Computational characterization of conserved and novel miRNAs in cotton

Cotton is one of the world's most valuable textiles and a significant oilseed crop. The fiber cells that emerge from the cotton ovule are specified from undifferentiated epidermal tissue and undergo a process of initiation, elongation, secondary cell wall synthesis, and maturation. Because of their unique development features, cotton fibers serve as ideal biological models for investigating the mechanisms of cellular elongation and cellulose biosynthesis. Despite their importance, little is known about how genes are regulated in the initial stages of fiber growth in order to coordinate their development. microRNAs (miRNAs) are small, ~21-nucleotide RNAs that are known to have broad post-transcriptional impact on gene expression and development. In this study, we sequenced nearly 4.1 million small RNAs derived from the early stages of fiber growth in an effort to characterize the diversity of cotton miRNAs and to identify their physiological roles. Comparative sequence analysis identified 26 conserved miRNA families as well as 5 novel, cotton-specific miRNAs. A Perl script was written that systematically predicted 242 miRNA targets in the cotton transcriptome. Nearly all of the targets that were experimentally tested for cleavage were experimentally validated, suggesting a low false-positive rate in the predictions. The results reveal that miRNAs often target families of transcription factors that mediate critical signaling pathways such as those involved in the phytohormonal response to auxin.