Transcriptome-based identification of small RNA in plants: The need for robust prediction algorithms

The world is abuzz with imploring discussions on climate change and how the human population will adapt to climatic fluctuations. One of the prime requirements is the availability of food and nutrition to the surviving populations around the world. Thus, the need of the hour is to understand, manipulate, and redesign the adaptability of major food crops around the world. As years of research have exhibited, small RNAs regulate almost every pathway of the plant’s life cycle, ranging from growth and organ differentiation, to stress response against both biotic and abiotic factors. Numerous literature exists detailing small RNA biology with emphasis on miRNA biogenesis, sub-cellular transport, degradation, and regulation of gene expression across a large plethora of plant species. However, we are still in a very nascent stage regarding the extent of control imparted by siRNAs and tasiRNAs, as well as tRNA-derived fragments. Transcriptome sequencing has been explored worldwide to detect the small RNAome of the plants under study as well as identify possible networks that exist between the various small RNAs and their target genes. However, the prediction of small RNAs from sequence data still remains an open challenge ranging from prediction of the mature sequence as well as prediction of their possible targets. This chapter will encompass the basics of transcriptome-based small RNA identification strategies and tools currently in use and investigate improvements on available prediction algorithms.