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

Ricardo A. Chávez Montes, Rosas-Cárdenas de Fátima Flor, Emanuele De Paoli, Monica Accerbi, Linda A. Rymarquis, Gayathri Mahalingam, Nayelli Marsch-Martínez, Blake C. Meyers (), Pamela J. Green () and Stefan de Folter ()
Additional contact information
Ricardo A. Chávez Montes: Laboratorio Nacional de Genómica para la Biodiversidad (LANGEBIO), Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN)
Rosas-Cárdenas de Fátima Flor: Laboratorio Nacional de Genómica para la Biodiversidad (LANGEBIO), Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN)
Emanuele De Paoli: University of Delaware
Monica Accerbi: University of Delaware
Linda A. Rymarquis: University of Delaware
Gayathri Mahalingam: University of Delaware
Nayelli Marsch-Martínez: CINVESTAV-IPN
Blake C. Meyers: University of Delaware
Pamela J. Green: University of Delaware
Stefan de Folter: Laboratorio Nacional de Genómica para la Biodiversidad (LANGEBIO), Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN)

Nature Communications, 2014, vol. 5, issue 1, 1-15

Abstract: Abstract 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.

Date: 2014
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DOI: 10.1038/ncomms4722

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