Deep Sequencing Reveals Divergent Expression Patterns Within the Small RNA Transcriptomes of Cultured and Vegetative Tissues of Sugarcane

Abstract

Deep sequencing has advanced the discovery and analysis of the small RNA component of transcriptomes and has revealed developmentally-regulated populations of small RNAs consistent with key roles in plant development. To study small RNA transcriptome complexity and explore their roles in sugarcane development, we obtained almost 50 million small RNA reads from suspension cells, embryogenic calli, leaf, apex and a developmental series of stem internodes. The complexity of the small RNA component of the transcriptome varied between tissues. The undifferentiated and young tissue type libraries had lower redundancy levels than libraries generated from maturing and mature tissues. The ratio of 21:24 nt small RNAs also varied widely between different tissue types, as did the proportion of abundant small RNAs derived from each putative origin of small RNA biogenesis. Cluster analysis indicates many abundant small RNAs display developmental expression patterns. There was substantial variation in isomiR composition, abundance and expression patterns within sugarcane microRNA (miRNA) families. Two hundred and fifty-six isomiRs from 36 miRNA families were identified by homology to known miRNA families from a range of plant species. Many isomiRs and miRNA families appear to be developmentally regulated, including a subset of miRNAs that are progressively upregulated during stem internode maturation. Transcribed sequences putatively targeted by abundant sugarcane small RNAs were predicted and miRNA directed cleavage of 18 predicted sugarcane targets were validated by 5′ RACE.