miRNAs. We also predicted 134 and 1002 potential target genes for these two sets of sequences. Using real time PCR, we verified the condition-specific expression of 5 cassava small RNAs relative to a non-stress control. We also found, using publicly available expression data, a significantly lower expression of the predicted target genes of conserved and nonconserved miRNAs under drought stress compared to other cassava genes. Gene Ontology enrichment analysis along with condition specific expression of predicted miRNA targets, allowed us to identify several interesting miRNAs which may play a role in stress-induced posttranscriptional regulation in cassava and other plants. 1. Introduction MicroRNAs (miRNAs) are short noncoding small RNA molecules that are transcribed in plants and animals and play key roles in posttranscriptional gene regulation [1]. Mature miRNAs are embedded into larger primary transcripts called pri-miRNAs and are released through a two-step cleavage process [2]. The first cleavage is performed by a Dicer homolog, called Dicer-like 1 (DCL1), which generates a stem-loop structure called precursor miRNA (premiRNA). Dicer makes a second set of cuts to produce the 20–24？nt mature miRNA duplexed with a complementary miRNA*. The double-stranded fragment is exported to the cytoplasm where it dissociates and the mature 21？nt miRNA is incorporated into the RNA-induced silencing complex (RISC). Guided by the miRNA sequence, the RISC complex down-regulates specific target genes either by cleaving or translational repression of their messenger RNAs [3–5]. In plants, regulation of gene expression by miRNAs is essential for normal growth and development, including leaf morphogenesis, patterning and polarity establishment, developmental timing, floral organ identity, and phytohormone signaling [3, 6]. Furthermore, miRNAs are also involved in plants’ adaptation to biotic
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