The jujube (Ziziphus jujuba Mill.), which is also known as Chinese date, is an important species in Rhamnaceae (buckthorn family) and regarded as a superfruit for the future due to its excellent survival mechanisms and adaptability to withstand water stress and drought conditions [1, 2]. The jujubes diverged from Cannabaceae and Musaceae families nearly 79.9 million years ago . It is indigenous to the lower and middle reaches of the Yellow River in China but widely distributed in Australia, Europe and south and east Asia [1, 4]. Jujube trees were found in northern China about 24 million years ago, but the domestication occurred at least 7240 years ago [5, 6]. The jujube is one of the oldest cultivated fruit trees in the world  and used as a fruit and a medicinal plant due to the presence of complex chemical substances with many curative properties . China has as many as 4000 years history of the use of jujube and is the largest exporter of this fruit in the world . At present, the extent of jujube cultivation in China is over 1.5 million hectares  and fresh jujube fruit production is as much as eight million tons . According to a report of the United Nation’s Food and Agriculture Organization, the China’s export volume of jujube exceeds 4700 tons of dry fruit per annum .
The jujube is an excellent source of biologically active phytochemical compounds with nutritional and nutraceutical properties . These compounds are found in many parts of the tree including bark, fruits, leaves and seeds . Thus, different plant parts of jujubes are used in alternative and complementary medicine to treat different ailments including fever, diarrhea, insomnia, wounds and ulcers, to purify blood and help in digestion . It is also used in traditional Chinese medicine to treat hysteria in women and anorexia, fatigue and diarrhea due to spleen-deficiency syndrome . While dry jujubes are generally used as food, food additives and flavoring agents, the fruits made into juice, confectionery, paste and puree are consumed to help in digestion and for general wellbeing [4, 13].
The jujube industry has well developed over the last 70 years in China and later in many different countries including Australia, Iran, South Korea and Japan, mainly due the application of modern scientific technology and innovations for crop production, protection and improvement [1, 14]. However, the industry is currently facing a series of new challenges due to increasing demands for the fruit worldwide. For example, fundamental research on genetic control of economically important traits is insufficient while modern and highly efficient breeding techniques are yet to be used for accelerated cultivar development of jujubes . Further, crop improvement practices by introducing single or multiple genes through marker assisted selection and conventional breeding or genetic engineering also present new challenges mainly due to the constraints in the direct use of many identified genes because of limited trait-enhancing alleles or gene pleiotropism [15, 16]. There is a growing body of evidence suggesting that miRNA act as genetic modulators which can fine-tune the regulation of gene expression at the post-transcriptional level by causing the cleavage of messenger RNAs or directing translational inhibition [17, 18]. The validated targets of most miRNAs are regulatory proteins, most of which are transcription factors that are crucial regulators of plant development process, metabolism and stress response [19–22]. Therefore, identification of miRNAs in plants such as jujuba is essential to utilize them in breeding for the improvement of yield, quality and stress resistance traits.
Computational approach has been widely used for the discovery of miRNAs in many economically important plant species including coffee, rapeseed, rice and watermelon [23–27]. These studies have used either whole genome sequences or expressed sequence tags (ESTs) for the identification of miRNAs. As genome information and ESTs are currently available for many plant species including jujuba, miRNA identification using computational approach is very feasible and useful for future validations and their use in crop improvement programs.
miRNA are endogenous single-stranded non-coding RNA molecules of approximately 19-25 nucleotides in length that has affinity to bind to partially complementary sequences in target messenger RNAs (mRNAs) thereby catalyzing posttranscriptional silencing of target genes [28–30]. miRNAs are transcribed from miRNA genes by RNA polymerase II and the immediate transcript is primary miRNAs (pri-miRNAs) which are processed into precursor miRNAs (pre-miRNAs) . Further processing of pre-miRNAs by the Dicer-like 1 enzyme with the help of HYPONASTIC LEAVES 1 and Serrate results in miRNA duplex [18, 31]. An RNA methyltransferase protein HUA ENHANCER 1 methylates the miRNA duplex and then the guide miRNA strand is incorporated into ARGONAUTE proteins to form a functional RNA-induced silencing complex (RISC) [18, 32]. When a successful pairing between miRNA and target gene occurs, the RISC instigates the inhibition of protein expression via cleavage of mRNA or inhibition of translation [29, 30].
As there is growing potential for genetic improvement of jujubes, identification of miRNAs is imperative to utilize them in the jujube breeding programs. Only a handful of studies have been undertaken in jujube to identify miRNAs, particularly the one which are involved in the response to witches’ broom disease caused by phytoplasma [33, 34]. This study embarked on the identification of other miRNAs in jujube and their putative target genes using ESTs and a computational approach.