Sample sequencing of vascular plants demonstrates widespread conservation and divergence of microRNAs

• DOI: 10.1038/ncomms4722
• Publication Date: 2014-04-23T14:15:19Z
• Authors: Ricardo A. Chávez...; de Fátima Flor Ro...; Emanuele De Paoli; Monica Accerbi; Linda A. Rymarquis; Gayathri Mahalingam; Nayelli Marsch-Ma...; Blake C. Meyers; Pamela J. Green; Stefan de Folter
• Keywords: MicroRNAs; 0303 health sciences; 03 medical and health sciences; Plants; Phylogeny

Small RNAs are pivotal regulators of gene expression that guide transcriptional and post-transcriptional silencing mechanisms in eukaryotes, including plants. Here we report a comprehensive atlas of sRNA and miRNA from 3 species of algae and 31 representative species across vascular plants, including non-model plants. We sequence and quantify sRNAs from 99 different tissues or treatments across species, resulting in a data set of over 132 million distinct sequences. Using miRBase mature sequences as a reference, we identify the miRNA sequences present in these libraries. We apply diverse profiling methods to examine critical sRNA and miRNA features, such as size distribution, tissue-specific regulation and sequence conservation between species, as well as to predict putative new miRNA sequences. We also develop database resources, computational analysis tools and a dedicated website, http://smallrna.udel.edu/. This study provides new insights on plant sRNAs and miRNAs, and a foundation for future studies.