Location: Vegetable ResearchTitle: Dynamic regulation of novel and conserved miRNAs across various tissues of diverse Cucurbit spp.) Author
Submitted to: Plant Molecular Biology Reporter
Publication Type: Peer reviewed journal
Publication Acceptance Date: 8/31/2012
Publication Date: 4/15/2013
Citation: Manohar, S., Jagadeeswaran, J., Nimmakayala, P., Almeida, A., Tomasson, Y., Sunkar, R., Levi, A., Reddy, U. 2013. Dynamic regulation of novel and conserved miRNAs across various tissues of diverse Cucurbit spp. Plant Molecular Biology Reporter. 2:335-343. Interpretive Summary: Cucurbits include important vegetable crops in the United States and throughout the world. However, there is limited knowledge on the genetics and genes that could be useful to improve these important vegetable crops. In this study, an ARS scientist at Charleston collaborated with scientists at West Virginia State University on identifying MicroRNA genes. The microRNAs are short ribonucleic acid (RNA) molecules that exist in plant genomes and play a key role in regulating a variety of biological mechanisms. The MicroRNA genes are also considered useful genetic markers because their gene sequences have remained highly conserved and not changed during many years of evolution. The researchers identified and evaluated 21 microRNA families among four different cucurbit species, including pumpkin, squash, bitter melon, and luffa. The knowledge gained in this study will be useful to researchers interested in studying gene regulation and different biological mechanisms, such as fruit setting and fruit growth in cucurbit species.
Technical Abstract: MicroRNA genes (miRNAs) encoding small non-coding RNAs are abundant in plant genomes and play a key role in regulating several biological mechanisms. Five conserved miRNAs, miR156, miR168-1, miR168-2, miR164, and miR166 were selected for analysis from the 21 known plant miRNA families that were recovered from deep sequencing data of small RNA libraries of pumpkin and squash. A total of six novel miRNAs were not reported before were found to have precursors with reliable fold back structures and hence considered novel and were designated as cuc-nov-miRNAs. A set of five conserved, six novel miRNAs and five uncharacterized small RNAs from deep sequencing data were profiled for dynamic regulation using qPCR. The miRNAs were evaluated for differential regulation across the tissues among four diverse cucurbit species, including pumpkin and squash (Cucurbita moschata Duch. Ex Poir. and Cucurbita pepo L.), bitter melon (Momordica charantia L.), and Luffa (Loofah) (Luffa acutangula Roxb.). Expression analysis revealed differential regulation of various miRNAs in leaf, stem and fruit tissues. Importantly, differences in the expression levels were also found in the leaves and fruits of closely related C. moschata and C. pepo. Comparative miRNA profiling and expression analysis in four cucurbits led to identification of conserved miRNAs in cucurbits. Predicted targets for two of the conserved miRNAs suggested miRNAs are involved in regulating similar biological mechanisms in various species of cucurbits.